229442	DRR084021	DRP003418	DRS039912	DRX077852	DRA004523	KYUSH-MIB	Kyushu University	piRNA profiles in mouse oocytes lacking Pld6, Mili, Miwi, or Dicer	Piwi-interacting RNAs (piRNAs) are approximately 26-30 nucleotide single-stranded RNAs bound to Piwi proteins. In mice, the piRNA pathway is well characterized in male germ cells, but its regulation and function in oocytes are less well understood. We have profiled piRNAs in normal ovaries and mutant ones lacking Pld6, Mili, Miwi, or Dicer using deep sequencing.	Piwi-interacting RNAs (piRNAs) are approximately 26-30 nucleotide single-stranded RNAs bound to Piwi proteins. In mice, the piRNA pathway is well characterized in male germ cells, but its regulation and function in oocytes are less well understood. We have profiled piRNAs in normal ovaries and mutant ones lacking Pld6, Mili, Miwi, or Dicer using deep sequencing.	Illumina HiSeq 1500 paired end sequencing of SAMD00048521			Mili WT RNA-seq replicate 1	RNA-Seq	TRANSCRIPTOMIC	RANDOM	paired	101			Illumina HiSeq 1500	dev_stage;;P20|sample_name;;mouse P20 ovaries|sex;;female|tissue_type;;ovary		202	SAMD00048521	mouse ovary small RNA-seq	5911418294	29264447	2017-01-27 00:37:12	3656091426	5911418294	29264447	2	29264447	index:0,count:29264447,average:101,stdev:0|index:1,count:29264447,average:101,stdev:0	DRR084021	KYUSH-MIB			in_mesa	28115634	18.78	2.86	0.04	4423371500	4296430631	4018571872	3926399897	97.13	97.71	27989869	26755267	177.617	523.587	139	263764	68.8	75.97	32541041	19255636	32541041	19255636	73.08	73.01	32541041	20453830	32541041	18506099	908441386	20.54	1.16	0	9.03	0	0.68	0	0.50	0	0.00	0	3.18	0	27989869	0	202	0	200.84	0	1.44	0	0.00	0	1.24	0	0.00	0	104.83	0	0.12	0	338997	0	29264447	0	2643163	0	197717	0	147322	0	0	0	929539	0	4918	0	0	0	57071	0	6897174	0	14764	0	6973927	0	86.61	0	25346706	0	210585	6142258	29.167595032885	29264447.0	27989869.0	338997.0	2643163.0	197717.0	147322.0	0.0	929539.0	25346706.0	95.6	1.2	9.0	0.7	0.5	0.0	3.2	86.6	101	101	101.00	38	2955709147	25.2	22.0	22.9	29.8	0.0	36.7	23.2	bulk
229474	DRR084031	DRP003418	DRS039912	DRX077862	DRA004523	KYUSH-MIB	Kyushu University	piRNA profiles in mouse oocytes lacking Pld6, Mili, Miwi, or Dicer	Piwi-interacting RNAs (piRNAs) are approximately 26-30 nucleotide single-stranded RNAs bound to Piwi proteins. In mice, the piRNA pathway is well characterized in male germ cells, but its regulation and function in oocytes are less well understood. We have profiled piRNAs in normal ovaries and mutant ones lacking Pld6, Mili, Miwi, or Dicer using deep sequencing.	Piwi-interacting RNAs (piRNAs) are approximately 26-30 nucleotide single-stranded RNAs bound to Piwi proteins. In mice, the piRNA pathway is well characterized in male germ cells, but its regulation and function in oocytes are less well understood. We have profiled piRNAs in normal ovaries and mutant ones lacking Pld6, Mili, Miwi, or Dicer using deep sequencing.	Illumina HiSeq 1500 paired end sequencing of SAMD00048521			Pld6 WT RNA-seq replicate 1	RNA-Seq	TRANSCRIPTOMIC	RANDOM	paired	101			Illumina HiSeq 1500	dev_stage;;P20|sample_name;;mouse P20 ovaries|sex;;female|tissue_type;;ovary		202	SAMD00048521	mouse ovary small RNA-seq	6788896800	33608400	2017-01-27 00:37:12	4241517658	6788896800	33608400	2	33608400	index:0,count:33608400,average:101,stdev:0|index:1,count:33608400,average:101,stdev:0	DRR084031	KYUSH-MIB			in_mesa	28115634	18.31	3.02	0.06	5158900051	4978893023	4739026747	4602718281	96.51	97.12	32199814	30798212	183.317	538.667	139	299842	62.65	68.39	36779807	20173121	36779807	20173121	66.81	66.25	36779807	21513875	36779807	19540414	1423079646	27.58	1.07	0	8.05	0	0.65	0	0.51	0	0.00	0	3.02	0	32199814	0	202	0	200.89	0	1.71	0	0.01	0	1.58	0	0.00	0	203.00	0	0.16	0	358122	0	33608400	0	2704600	0	219422	0	172513	0	0	0	1016651	0	4795	0	0	0	155380	0	6946418	0	17632	0	7124225	0	87.76	0	29495214	0	222827	6348693	28.491578668653	33608400.0	32199814.0	358122.0	2704600.0	219422.0	172513.0	0.0	1016651.0	29495214.0	95.8	1.1	8.0	0.7	0.5	0.0	3.0	87.8	101	101	101.00	38	3394448400	25.7	21.3	22.5	30.5	0.0	36.8	23.3	bulk
725006	ERR505201	ERP005852	ERS459877	ERX470567	ERA311846	EBI	ArrayExpress	An mRNA-sequencing atlas of mouse CD4+ T cell transcriptomes	PolyA+ mRNA-seq was performed on naive, Th1, Th2, Th17, splenic Treg, and in vitro-induced Treg (iTreg) cells.	PolyA+ mRNA-seq was performed on naive, Th1, Th2, Th17, splenic Treg, and in vitro-induced Treg (iTreg) cells.	Illumina HiSeq 2000 paired end sequencing; An mRNA-sequencing atlas of mouse CD4+ T cell transcriptomes	An mRNA-sequencing atlas of mouse CD4+ T cell transcriptomes	Protocols: CD4+, CD62L+ cells were purified with CD4+CD62L+ T Cell Isolation Kit II (Miltenyi Biotec). Cells were seeded into anti-CD3 (2 ug/ml, clone 145-2C11, eBioscience) and anti-CD28 (5 ug/ml, clone 37.51, eBioscience) coated 96-well plates, at a density of 250,000-500,000 cells/ml and cultured in a total volume of 200 ul in the presence of recombinant murine IL-12 (10 ng/ml, RD Systems) and neutralising anti-IL4 (10 ug/ml, clone 11B11, eBioscience). Cells were cultured for another four days in absence of CD3 and CD28 stimulation to rest them. The original medium was kept and fresh medium containing the same cytokines as before was added to dilute the cultures 1:3. Finally, the cells were labelled with anti-CXCR3-APC (1:200, clone CXCR3-173, BioLegend) and Propidium Iodide and FITC-conjugated antibodies against CD11b, CD11c, Ly6G, CD8a and CD19. The cultures were then FACS-sorted to obtain Propidium Iodide-, FITC-negative and CXCR3-positive cells. RNA was purified using the Qiagen RNEasy Plus Mini Kit automated using a QIAcube Samples were processed using the TruSeq RNA Sample Prep v2 kit (Illumina) according to the manufacturers instructions with an alteration to use KAPA Hifi polymerase for PCR amplification instead of the one supplied with the kit.	Th1_B	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	paired	264	69.5	CD4+, CD62L+ cells were purified with CD4+CD62L+ T Cell Isolation Kit II (Miltenyi Biotec). Cells were seeded into anti-CD3 (2 ug/ml, clone 145-2C11, eBioscience) and anti-CD28 (5 ug/ml, clone 37.51, eBioscience) coated 96-well plates, at a density of 250,000-500,000 cells/ml and cultured in a total volume of 200 ul in the presence of recombinant murine IL-12 (10 ng/ml, RD Systems) and neutralising anti-IL4 (10 ug/ml, clone 11B11, eBioscience). Cells were cultured for another four days in absence of CD3 and CD28 stimulation to rest them. The original medium was kept and fresh medium containing the same cytokines as before was added to dilute the cultures 1:3. Finally, the cells were labelled with anti-CXCR3-APC (1:200, clone CXCR3-173, BioLegend) and Propidium Iodide and FITC-conjugated antibodies against CD11b, CD11c, Ly6G, CD8a and CD19. The cultures were then FACS-sorted to obtain Propidium Iodide-, FITC-negative and CXCR3-positive cells. RNA was purified using the Qiagen RNEasy Plus Mini Kit automated using a QIAcube Samples were processed using the TruSeq RNA Sample Prep v2 kit (Illumina) according to the manufacturers instructions with an alteration to use KAPA Hifi polymerase for PCR amplification instead of the one supplied with the kit.	Illumina HiSeq 2000	alias;;E-MTAB-2582:Th1 rep2|broker name;;ArrayExpress|cell type;;T-helper 1 cell|ENA checklist;;ERC000011|INSDC center alias;;EBI|INSDC center name;;European Bioinformatics Institute|INSDC first public;;2015-04-05T17:04:12Z|INSDC last update;;2018-03-08T17:48:54Z|INSDC status;;public|organism;;Mus musculus|Sample Name;;ERS459877|SRA accession;;ERS459877|title;;Th1 rep2	Experimental Factor: cell type;;T-helper 1 cell	200	SAMEA2536561	E-MTAB-2582:Th1 rep2	8708271600	43541358	2015-04-06 04:39:03	6295814845	8708271600	43541358	2	43541358	index:0,count:43541358,average:100,stdev:0|index:1,count:43541358,average:100,stdev:0	E-MTAB-2582:Teichmann-ThExpress_Th1_B		ArrayExpress	SC	in_mesa	25886751	3.21	3.55	0.07	8264952046	8166826994	7441603601	7405585031	98.81	99.52	42597149	35962616	296.749	1228.695	227	219028	84.66	94.05	49576095	36062481	49576095	36062481	90.51	90.95	49576095	38553520	49576095	34873928	400173254	4.84	0.70	0	9.77	0	0.42	0	0.09	0	0.00	0	1.66	0	42597149	0	200	0	198.35	0	1.49	0	0.01	0	1.22	0	0.01	0	381.38	0	0.30	0	304733	0	43541358	0	4252101	0	182728	0	39818	0	0	0	721663	0	13930	0	0	0	153468	0	20475723	0	34681	0	20677802	0	88.07	0	38345048	0	219639	21949645	99.935098047250	43541358.0	42597149.0	304733.0	4252101.0	182728.0	39818.0	0.0	721663.0	38345048.0	97.8	0.7	9.8	0.4	0.1	0.0	1.7	88.1	100	100	100.00	44	4354135800	24.9	25.2	25.0	24.9	0.0	36.7	25.6	bulk
725030	ERR505204	ERP005852	ERS459874	ERX470564	ERA311846	EBI	ArrayExpress	An mRNA-sequencing atlas of mouse CD4+ T cell transcriptomes	PolyA+ mRNA-seq was performed on naive, Th1, Th2, Th17, splenic Treg, and in vitro-induced Treg (iTreg) cells.	PolyA+ mRNA-seq was performed on naive, Th1, Th2, Th17, splenic Treg, and in vitro-induced Treg (iTreg) cells.	Illumina HiSeq 2000 paired end sequencing; An mRNA-sequencing atlas of mouse CD4+ T cell transcriptomes	An mRNA-sequencing atlas of mouse CD4+ T cell transcriptomes	Protocols: CD4+, CD62L+ cells were purified with CD4+CD62L+ T Cell Isolation Kit II (Miltenyi Biotec) and further purification was performed by FACS using anti-CD62L and anti-CD4 Fab fragments. Poly-(A)+ RNA was purified from ~500,000 cells using the Oligotex kit (Qiagen). The manufacturers protocol was modified slightly to include additional final elution steps resulting in a larger volume. RNA was purified, reverse transcribed and prepared for sequencing described in http://msb.embopress.org/content/7/1/497	Naive 3b	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	paired	121	16.6	CD4+, CD62L+ cells were purified with CD4+CD62L+ T Cell Isolation Kit II (Miltenyi Biotec) and further purification was performed by FACS using anti-CD62L and anti-CD4 Fab fragments. Poly-(A)+ RNA was purified from ~500,000 cells using the Oligotex kit (Qiagen). The manufacturers protocol was modified slightly to include additional final elution steps resulting in a larger volume. RNA was purified, reverse transcribed and prepared for sequencing described in http://msb.embopress.org/content/7/1/497	Illumina HiSeq 2000	alias;;E-MTAB-2582:Naive rep1|broker name;;ArrayExpress|cell type;;naive thymus-derived CD4-positive, alpha-beta T cell|ENA checklist;;ERC000011|INSDC center alias;;EBI|INSDC center name;;European Bioinformatics Institute|INSDC first public;;2015-04-05T17:04:12Z|INSDC last update;;2018-03-08T17:48:51Z|INSDC status;;public|organism;;Mus musculus|Sample Name;;ERS459874|SRA accession;;ERS459874|title;;Naive rep1	Experimental Factor: cell type;;naive thymus-derived CD4-positive, alpha-beta T cell	200	SAMEA2536558	E-MTAB-2582:Naive rep1	25503717000	127518585	2015-04-06 04:39:03	17545194237	25503717000	127518585	2	127518585	index:0,count:127518585,average:100,stdev:0|index:1,count:127518585,average:100,stdev:0	E-MTAB-2582:Teichmann-ThExpress_naive_3b		ArrayExpress	CRUK	in_mesa	25886751	0.21	2.28	0.32	6463217015	6389321671	5997097037	5980948759	98.86	99.73	58665042	55685250	126.623	911.412	101	839776	66.05	71.3	67127657	38746738	67127657	38746738	66.83	66.58	67127657	39203981	67127657	36182131	1745241373	27.00	1.72	0	3.39	0	1.10	0	0.15	0	0.00	0	52.75	0	58665042	0	200	0	185.56	0	1.66	0	0.03	0	1.34	0	0.00	0	127.45	0	0.52	0	2189290	0	127518585	0	4323786	0	1402827	0	188816	0	0	0	67261900	0	9492	0	0	0	125371	0	15499181	0	157176	0	15791220	0	42.61	0	54341256	0	156674	10930135	69.763553620894	127518585.0	58665042.0	2189290.0	4323786.0	1402827.0	188816.0	0.0	67261900.0	54341256.0	46.0	1.7	3.4	1.1	0.1	0.0	52.7	42.6	100	100	100.00	38	12751858500	22.9	26.7	29.9	20.1	0.3	33.6	16.0	bulk
725039	ERR505205	ERP005852	ERS459869	ERX470559	ERA311846	EBI	ArrayExpress	An mRNA-sequencing atlas of mouse CD4+ T cell transcriptomes	PolyA+ mRNA-seq was performed on naive, Th1, Th2, Th17, splenic Treg, and in vitro-induced Treg (iTreg) cells.	PolyA+ mRNA-seq was performed on naive, Th1, Th2, Th17, splenic Treg, and in vitro-induced Treg (iTreg) cells.	Illumina HiSeq 2000 paired end sequencing; An mRNA-sequencing atlas of mouse CD4+ T cell transcriptomes	An mRNA-sequencing atlas of mouse CD4+ T cell transcriptomes		Th2_A	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	paired	258	68	CD4+, CD62L+ cells were purified with CD4+CD62L+ T Cell Isolation Kit II (Miltenyi Biotec). Cells were seeded into anti-CD3 (2 ug/ml, clone 145-2C11, eBioscience) and anti-CD28 (5 ug/ml, clone 37.51, eBioscience) coated 96-well plates, at a density of 250,000-500,000 cells/ml and cultured in a total volume of 200 ul in the presence of recombinant murine IL-4 (10 ng/ml, RD Systems) and neutralizing anti-IFN-gamma (10 ug/ml, clone XMG1.2, eBioscience). Cells were cultured for another four days in absence of CD3 and CD28 stimulation to rest them. The original medium was kept and fresh medium containing the same cytokines as before was added to dilute the cultures 1:3. Finally, the cells were labelled with Propidium Iodide and FITC-conjugated antibodies against CD11b, CD11c, Ly6G, CD8a and CD19. The cultures were then FACS-sorted to obtain Propidium Iodide-, FITC-negative cells. RNA was purified using the Qiagen RNEasy Plus Mini Kit automated using a QIAcube Samples were processed using the TruSeq RNA Sample Prep v2 kit (Illumina) according to the manufacturers instructions with an alteration to use KAPA Hifi polymerase for PCR amplification instead of the one supplied with the kit.	Illumina HiSeq 2000	Alias;;E-MTAB-2582:Th2 rep1|Broker name;;ArrayExpress|cell type;;T-helper 2 cell|Description;;Protocols: CD4+, CD62L+ cells were purified with CD4+CD62L+ T Cell Isolation Kit II (Miltenyi Biotec). Cells were seeded into anti-CD3 (2 ug/ml, clone 145-2C11, eBioscience) and anti-CD28 (5 ug/ml, clone 37.51, eBioscience) coated 96-well plates, at a density of 250,000-500,000 cells/ml and cultured in a total volume of 200 ul in the presence of recombinant murine IL-4 (10 ng/ml, RD Systems) and neutralizing anti-IFN-gamma (10 ug/ml, clone XMG1.2, eBioscience). Cells were cultured for another four days in absence of CD3 and CD28 stimulation to rest them. The original medium was kept and fresh medium containing the same cytokines as before was added to dilute the cultures 1:3. Finally, the cells were labelled with Propidium Iodide and FITC-conjugated antibodies against CD11b, CD11c, Ly6G, CD8a and CD19. The cultures were then FACS-sorted to obtain Propidium Iodide-, FITC-negative cells. RNA was purified using the Qiagen RNEasy Plus Mini Kit automated using a QIAcube Samples were processed using the TruSeq RNA Sample Prep v2 kit (Illumina) according to the manufacturers instructions with an alteration to use KAPA Hifi polymerase for PCR amplification instead of the one supplied with the kit.|ENA checklist;;ERC000011|INSDC center alias;;EBI|INSDC center name;;European Bioinformatics Institute|INSDC first public;;2015-04-05T17:04:12Z|INSDC last update;;2018-03-08T17:48:50Z|INSDC status;;public|organism;;Mus musculus|Sample Name;;ERS459869|SRA accession;;ERS459869|Title;;Th2 rep1	Experimental Factor: cell type;;T-helper 2 cell	200	SAMEA2536553	E-MTAB-2582:Th2 rep1	10286746400	51433732	2015-04-06 04:39:03	7450242509	10286746400	51433732	2	51433732	index:0,count:51433732,average:100,stdev:0|index:1,count:51433732,average:100,stdev:0	E-MTAB-2582:Teichmann-ThExpress_Th2_A		ArrayExpress	SC	in_mesa	25886751	7.52	3.4	0.09	9712581546	9570261059	8558201888	8494881347	98.53	99.26	50269311	43799692	287.826	1079.599	218	273918	82.13	93.25	59185623	41288559	59185623	41288559	89.72	89.94	59185623	45102447	59185623	39823806	511051187	5.26	0.70	0	11.65	0	0.31	0	0.07	0	0.00	0	1.88	0	50269311	0	200	0	198.37	0	1.59	0	0.01	0	1.24	0	0.01	0	308.09	0	0.31	0	361264	0	51433732	0	5991820	0	161800	0	38115	0	0	0	964506	0	15055	0	0	0	159856	0	21743853	0	39917	0	21958681	0	86.09	0	44277491	0	221245	23363444	105.599873443468	51433732.0	50269311.0	361264.0	5991820.0	161800.0	38115.0	0.0	964506.0	44277491.0	97.7	0.7	11.6	0.3	0.1	0.0	1.9	86.1	100	100	100.00	44	5143373200	24.8	25.2	25.0	24.9	0.0	36.7	25.5	bulk
725060	ERR505208	ERP005852	ERS459873	ERX470563	ERA311846	EBI	ArrayExpress	An mRNA-sequencing atlas of mouse CD4+ T cell transcriptomes	PolyA+ mRNA-seq was performed on naive, Th1, Th2, Th17, splenic Treg, and in vitro-induced Treg (iTreg) cells.	PolyA+ mRNA-seq was performed on naive, Th1, Th2, Th17, splenic Treg, and in vitro-induced Treg (iTreg) cells.	Illumina HiSeq 2000 paired end sequencing; An mRNA-sequencing atlas of mouse CD4+ T cell transcriptomes	An mRNA-sequencing atlas of mouse CD4+ T cell transcriptomes		Th17_B	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	paired	213	54.2	CD4+, CD62L+ cells were purified with CD4+CD62L+ T Cell Isolation Kit II (Miltenyi Biotec) and further purification was performed by FACS using anti-CD62L and anti-CD4 Fab fragments. Cells were seeded into anti-CD3 (1 ug/ml, clone 145-2C11, eBioscience) and anti-CD28 (5 ug/ml, clone 37.51, eBioscience) coated 96-well plates, at a density of 250,000-500,000 cells/ml and cultured in a total volume of 200 ul in the presence of recombinant human IL-6 (30ng/ml, Immunotools), recombinant human TGF-beta1 (5ng/ml, Sigma), recombinant murine IL-1beta (10ng/ml, Immunotools), recombinant murine IL-23 (10ng/ ml, R&D systems), neutralizing anti-IL4 (5ug/ml, clone 11B11, eBioscience), neutralizing anti-IFN-gamma (5ug/ml, clone XMG1.2, eBioscience), and neutralizing anti-IL2 (5ug/ml, clone JES6-5H4, eBioscience). Cells were labelled with anti-CCR6-APC (1:200, clone 29-2L17, BioLegend), anti-CD8a-FITC (1:1500, clone 53-6.7, eBioscience), and propidium iodide. FACS sorting was then performed to select FITC-negative, APC-positive, propidium iodide-negative cells. Poly-(A)+ RNA was purified from ~500,000 cells using the Oligotex kit (Qiagen). The manufacturers protocol was modified slightly to include additional final elution steps resulting in a larger volume. RNA was purified, reverse transcribed and prepared for sequencing described in http://msb.embopress.org/content/7/1/497	Illumina HiSeq 2000	Alias;;E-MTAB-2582:Th17 rep2|Broker name;;ArrayExpress|cell type;;T-helper 17 cell|Description;;Protocols: CD4+, CD62L+ cells were purified with CD4+CD62L+ T Cell Isolation Kit II (Miltenyi Biotec) and further purification was performed by FACS using anti-CD62L and anti-CD4 Fab fragments. Cells were seeded into anti-CD3 (1 ug/ml, clone 145-2C11, eBioscience) and anti-CD28 (5 ug/ml, clone 37.51, eBioscience) coated 96-well plates, at a density of 250,000-500,000 cells/ml and cultured in a total volume of 200 ul in the presence of recombinant human IL-6 (30ng/ml, Immunotools), recombinant human TGF-beta1 (5ng/ml, Sigma), recombinant murine IL-1beta (10ng/ml, Immunotools), recombinant murine IL-23 (10ng/ ml, RD systems), neutralizing anti-IL4 (5ug/ml, clone 11B11, eBioscience), neutralizing anti-IFN-gamma (5ug/ml, clone XMG1.2, eBioscience), and neutralizing anti-IL2 (5ug/ml, clone JES6-5H4, eBioscience). Cells were labelled with anti-CCR6-APC (1:200, clone 29-2L17, BioLegend), anti-CD8a-FITC (1:1500, clone 53-6.7, eBioscience), and propidium iodide. FACS sorting was then performed to select FITC-negative, APC-positive, propidium iodide-negative cells. Poly-(A)+ RNA was purified from ~500,000 cells using the Oligotex kit (Qiagen). The manufacturers protocol was modified slightly to include additional final elution steps resulting in a larger volume. RNA was purified, reverse transcribed and prepared for sequencing described in http://msb.embopress.org/content/7/1/497|ENA checklist;;ERC000011|INSDC center alias;;EBI|INSDC center name;;European Bioinformatics Institute|INSDC first public;;2015-04-05T17:04:12Z|INSDC last update;;2018-03-08T17:48:51Z|INSDC status;;public|organism;;Mus musculus|Sample Name;;ERS459873|SRA accession;;ERS459873|Title;;Th17 rep2	Experimental Factor: cell type;;T-helper 17 cell	200	SAMEA2536557	E-MTAB-2582:Th17 rep2	30131552400	150657762	2015-04-06 04:39:03	22329773707	30131552400	150657762	2	150657762	index:0,count:150657762,average:100,stdev:0|index:1,count:150657762,average:100,stdev:0	E-MTAB-2582:Teichmann-ThExpress_Th17_B		ArrayExpress	CRUK	in_mesa	25886751	2.04	3.43	0.2	19755965604	19269750140	18348069835	18068161611	97.54	98.47	111261911	102410470	228.832	757.414	193	665082	70.1	75.57	125545761	77995043	125545761	77995043	72.69	72.52	125545761	80881376	125545761	74851262	4453249173	22.54	0.85	0	5.34	0	0.32	0	0.06	0	0.00	0	25.77	0	111261911	0	200	0	193.22	0	1.89	0	0.01	0	1.35	0	0.00	0	169.28	0	2.16	0	1282508	0	150657762	0	8052439	0	481009	0	83623	0	0	0	38831219	0	21295	0	0	0	176487	0	30790344	0	155934	0	31144060	0	68.51	0	103209472	0	312080	31430187	100.711955267880	150657762.0	111261911.0	1282508.0	8052439.0	481009.0	83623.0	0.0	38831219.0	103209472.0	73.9	0.9	5.3	0.3	0.1	0.0	25.8	68.5	100	100	100.00	38	15065776200	25.6	23.7	24.5	25.8	0.3	29.9	13.0	bulk
725125	ERR505210	ERP005852	ERS459875	ERX470565	ERA311846	EBI	ArrayExpress	An mRNA-sequencing atlas of mouse CD4+ T cell transcriptomes	PolyA+ mRNA-seq was performed on naive, Th1, Th2, Th17, splenic Treg, and in vitro-induced Treg (iTreg) cells.	PolyA+ mRNA-seq was performed on naive, Th1, Th2, Th17, splenic Treg, and in vitro-induced Treg (iTreg) cells.	Illumina HiSeq 2000 paired end sequencing; An mRNA-sequencing atlas of mouse CD4+ T cell transcriptomes	An mRNA-sequencing atlas of mouse CD4+ T cell transcriptomes		Naive C	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	paired	122	18	CD4+, CD62L+ cells were purified with CD4+CD62L+ T Cell Isolation Kit II (Miltenyi Biotec) and further purification was performed by FACS using anti-CD62L and anti-CD4 Fab fragments. Poly-(A)+ RNA was purified from ~500,000 cells using the Oligotex kit (Qiagen). The manufacturers protocol was modified slightly to include additional final elution steps resulting in a larger volume. RNA was purified, reverse transcribed and prepared for sequencing described in http://msb.embopress.org/content/7/1/497	Illumina HiSeq 2000	Alias;;E-MTAB-2582:Naive rep2|Broker name;;ArrayExpress|cell type;;naive thymus-derived CD4-positive, alpha-beta T cell|Description;;Protocols: CD4+, CD62L+ cells were purified with CD4+CD62L+ T Cell Isolation Kit II (Miltenyi Biotec) and further purification was performed by FACS using anti-CD62L and anti-CD4 Fab fragments. Poly-(A)+ RNA was purified from ~500,000 cells using the Oligotex kit (Qiagen). The manufacturers protocol was modified slightly to include additional final elution steps resulting in a larger volume. RNA was purified, reverse transcribed and prepared for sequencing described in http://msb.embopress.org/content/7/1/497|ENA checklist;;ERC000011|INSDC center alias;;EBI|INSDC center name;;European Bioinformatics Institute|INSDC first public;;2015-04-05T17:04:12Z|INSDC last update;;2018-03-08T17:48:51Z|INSDC status;;public|organism;;Mus musculus|Sample Name;;ERS459875|SRA accession;;ERS459875|Title;;Naive rep2	Experimental Factor: cell type;;naive thymus-derived CD4-positive, alpha-beta T cell	200	SAMEA2536559	E-MTAB-2582:Naive rep2	38097765000	190488825	2015-04-06 04:39:03	27489229064	38097765000	190488825	2	190488825	index:0,count:190488825,average:100,stdev:0|index:1,count:190488825,average:100,stdev:0	E-MTAB-2582:Teichmann-ThExpress_naive_C		ArrayExpress	CRUK	in_mesa	25886751	0.36	2.49	0.31	4173906522	4069592714	3939392529	3881143505	97.5	98.52	41862350	39962731	111.317	1207.140	69	1045629	55.19	58.45	46886083	23103338	46886083	23103338	55.44	55.21	46886083	23210539	46886083	21820862	1617408224	38.75	0.92	0	1.23	0	0.24	0	0.08	0	0.00	0	77.71	0	41862350	0	200	0	175.83	0	1.59	0	0.01	0	1.23	0	0.00	0	111.96	0	0.44	0	1761632	0	190488825	0	2335590	0	459854	0	144131	0	0	0	148022490	0	5037	0	0	0	66067	0	8152736	0	64886	0	8288726	0	20.75	0	39526760	0	156938	5471897	34.866616115918	190488825.0	41862350.0	1761632.0	2335590.0	459854.0	144131.0	0.0	148022490.0	39526760.0	22.0	0.9	1.2	0.2	0.1	0.0	77.7	20.8	100	100	100.00	38	19048882500	25.0	24.8	29.2	20.8	0.3	32.4	14.6	bulk
725133	ERR505211	ERP005852	ERS459871	ERX470561	ERA311846	EBI	ArrayExpress	An mRNA-sequencing atlas of mouse CD4+ T cell transcriptomes	PolyA+ mRNA-seq was performed on naive, Th1, Th2, Th17, splenic Treg, and in vitro-induced Treg (iTreg) cells.	PolyA+ mRNA-seq was performed on naive, Th1, Th2, Th17, splenic Treg, and in vitro-induced Treg (iTreg) cells.	Illumina HiSeq 2000 paired end sequencing; An mRNA-sequencing atlas of mouse CD4+ T cell transcriptomes	An mRNA-sequencing atlas of mouse CD4+ T cell transcriptomes	Protocols: CD4+, CD62L+ cells were purified with CD4+CD62L+ T Cell Isolation Kit II (Miltenyi Biotec). Cells were seeded into anti-CD3 (2 ug/ml, clone 145-2C11, eBioscience) and anti-CD28 (5 ug/ml, clone 37.51, eBioscience) coated 96-well plates, at a density of 250,000-500,000 cells/ml and cultured in a total volume of 200 ul in the presence of recombinant murine IL-12 (10 ng/ml, RD Systems) and neutralising anti-IL4 (10 ug/ml, clone 11B11, eBioscience). Cells were cultured for another four days in absence of CD3 and CD28 stimulation to rest them. The original medium was kept and fresh medium containing the same cytokines as before was added to dilute the cultures 1:3. Finally, the cells were labelled with anti-CXCR3-APC (1:200, clone CXCR3-173, BioLegend) and Propidium Iodide and FITC-conjugated antibodies against CD11b, CD11c, Ly6G, CD8a and CD19. The cultures were then FACS-sorted to obtain Propidium Iodide-, FITC-negative and CXCR3-positive cells. RNA was purified using the Qiagen RNEasy Plus Mini Kit automated using a QIAcube Samples were processed using the TruSeq RNA Sample Prep v2 kit (Illumina) according to the manufacturers instructions with an alteration to use KAPA Hifi polymerase for PCR amplification instead of the one supplied with the kit.	Th1_A	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	paired	262	68.6	CD4+, CD62L+ cells were purified with CD4+CD62L+ T Cell Isolation Kit II (Miltenyi Biotec). Cells were seeded into anti-CD3 (2 ug/ml, clone 145-2C11, eBioscience) and anti-CD28 (5 ug/ml, clone 37.51, eBioscience) coated 96-well plates, at a density of 250,000-500,000 cells/ml and cultured in a total volume of 200 ul in the presence of recombinant murine IL-12 (10 ng/ml, RD Systems) and neutralising anti-IL4 (10 ug/ml, clone 11B11, eBioscience). Cells were cultured for another four days in absence of CD3 and CD28 stimulation to rest them. The original medium was kept and fresh medium containing the same cytokines as before was added to dilute the cultures 1:3. Finally, the cells were labelled with anti-CXCR3-APC (1:200, clone CXCR3-173, BioLegend) and Propidium Iodide and FITC-conjugated antibodies against CD11b, CD11c, Ly6G, CD8a and CD19. The cultures were then FACS-sorted to obtain Propidium Iodide-, FITC-negative and CXCR3-positive cells. RNA was purified using the Qiagen RNEasy Plus Mini Kit automated using a QIAcube Samples were processed using the TruSeq RNA Sample Prep v2 kit (Illumina) according to the manufacturers instructions with an alteration to use KAPA Hifi polymerase for PCR amplification instead of the one supplied with the kit.	Illumina HiSeq 2000	alias;;E-MTAB-2582:Th1 rep1|broker name;;ArrayExpress|cell type;;T-helper 1 cell|ENA checklist;;ERC000011|INSDC center alias;;EBI|INSDC center name;;European Bioinformatics Institute|INSDC first public;;2015-04-05T17:04:12Z|INSDC last update;;2018-03-08T17:48:50Z|INSDC status;;public|organism;;Mus musculus|Sample Name;;ERS459871|SRA accession;;ERS459871|title;;Th1 rep1	Experimental Factor: cell type;;T-helper 1 cell	200	SAMEA2536555	E-MTAB-2582:Th1 rep1	10164746600	50823733	2015-04-06 04:39:04	7344222623	10164746600	50823733	2	50823733	index:0,count:50823733,average:100,stdev:0|index:1,count:50823733,average:100,stdev:0	E-MTAB-2582:Teichmann-ThExpress_Th1_A		ArrayExpress	SC	in_mesa	25886751	3.4	3.43	0.08	9636893796	9497730474	8765524603	8702568962	98.56	99.28	49715955	41987734	294.134	1217.331	227	256875	85.29	93.79	57141474	42400872	57141474	42400872	90.35	90.83	57141474	44917769	57141474	41066000	470283174	4.88	0.69	0	8.87	0	0.41	0	0.08	0	0.00	0	1.68	0	49715955	0	200	0	198.38	0	1.49	0	0.01	0	1.23	0	0.00	0	365.93	0	0.29	0	348672	0	50823733	0	4506408	0	210323	0	41500	0	0	0	855955	0	16016	0	0	0	176694	0	23976448	0	42131	0	24211289	0	88.95	0	45209547	0	227383	25424407	111.813139064926	50823733.0	49715955.0	348672.0	4506408.0	210323.0	41500.0	0.0	855955.0	45209547.0	97.8	0.7	8.9	0.4	0.1	0.0	1.7	89.0	100	100	100.00	44	5082373300	25.0	25.0	24.9	25.1	0.0	36.7	25.6	bulk
725142	ERR505212	ERP005852	ERS459879	ERX470569	ERA311846	EBI	ArrayExpress	An mRNA-sequencing atlas of mouse CD4+ T cell transcriptomes	PolyA+ mRNA-seq was performed on naive, Th1, Th2, Th17, splenic Treg, and in vitro-induced Treg (iTreg) cells.	PolyA+ mRNA-seq was performed on naive, Th1, Th2, Th17, splenic Treg, and in vitro-induced Treg (iTreg) cells.	Illumina HiSeq 2000 paired end sequencing; An mRNA-sequencing atlas of mouse CD4+ T cell transcriptomes	An mRNA-sequencing atlas of mouse CD4+ T cell transcriptomes	Protocols: CD4+, CD62L+ cells were purified with CD4+CD62L+ T Cell Isolation Kit II (Miltenyi Biotec). Cells were seeded into anti-CD3 (2 ug/ml, clone 145-2C11, eBioscience) and anti-CD28 (5 ug/ml, clone 37.51, eBioscience) coated 96-well plates, at a density of 250,000-500,000 cells/ml and cultured in a total volume of 200 ul in the presence of recombinant murine IL-4 (10 ng/ml, R&D Systems) and neutralizing anti-IFN-gamma (10 ug/ml, clone XMG1.2, eBioscience). Cells were cultured for another four days in absence of CD3 and CD28 stimulation to rest them. The original medium was kept and fresh medium containing the same cytokines as before was added to dilute the cultures 1:3. Finally, the cells were labelled with Propidium Iodide and FITC-conjugated antibodies against CD11b, CD11c, Ly6G, CD8a and CD19. The cultures were then FACS-sorted to obtain Propidium Iodide-, FITC-negative cells. RNA was purified using the Qiagen RNEasy Plus Mini Kit automated using a QIAcube Samples were processed using the TruSeq RNA Sample Prep v2 kit (Illumina) according to the manufacturers instructions with an alteration to use KAPA Hifi polymerase for PCR amplification instead of the one supplied with the kit.	Th2_B	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	paired	260	68.3	CD4+, CD62L+ cells were purified with CD4+CD62L+ T Cell Isolation Kit II (Miltenyi Biotec). Cells were seeded into anti-CD3 (2 ug/ml, clone 145-2C11, eBioscience) and anti-CD28 (5 ug/ml, clone 37.51, eBioscience) coated 96-well plates, at a density of 250,000-500,000 cells/ml and cultured in a total volume of 200 ul in the presence of recombinant murine IL-4 (10 ng/ml, RD Systems) and neutralizing anti-IFN-gamma (10 ug/ml, clone XMG1.2, eBioscience). Cells were cultured for another four days in absence of CD3 and CD28 stimulation to rest them. The original medium was kept and fresh medium containing the same cytokines as before was added to dilute the cultures 1:3. Finally, the cells were labelled with Propidium Iodide and FITC-conjugated antibodies against CD11b, CD11c, Ly6G, CD8a and CD19. The cultures were then FACS-sorted to obtain Propidium Iodide-, FITC-negative cells. RNA was purified using the Qiagen RNEasy Plus Mini Kit automated using a QIAcube Samples were processed using the TruSeq RNA Sample Prep v2 kit (Illumina) according to the manufacturers instructions with an alteration to use KAPA Hifi polymerase for PCR amplification instead of the one supplied with the kit.	Illumina HiSeq 2000	alias;;E-MTAB-2582:Th2 rep2|broker name;;ArrayExpress|cell type;;T-helper 2 cell|ENA checklist;;ERC000011|INSDC center alias;;EBI|INSDC center name;;European Bioinformatics Institute|INSDC first public;;2015-04-05T17:04:12Z|INSDC last update;;2018-03-08T17:50:42Z|INSDC status;;public|organism;;Mus musculus|Sample Name;;ERS459879|SRA accession;;ERS459879|title;;Th2 rep2	Experimental Factor: cell type;;T-helper 2 cell	200	SAMEA2536563	E-MTAB-2582:Th2 rep2	10416061000	52080305	2015-04-06 04:39:04	7515996459	10416061000	52080305	2	52080305	index:0,count:52080305,average:100,stdev:0|index:1,count:52080305,average:100,stdev:0	E-MTAB-2582:Teichmann-ThExpress_Th2_B		ArrayExpress	SC	in_mesa	25886751	7.94	3.39	0.09	9856476660	9743231117	8722054874	8677479789	98.85	99.49	50943008	44815546	288.899	998.324	218	280711	80.31	90.78	59486341	40910556	59486341	40910556	87.65	87.49	59486341	44649506	59486341	39425317	824597356	8.37	0.72	0	11.29	0	0.29	0	0.09	0	0.00	0	1.81	0	50943008	0	200	0	198.41	0	1.54	0	0.01	0	1.20	0	0.01	0	347.20	0	0.30	0	373496	0	52080305	0	5879323	0	148430	0	45527	0	0	0	943340	0	14270	0	0	0	154123	0	20622131	0	39624	0	20830148	0	86.53	0	45063685	0	230716	22178807	96.130337731237	52080305.0	50943008.0	373496.0	5879323.0	148430.0	45527.0	0.0	943340.0	45063685.0	97.8	0.7	11.3	0.3	0.1	0.0	1.8	86.5	100	100	100.00	44	5208030500	25.0	25.0	24.9	25.1	0.0	36.7	25.5	bulk
896076	ERR525589	ERP005997	ERS472808	ERX490829	ERA315790	UCSF	ArrayExpress	RNA-seq comparison of primary mouse classical brown, beige, and white adipocytes	Classical brown adipocytes in interscapular BAT (Myf-5 derived) and "inducible" beige cells in WAT (non-Myf-5 derived) have distinct developmental origins, although both cell types have morphological and biochemical characteristics of brown fat such as the expression of UCP1. This raises an important question as to how similar the two types of brown adipocytes are at molecular and functional levels. To this end, we employed RNA-seq to systematically determine the transcriptional signatures unique to each cell type.	Classical brown adipocytes in interscapular BAT (Myf-5 derived) and "inducible" beige cells in WAT (non-Myf-5 derived) have distinct developmental origins, although both cell types have morphological and biochemical characteristics of brown fat such as the expression of UCP1. This raises an important question as to how similar the two types of brown adipocytes are at molecular and functional levels. To this end, we employed RNA-seq to systematically determine the transcriptional signatures unique to each cell type.	Illumina HiSeq 2500 paired end sequencing; RNA-seq comparison of primary mouse classical brown, beige, and white adipocytes	RNA-seq comparison of primary mouse classical brown, beige, and white adipocytes	Protocols: Primary stromal vascular (SV) cells were isolated from inguinal WAT or from interscapular BAT of the same C57BL/6 mice using Collagenase D (1.5 u/ml) and Dispase II (2.4 u/ml). To clearly define the molecular signatures of PPAR-gamma ligand-induced beige cells, we used C57BL/6 mice that possess less beige cells in the absence of environmental stimuli. SV cells were plated in collagen coated culture dishes in DMEM/F12 medium (D-glucose 17.51 mM) and differentiated as described previously (DOI: 10.1371/journal.pone.0049452). Beige cells were induced by a specific PPAR-gamma agonist rosiglitazone (1uM). RiboZol reagent (AMRESCO) following the manufacturer's protocol Ultralow DR library kit (NuGEN): www.nugeninc.com/nugen/index.cfm/products/cs/ngs/rna-seq-v2	Brown_biolrepli2	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	paired	315	33	Primary stromal vascular (SV) cells were isolated from inguinal WAT or from interscapular BAT of the same C57BL/6 mice using Collagenase D (1.5 u/ml) and Dispase II (2.4 u/ml). To clearly define the molecular signatures of PPAR-gamma ligand-induced beige cells, we used C57BL/6 mice that possess less beige cells in the absence of environmental stimuli. SV cells were plated in collagen coated culture dishes in DMEM/F12 medium (D-glucose 17.51 mM) and differentiated as described previously (DOI: 10.1371/journal.pone.0049452). Beige cells were induced by a specific PPAR-gamma agonist rosiglitazone (1uM). RiboZol reagent (AMRESCO) following the manufacturer's protocol Ultralow DR library kit (NuGEN): www.nugeninc.com/nugen/index.cfm/products/cs/ngs/rna-seq-v2	Illumina HiSeq 2500	alias;;E-MTAB-2624:Brown_biolrepli2|broker name;;ArrayExpress|cell type;;claical brown adipocyte|ENA checklist;;ERC000011|INSDC center alias;;UCSF|INSDC center name;;University of California, San Francisco|INSDC first public;;2015-02-16T17:01:59Z|INSDC last update;;2018-03-08T18:23:10Z|INSDC status;;public|organism;;Mus musculus|Sample Name;;ERS472808|SRA accession;;ERS472808|title;;Brown_biolrepli2	Experimental Factor: cell type;;Classical brown adipocyte	202	SAMEA2579686	E-MTAB-2624:Brown_biolrepli2	9544367084	47249342	2015-02-17 06:11:42	6326450204	9544367084	47249342	2	47249342	index:0,count:47249342,average:101,stdev:0|index:1,count:47249342,average:101,stdev:0	E-MTAB-2624:RNA2_read		ArrayExpress	UCSF Genomics Core	in_mesa	25774848	69.4	0.85	0.1	5352002051	5339289621	5210446100	5215095436	99.76	100.09	35339003	34660696	173.776	356.125	104	263743	91.2	93.96	36782305	32229717	36782305	32229717	91.77	92.23	36782305	32430202	36782305	31635972	274731730	5.13	5.66	0	2.19	0	0.12	0	0.03	0	0.00	0	25.05	0	35339003	0	202	0	195.28	0	1.60	0	0.02	0	1.96	0	0.01	0	255.40	0	0.46	0	2673061	0	47249342	0	1036708	0	58121	0	16426	0	0	0	11835792	0	1701	0	0	0	15296	0	2870864	0	26674	0	2914535	0	72.60	0	34302295	0	104267	2507807	24.051780524998	47249342.0	35339003.0	2673061.0	1036708.0	58121.0	16426.0	0.0	11835792.0	34302295.0	74.8	5.7	2.2	0.1	0.0	0.0	25.0	72.6	101	101	101.00	38	4772183542	31.3	19.2	19.3	30.2	0.0	36.0	20.3	bulk
896132	ERR525590	ERP005997	ERS472804	ERX490825	ERA315790	UCSF	ArrayExpress	RNA-seq comparison of primary mouse classical brown, beige, and white adipocytes	Classical brown adipocytes in interscapular BAT (Myf-5 derived) and "inducible" beige cells in WAT (non-Myf-5 derived) have distinct developmental origins, although both cell types have morphological and biochemical characteristics of brown fat such as the expression of UCP1. This raises an important question as to how similar the two types of brown adipocytes are at molecular and functional levels. To this end, we employed RNA-seq to systematically determine the transcriptional signatures unique to each cell type.	Classical brown adipocytes in interscapular BAT (Myf-5 derived) and "inducible" beige cells in WAT (non-Myf-5 derived) have distinct developmental origins, although both cell types have morphological and biochemical characteristics of brown fat such as the expression of UCP1. This raises an important question as to how similar the two types of brown adipocytes are at molecular and functional levels. To this end, we employed RNA-seq to systematically determine the transcriptional signatures unique to each cell type.	Illumina HiSeq 2500 paired end sequencing; RNA-seq comparison of primary mouse classical brown, beige, and white adipocytes	RNA-seq comparison of primary mouse classical brown, beige, and white adipocytes		White_biolrepli1	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	paired	340	38.7	Primary stromal vascular (SV) cells were isolated from inguinal WAT or from interscapular BAT of the same C57BL/6 mice using Collagenase D (1.5 u/ml) and Dispase II (2.4 u/ml). To clearly define the molecular signatures of PPAR-gamma ligand-induced beige cells, we used C57BL/6 mice that possess less beige cells in the absence of environmental stimuli. SV cells were plated in collagen coated culture dishes in DMEM/F12 medium (D-glucose 17.51 mM) and differentiated as described previously (DOI: 10.1371/journal.pone.0049452). Beige cells were induced by a specific PPAR-gamma agonist rosiglitazone (1uM). RiboZol reagent (AMRESCO) following the manufacturer's protocol Ultralow DR library kit (NuGEN): www.nugeninc.com/nugen/index.cfm/products/cs/ngs/rna-seq-v2	Illumina HiSeq 2500	Alias;;E-MTAB-2624:White_biolrepli1|Broker name;;ArrayExpress|cell type;;inguinal white adipocyte|Description;;Protocols: Primary stromal vascular (SV) cells were isolated from inguinal WAT or from interscapular BAT of the same C57BL/6 mice using Collagenase D (1.5 u/ml) and Dispase II (2.4 u/ml). To clearly define the molecular signatures of PPAR-gamma ligand-induced beige cells, we used C57BL/6 mice that possess less beige cells in the absence of environmental stimuli. SV cells were plated in collagen coated culture dishes in DMEM/F12 medium (D-glucose 17.51 mM) and differentiated as described previously (DOI: 10.1371/journal.pone.0049452). Beige cells were induced by a specific PPAR-gamma agonist rosiglitazone (1uM). RiboZol reagent (AMRESCO) following the manufacturer's protocol Ultralow DR library kit (NuGEN): www.nugeninc.com/nugen/index.cfm/products/cs/ngs/rna-seq-v2|ENA checklist;;ERC000011|INSDC center alias;;UCSF|INSDC center name;;University of California, San Francisco|INSDC first public;;2015-02-16T17:01:59Z|INSDC last update;;2018-03-08T18:23:10Z|INSDC status;;public|organism;;Mus musculus|Sample Name;;ERS472804|SRA accession;;ERS472804|Title;;White_biolrepli1	Experimental Factor: cell type;;inguinal white adipocyte	202	SAMEA2579682	E-MTAB-2624:White_biolrepli1	9963114296	49322348	2015-02-17 06:11:42	6751759764	9963114296	49322348	2	49322348	index:0,count:49322348,average:101,stdev:0|index:1,count:49322348,average:101,stdev:0	E-MTAB-2624:RNA3_read		ArrayExpress	UCSF Genomics Core	in_mesa	25774848	35.89	1.45	0.12	5243695848	5282325114	4999640189	5069263128	100.74	101.39	35110311	33702023	175.219	563.143	103	255708	83.44	88.13	38316160	29296614	38316160	29296614	80.56	82.11	38316160	28283118	38316160	27293477	482098147	9.19	4.81	0	3.79	0	0.33	0	0.14	0	0.00	0	28.35	0	35110311	0	202	0	193.77	0	2.21	0	0.03	0	2.87	0	0.03	0	183.62	0	0.60	0	2372091	0	49322348	0	1868688	0	160913	0	68914	0	0	0	13982210	0	4688	0	0	0	31633	0	6095842	0	35438	0	6167601	0	67.40	0	33241623	0	144693	5365901	37.084731120372	49322348.0	35110311.0	2372091.0	1868688.0	160913.0	68914.0	0.0	13982210.0	33241623.0	71.2	4.8	3.8	0.3	0.1	0.0	28.3	67.4	101	101	101.00	38	4981557148	27.7	22.5	22.8	27.0	0.0	35.1	18.3	bulk
896140	ERR525591	ERP005997	ERS472807	ERX490828	ERA315790	UCSF	ArrayExpress	RNA-seq comparison of primary mouse classical brown, beige, and white adipocytes	Classical brown adipocytes in interscapular BAT (Myf-5 derived) and "inducible" beige cells in WAT (non-Myf-5 derived) have distinct developmental origins, although both cell types have morphological and biochemical characteristics of brown fat such as the expression of UCP1. This raises an important question as to how similar the two types of brown adipocytes are at molecular and functional levels. To this end, we employed RNA-seq to systematically determine the transcriptional signatures unique to each cell type.	Classical brown adipocytes in interscapular BAT (Myf-5 derived) and "inducible" beige cells in WAT (non-Myf-5 derived) have distinct developmental origins, although both cell types have morphological and biochemical characteristics of brown fat such as the expression of UCP1. This raises an important question as to how similar the two types of brown adipocytes are at molecular and functional levels. To this end, we employed RNA-seq to systematically determine the transcriptional signatures unique to each cell type.	Illumina HiSeq 2500 paired end sequencing; RNA-seq comparison of primary mouse classical brown, beige, and white adipocytes	RNA-seq comparison of primary mouse classical brown, beige, and white adipocytes	Protocols: Primary stromal vascular (SV) cells were isolated from inguinal WAT or from interscapular BAT of the same C57BL/6 mice using Collagenase D (1.5 u/ml) and Dispase II (2.4 u/ml). To clearly define the molecular signatures of PPAR-gamma ligand-induced beige cells, we used C57BL/6 mice that possess less beige cells in the absence of environmental stimuli. SV cells were plated in collagen coated culture dishes in DMEM/F12 medium (D-glucose 17.51 mM) and differentiated as described previously (DOI: 10.1371/journal.pone.0049452). Beige cells were induced by a specific PPAR-gamma agonist rosiglitazone (1uM). RiboZol reagent (AMRESCO) following the manufacturer's protocol Ultralow DR library kit (NuGEN): www.nugeninc.com/nugen/index.cfm/products/cs/ngs/rna-seq-v2	Beige_biolrepli1	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	paired	304	27.3	Primary stromal vascular (SV) cells were isolated from inguinal WAT or from interscapular BAT of the same C57BL/6 mice using Collagenase D (1.5 u/ml) and Dispase II (2.4 u/ml). To clearly define the molecular signatures of PPAR-gamma ligand-induced beige cells, we used C57BL/6 mice that possess less beige cells in the absence of environmental stimuli. SV cells were plated in collagen coated culture dishes in DMEM/F12 medium (D-glucose 17.51 mM) and differentiated as described previously (DOI: 10.1371/journal.pone.0049452). Beige cells were induced by a specific PPAR-gamma agonist rosiglitazone (1uM). RiboZol reagent (AMRESCO) following the manufacturer's protocol Ultralow DR library kit (NuGEN): www.nugeninc.com/nugen/index.cfm/products/cs/ngs/rna-seq-v2	Illumina HiSeq 2500	alias;;E-MTAB-2624:Beige_biolrepli1|broker name;;ArrayExpress|cell type;;rosiglitazone-treated adipocyte (beige cell)|ENA checklist;;ERC000011|INSDC center alias;;UCSF|INSDC center name;;University of California, San Francisco|INSDC first public;;2015-02-16T17:01:59Z|INSDC last update;;2018-03-08T18:23:10Z|INSDC status;;public|organism;;Mus musculus|Sample Name;;ERS472807|SRA accession;;ERS472807|title;;Beige_biolrepli1	Experimental Factor: cell type;;rosiglitazone-treated adipocyte (beige cell)	202	SAMEA2579685	E-MTAB-2624:Beige_biolrepli1	8117348790	40184895	2015-02-17 06:11:42	5454071296	8117348790	40184895	2	40184895	index:0,count:40184895,average:101,stdev:0|index:1,count:40184895,average:101,stdev:0	E-MTAB-2624:RNA5_read		ArrayExpress	UCSF Genomics Core	in_mesa	25774848	56.17	1.01	0.09	4255502154	4283033481	4067915904	4118035621	100.65	101.23	28682372	27926943	170.161	427.931	102	220623	88.42	93.04	30908795	25360623	30908795	25360623	87.47	88.69	30908795	25088593	30908795	24175188	217013552	5.10	5.12	0	3.54	0	0.25	0	0.01	0	0.00	0	28.36	0	28682372	0	202	0	193.90	0	2.07	0	0.03	0	2.49	0	0.02	0	227.10	0	0.56	0	2058860	0	40184895	0	1424249	0	100779	0	5898	0	0	0	11395846	0	2542	0	0	0	16396	0	3346102	0	27173	0	3392213	0	67.83	0	27258123	0	119302	2926754	24.532312953681	40184895.0	28682372.0	2058860.0	1424249.0	100779.0	5898.0	0.0	11395846.0	27258123.0	71.4	5.1	3.5	0.3	0.0	0.0	28.4	67.8	101	101	101.00	38	4058674395	29.4	21.2	21.2	28.1	0.0	35.4	18.8	bulk
896148	ERR525592	ERP005997	ERS472803	ERX490824	ERA315790	UCSF	ArrayExpress	RNA-seq comparison of primary mouse classical brown, beige, and white adipocytes	Classical brown adipocytes in interscapular BAT (Myf-5 derived) and "inducible" beige cells in WAT (non-Myf-5 derived) have distinct developmental origins, although both cell types have morphological and biochemical characteristics of brown fat such as the expression of UCP1. This raises an important question as to how similar the two types of brown adipocytes are at molecular and functional levels. To this end, we employed RNA-seq to systematically determine the transcriptional signatures unique to each cell type.	Classical brown adipocytes in interscapular BAT (Myf-5 derived) and "inducible" beige cells in WAT (non-Myf-5 derived) have distinct developmental origins, although both cell types have morphological and biochemical characteristics of brown fat such as the expression of UCP1. This raises an important question as to how similar the two types of brown adipocytes are at molecular and functional levels. To this end, we employed RNA-seq to systematically determine the transcriptional signatures unique to each cell type.	Illumina HiSeq 2500 paired end sequencing; RNA-seq comparison of primary mouse classical brown, beige, and white adipocytes	RNA-seq comparison of primary mouse classical brown, beige, and white adipocytes		Brown_biolrepli1	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	paired	250	17.3	Primary stromal vascular (SV) cells were isolated from inguinal WAT or from interscapular BAT of the same C57BL/6 mice using Collagenase D (1.5 u/ml) and Dispase II (2.4 u/ml). To clearly define the molecular signatures of PPAR-gamma ligand-induced beige cells, we used C57BL/6 mice that possess less beige cells in the absence of environmental stimuli. SV cells were plated in collagen coated culture dishes in DMEM/F12 medium (D-glucose 17.51 mM) and differentiated as described previously (DOI: 10.1371/journal.pone.0049452). Beige cells were induced by a specific PPAR-gamma agonist rosiglitazone (1uM). RiboZol reagent (AMRESCO) following the manufacturer's protocol Ultralow DR library kit (NuGEN): www.nugeninc.com/nugen/index.cfm/products/cs/ngs/rna-seq-v2	Illumina HiSeq 2500	Alias;;E-MTAB-2624:Brown_biolrepli1|Broker name;;ArrayExpress|cell type;;claical brown adipocyte|Description;;Protocols: Primary stromal vascular (SV) cells were isolated from inguinal WAT or from interscapular BAT of the same C57BL/6 mice using Collagenase D (1.5 u/ml) and Dispase II (2.4 u/ml). To clearly define the molecular signatures of PPAR-gamma ligand-induced beige cells, we used C57BL/6 mice that possess less beige cells in the absence of environmental stimuli. SV cells were plated in collagen coated culture dishes in DMEM/F12 medium (D-glucose 17.51 mM) and differentiated as described previously (DOI: 10.1371/journal.pone.0049452). Beige cells were induced by a specific PPAR-gamma agonist rosiglitazone (1uM). RiboZol reagent (AMRESCO) following the manufacturer's protocol Ultralow DR library kit (NuGEN): www.nugeninc.com/nugen/index.cfm/products/cs/ngs/rna-seq-v2|ENA checklist;;ERC000011|INSDC center alias;;UCSF|INSDC center name;;University of California, San Francisco|INSDC first public;;2015-02-16T17:01:59Z|INSDC last update;;2018-03-08T18:23:10Z|INSDC status;;public|organism;;Mus musculus|Sample Name;;ERS472803|SRA accession;;ERS472803|Title;;Brown_biolrepli1	Experimental Factor: cell type;;Classical brown adipocyte	202	SAMEA2579681	E-MTAB-2624:Brown_biolrepli1	9444402536	46754468	2015-02-17 06:11:42	6358686090	9444402536	46754468	2	46754468	index:0,count:46754468,average:101,stdev:0|index:1,count:46754468,average:101,stdev:0	E-MTAB-2624:RNA1_read		ArrayExpress	UCSF Genomics Core	in_mesa	25774848	53.15	0.97	0.07	5446652802	5494651048	5223130405	5298162690	100.88	101.44	35398606	34355770	181.015	413.635	113	240058	87.3	91.58	37933435	30903046	37933435	30903046	85.53	86.86	37933435	30276452	37933435	29309961	363466229	6.67	4.96	0	3.54	0	0.16	0	0.02	0	0.00	0	24.11	0	35398606	0	202	0	194.94	0	2.24	0	0.03	0	2.15	0	0.02	0	331.98	0	0.55	0	2319405	0	46754468	0	1653684	0	75898	0	7200	0	0	0	11272764	0	2880	0	0	0	21115	0	4283777	0	28981	0	4336753	0	72.17	0	33744922	0	130938	3800154	29.022545021308	46754468.0	35398606.0	2319405.0	1653684.0	75898.0	7200.0	0.0	11272764.0	33744922.0	75.7	5.0	3.5	0.2	0.0	0.0	24.1	72.2	101	101	101.00	38	4722201268	29.0	21.4	21.5	28.1	0.0	35.4	18.9	bulk
896156	ERR525593	ERP005997	ERS472805	ERX490826	ERA315790	UCSF	ArrayExpress	RNA-seq comparison of primary mouse classical brown, beige, and white adipocytes	Classical brown adipocytes in interscapular BAT (Myf-5 derived) and "inducible" beige cells in WAT (non-Myf-5 derived) have distinct developmental origins, although both cell types have morphological and biochemical characteristics of brown fat such as the expression of UCP1. This raises an important question as to how similar the two types of brown adipocytes are at molecular and functional levels. To this end, we employed RNA-seq to systematically determine the transcriptional signatures unique to each cell type.	Classical brown adipocytes in interscapular BAT (Myf-5 derived) and "inducible" beige cells in WAT (non-Myf-5 derived) have distinct developmental origins, although both cell types have morphological and biochemical characteristics of brown fat such as the expression of UCP1. This raises an important question as to how similar the two types of brown adipocytes are at molecular and functional levels. To this end, we employed RNA-seq to systematically determine the transcriptional signatures unique to each cell type.	Illumina HiSeq 2500 paired end sequencing; RNA-seq comparison of primary mouse classical brown, beige, and white adipocytes	RNA-seq comparison of primary mouse classical brown, beige, and white adipocytes	Protocols: Primary stromal vascular (SV) cells were isolated from inguinal WAT or from interscapular BAT of the same C57BL/6 mice using Collagenase D (1.5 u/ml) and Dispase II (2.4 u/ml). To clearly define the molecular signatures of PPAR-gamma ligand-induced beige cells, we used C57BL/6 mice that possess less beige cells in the absence of environmental stimuli. SV cells were plated in collagen coated culture dishes in DMEM/F12 medium (D-glucose 17.51 mM) and differentiated as described previously (DOI: 10.1371/journal.pone.0049452). Beige cells were induced by a specific PPAR-gamma agonist rosiglitazone (1uM). RiboZol reagent (AMRESCO) following the manufacturer's protocol Ultralow DR library kit (NuGEN): www.nugeninc.com/nugen/index.cfm/products/cs/ngs/rna-seq-v2	Beige_biolrepli2	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	paired	372	33.5	Primary stromal vascular (SV) cells were isolated from inguinal WAT or from interscapular BAT of the same C57BL/6 mice using Collagenase D (1.5 u/ml) and Dispase II (2.4 u/ml). To clearly define the molecular signatures of PPAR-gamma ligand-induced beige cells, we used C57BL/6 mice that possess less beige cells in the absence of environmental stimuli. SV cells were plated in collagen coated culture dishes in DMEM/F12 medium (D-glucose 17.51 mM) and differentiated as described previously (DOI: 10.1371/journal.pone.0049452). Beige cells were induced by a specific PPAR-gamma agonist rosiglitazone (1uM). RiboZol reagent (AMRESCO) following the manufacturer's protocol Ultralow DR library kit (NuGEN): www.nugeninc.com/nugen/index.cfm/products/cs/ngs/rna-seq-v2	Illumina HiSeq 2500	alias;;E-MTAB-2624:Beige_biolrepli2|broker name;;ArrayExpress|cell type;;rosiglitazone-treated adipocyte (beige cell)|ENA checklist;;ERC000011|INSDC center alias;;UCSF|INSDC center name;;University of California, San Francisco|INSDC first public;;2015-02-16T17:01:59Z|INSDC last update;;2018-03-08T18:23:10Z|INSDC status;;public|organism;;Mus musculus|Sample Name;;ERS472805|SRA accession;;ERS472805|title;;Beige_biolrepli2	Experimental Factor: cell type;;rosiglitazone-treated adipocyte (beige cell)	202	SAMEA2579683	E-MTAB-2624:Beige_biolrepli2	14372387062	71150431	2015-02-17 06:11:43	9641746184	14372387062	71150431	2	71150431	index:0,count:71150431,average:101,stdev:0|index:1,count:71150431,average:101,stdev:0	E-MTAB-2624:RNA6_read		ArrayExpress	UCSF Genomics Core	in_mesa	25774848	55.76	1.04	0.07	9179701788	9223579306	8834755920	8919721754	100.48	100.96	57379432	55485007	191.261	452.877	124	341783	88.66	92.51	61071796	50872565	61071796	50872565	87.74	88.73	61071796	50346189	61071796	48789272	550711077	6.00	5.42	0	3.36	0	0.24	0	0.02	0	0.00	0	19.10	0	57379432	0	202	0	195.88	0	2.04	0	0.03	0	2.45	0	0.02	0	256.65	0	0.53	0	3855628	0	71150431	0	2390272	0	172653	0	11088	0	0	0	13587258	0	5661	0	0	0	38674	0	7417026	0	49480	0	7510841	0	77.29	0	54989160	0	152618	6794222	44.517828827530	71150431.0	57379432.0	3855628.0	2390272.0	172653.0	11088.0	0.0	13587258.0	54989160.0	80.6	5.4	3.4	0.2	0.0	0.0	19.1	77.3	101	101	101.00	38	7186193531	29.2	21.0	21.1	28.7	0.0	35.6	19.1	bulk
896164	ERR525594	ERP005997	ERS472806	ERX490827	ERA315790	UCSF	ArrayExpress	RNA-seq comparison of primary mouse classical brown, beige, and white adipocytes	Classical brown adipocytes in interscapular BAT (Myf-5 derived) and "inducible" beige cells in WAT (non-Myf-5 derived) have distinct developmental origins, although both cell types have morphological and biochemical characteristics of brown fat such as the expression of UCP1. This raises an important question as to how similar the two types of brown adipocytes are at molecular and functional levels. To this end, we employed RNA-seq to systematically determine the transcriptional signatures unique to each cell type.	Classical brown adipocytes in interscapular BAT (Myf-5 derived) and "inducible" beige cells in WAT (non-Myf-5 derived) have distinct developmental origins, although both cell types have morphological and biochemical characteristics of brown fat such as the expression of UCP1. This raises an important question as to how similar the two types of brown adipocytes are at molecular and functional levels. To this end, we employed RNA-seq to systematically determine the transcriptional signatures unique to each cell type.	Illumina HiSeq 2500 paired end sequencing; RNA-seq comparison of primary mouse classical brown, beige, and white adipocytes	RNA-seq comparison of primary mouse classical brown, beige, and white adipocytes	Protocols: Primary stromal vascular (SV) cells were isolated from inguinal WAT or from interscapular BAT of the same C57BL/6 mice using Collagenase D (1.5 u/ml) and Dispase II (2.4 u/ml). To clearly define the molecular signatures of PPAR-gamma ligand-induced beige cells, we used C57BL/6 mice that possess less beige cells in the absence of environmental stimuli. SV cells were plated in collagen coated culture dishes in DMEM/F12 medium (D-glucose 17.51 mM) and differentiated as described previously (DOI: 10.1371/journal.pone.0049452). Beige cells were induced by a specific PPAR-gamma agonist rosiglitazone (1uM). RiboZol reagent (AMRESCO) following the manufacturer's protocol Ultralow DR library kit (NuGEN): www.nugeninc.com/nugen/index.cfm/products/cs/ngs/rna-seq-v2	White_biolrepli2	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	paired	391	35.5	Primary stromal vascular (SV) cells were isolated from inguinal WAT or from interscapular BAT of the same C57BL/6 mice using Collagenase D (1.5 u/ml) and Dispase II (2.4 u/ml). To clearly define the molecular signatures of PPAR-gamma ligand-induced beige cells, we used C57BL/6 mice that possess less beige cells in the absence of environmental stimuli. SV cells were plated in collagen coated culture dishes in DMEM/F12 medium (D-glucose 17.51 mM) and differentiated as described previously (DOI: 10.1371/journal.pone.0049452). Beige cells were induced by a specific PPAR-gamma agonist rosiglitazone (1uM). RiboZol reagent (AMRESCO) following the manufacturer's protocol Ultralow DR library kit (NuGEN): www.nugeninc.com/nugen/index.cfm/products/cs/ngs/rna-seq-v2	Illumina HiSeq 2500	alias;;E-MTAB-2624:White_biolrepli2|broker name;;ArrayExpress|cell type;;inguinal white adipocyte|ENA checklist;;ERC000011|INSDC center alias;;UCSF|INSDC center name;;University of California, San Francisco|INSDC first public;;2015-02-16T17:01:59Z|INSDC last update;;2018-03-08T18:23:10Z|INSDC status;;public|organism;;Mus musculus|Sample Name;;ERS472806|SRA accession;;ERS472806|title;;White_biolrepli2	Experimental Factor: cell type;;inguinal white adipocyte	202	SAMEA2579684	E-MTAB-2624:White_biolrepli2	7531707158	37285679	2015-02-17 06:11:43	5093935817	7531707158	37285679	2	37285679	index:0,count:37285679,average:101,stdev:0|index:1,count:37285679,average:101,stdev:0	E-MTAB-2624:RNA4_read		ArrayExpress	UCSF Genomics Core	in_mesa	25774848	35.4	1.53	0.09	4755535538	4795339132	4560492548	4624282308	100.84	101.4	29266680	27798805	202.241	608.074	124	157771	83.62	87.67	31559100	24472430	31559100	24472430	81.03	82.27	31559100	23713727	31559100	22965718	491934716	10.34	5.30	0	3.63	0	0.30	0	0.13	0	0.00	0	21.08	0	29266680	0	202	0	195.60	0	2.22	0	0.03	0	2.47	0	0.03	0	200.94	0	0.58	0	1975939	0	37285679	0	1352707	0	112683	0	48128	0	0	0	7858188	0	3657	0	0	0	28169	0	5295806	0	28383	0	5356015	0	74.87	0	27913973	0	143901	4927948	34.245404826930	37285679.0	29266680.0	1975939.0	1352707.0	112683.0	48128.0	0.0	7858188.0	27913973.0	78.5	5.3	3.6	0.3	0.1	0.0	21.1	74.9	101	101	101.00	38	3765853579	27.8	22.2	22.6	27.4	0.0	35.3	18.6	bulk
1671816	ERR789828	ERP009875	ERS685125	ERX780123	ERA419903	Massachusetts Institute of Technology		RNA-seq of Pdx1+ mouse Islet during development	The aim of this experiment was to observe the transcriptional profile of mouse islets during development (at timepoints E18.5, P10, Adult). RNA-seq was performed on the same RNA that was used for an earlier microarray. No MARIS sorting.	The aim of this experiment was to observe the transcriptional profile of mouse islets during development (at timepoints E18.5, P10, Adult). RNA-seq was performed on the same RNA that was used for an earlier microarray. No MARIS sorting.	Illumina HiSeq 2000 paired end sequencing; RNA-seq of Pdx1+ mouse Islet during development	RNA-seq of Pdx1+ mouse Islet during development	Protocols: Isolated islets were GFP sorted using mouse lines that expressed GFP with a minimal Pdx1 promoter. No MARIS sorting. After sorting, cells were pelleted by centrifugation at 3000 g for 5min at 4C. The supernatant was discarded. Total RNA was isolated from the pellet using the RecoverAll Total Nucleic Acid Isolation kit (Ambion), starting at the protease digestion stage of manufacturer-recommended protocol. The following modification to the isolation procedure was made: instead of incubating cells in digestion buffer for 15 minutes at 50C and 15 minutes at 80C, we carried out the incubation for 3 hours at 50C. Cell lysates were frozen at -80C overnight before continuing the RNA isolation by the manufacturer's instructions. NA	Mouse Islet P10 RNA	RNA-Seq	TRANSCRIPTOMIC	cDNA	paired	400	200	Isolated islets were GFP sorted using mouse lines that expressed GFP with a minimal Pdx1 promoter. No MARIS sorting. After sorting, cells were pelleted by centrifugation at 3000 g for 5min at 4C. The supernatant was discarded. Total RNA was isolated from the pellet using the RecoverAll Total Nucleic Acid Isolation kit (Ambion), starting at the protease digestion stage of manufacturer-recommended protocol. The following modification to the isolation procedure was made: instead of incubating cells in digestion buffer for 15 minutes at 50C and 15 minutes at 80C, we carried out the incubation for 3 hours at 50C. Cell lysates were frozen at -80C overnight before continuing the RNA isolation by the manufacturer's instructions. NA	Illumina HiSeq 2000	alias;;E-MTAB-3417:P10 pancreas islets|broker name;;ArrayExpress|developmental stage;;P10|ENA checklist;;ERC000011|INSDC center alias;;Massachusetts Institute of Technology|INSDC center name;;Massachusetts Institute of Technology|INSDC first public;;2015-03-17T16:40:38Z|INSDC last update;;2018-03-08T23:43:19Z|INSDC status;;public|organism part;;islet|organism;;Mus musculus|Sample Name;;ERS685125|SRA accession;;ERS685125|strain or line;;Pdx1 minimal promoter-GFP on mixed/outbred background|title;;P10 pancreas islets	Experimental Factor: developmental stage;;P10	200	SAMEA3307738	E-MTAB-3417:P10 pancreas islets	8026981600	40134908	2015-03-18 05:46:06	5409789509	8026981600	40134908	2	40134908	index:0,count:40134908,average:100,stdev:0|index:1,count:40134908,average:100,stdev:0	E-MTAB-3417:RNAseq_Mouse_Islet_P10	Massachusetts Institute of Technology	ArrayExpress	MIT BioMicroCenter			4.66	2.93	0.09	5076545323	5048197037	4790251276	4783428244	99.44	99.86	31273003	29946391	180.144	458.862	157	376766	87.48	92.75	33894365	27356274	33894365	27356274	89.52	89.83	33894365	27995753	33894365	26495989	321955261	6.34	0.40	0	4.43	0	0.24	0	0.06	0	0.00	0	21.78	0	31273003	0	200	0	197.18	0	2.10	0	0.01	0	1.93	0	0.01	0	240.41	0	0.81	0	160250	0	40134908	0	1777885	0	96872	0	22922	0	0	0	8742111	0	7758	0	0	0	71522	0	13085164	0	31705	0	13196149	0	73.49	0	29495118	0	119348	12236404	102.527097228274	40134908.0	31273003.0	160250.0	1777885.0	96872.0	22922.0	0.0	8742111.0	29495118.0	77.9	0.4	4.4	0.2	0.1	0.0	21.8	73.5	100	100	100.00	38	4013490800	24.2	25.7	25.2	24.7	0.2	34.8	18.5	bulk
1671832	ERR789829	ERP009875	ERS685124	ERX780122	ERA419903	Massachusetts Institute of Technology		RNA-seq of Pdx1+ mouse Islet during development	The aim of this experiment was to observe the transcriptional profile of mouse islets during development (at timepoints E18.5, P10, Adult). RNA-seq was performed on the same RNA that was used for an earlier microarray. No MARIS sorting.	The aim of this experiment was to observe the transcriptional profile of mouse islets during development (at timepoints E18.5, P10, Adult). RNA-seq was performed on the same RNA that was used for an earlier microarray. No MARIS sorting.	Illumina HiSeq 2000 paired end sequencing; RNA-seq of Pdx1+ mouse Islet during development	RNA-seq of Pdx1+ mouse Islet during development	Protocols: Isolated islets were GFP sorted using mouse lines that expressed GFP with a minimal Pdx1 promoter. No MARIS sorting. After sorting, cells were pelleted by centrifugation at 3000 g for 5min at 4C. The supernatant was discarded. Total RNA was isolated from the pellet using the RecoverAll Total Nucleic Acid Isolation kit (Ambion), starting at the protease digestion stage of manufacturer-recommended protocol. The following modification to the isolation procedure was made: instead of incubating cells in digestion buffer for 15 minutes at 50C and 15 minutes at 80C, we carried out the incubation for 3 hours at 50C. Cell lysates were frozen at -80C overnight before continuing the RNA isolation by the manufacturer's instructions. NA	Mouse Islet Adult RNA	RNA-Seq	TRANSCRIPTOMIC	cDNA	paired	400	200	Isolated islets were GFP sorted using mouse lines that expressed GFP with a minimal Pdx1 promoter. No MARIS sorting. After sorting, cells were pelleted by centrifugation at 3000 g for 5min at 4C. The supernatant was discarded. Total RNA was isolated from the pellet using the RecoverAll Total Nucleic Acid Isolation kit (Ambion), starting at the protease digestion stage of manufacturer-recommended protocol. The following modification to the isolation procedure was made: instead of incubating cells in digestion buffer for 15 minutes at 50C and 15 minutes at 80C, we carried out the incubation for 3 hours at 50C. Cell lysates were frozen at -80C overnight before continuing the RNA isolation by the manufacturer's instructions. NA	Illumina HiSeq 2000	alias;;E-MTAB-3417:Adult pancreas islets|broker name;;ArrayExpress|developmental stage;;adult|ENA checklist;;ERC000011|INSDC center alias;;Massachusetts Institute of Technology|INSDC center name;;Massachusetts Institute of Technology|INSDC first public;;2015-03-17T16:40:38Z|INSDC last update;;2018-03-08T23:43:19Z|INSDC status;;public|organism part;;islet|organism;;Mus musculus|Sample Name;;ERS685124|SRA accession;;ERS685124|strain or line;;Pdx1 minimal promoter-GFP on mixed/outbred background|title;;Adult pancreas islets	Experimental Factor: developmental stage;;adult	200	SAMEA3307737	E-MTAB-3417:Adult pancreas islets	20319963000	101599815	2015-03-18 05:46:07	13658982527	20319963000	101599815	2	101599815	index:0,count:101599815,average:100,stdev:0|index:1,count:101599815,average:100,stdev:0	E-MTAB-3417:RNAseq_Mouse_Islet_Adult	Massachusetts Institute of Technology	ArrayExpress	MIT BioMicroCenter			4.21	2.76	0.07	12753936690	12673804418	12072115149	12039576173	99.37	99.73	79487403	76161793	178.527	458.585	157	1008177	87.91	92.93	86263652	69875913	86263652	69875913	89.88	90.18	86263652	71444066	86263652	67804432	779027418	6.11	0.33	0	4.23	0	0.39	0	0.05	0	0.00	0	21.33	0	79487403	0	200	0	197.32	0	2.05	0	0.01	0	1.87	0	0.01	0	285.53	0	0.79	0	334617	0	101599815	0	4297283	0	396129	0	48858	0	0	0	21667425	0	16780	0	0	0	177566	0	33351001	0	78757	0	33624104	0	74.01	0	75190120	0	158320	31431805	198.533381758464	101599815.0	79487403.0	334617.0	4297283.0	396129.0	48858.0	0.0	21667425.0	75190120.0	78.2	0.3	4.2	0.4	0.0	0.0	21.3	74.0	100	100	100.00	38	10159981500	24.1	25.8	25.4	24.6	0.2	34.7	18.3	bulk
1671944	ERR789830	ERP009875	ERS685123	ERX780121	ERA419903	Massachusetts Institute of Technology		RNA-seq of Pdx1+ mouse Islet during development	The aim of this experiment was to observe the transcriptional profile of mouse islets during development (at timepoints E18.5, P10, Adult). RNA-seq was performed on the same RNA that was used for an earlier microarray. No MARIS sorting.	The aim of this experiment was to observe the transcriptional profile of mouse islets during development (at timepoints E18.5, P10, Adult). RNA-seq was performed on the same RNA that was used for an earlier microarray. No MARIS sorting.	RNA-seq of Pdx1+ mouse Islet during development	RNA-seq of Pdx1+ mouse Islet during development		Mouse Islet E18.5 RNA	RNA-Seq	TRANSCRIPTOMIC	cDNA	paired	400	200	Isolated islets were GFP sorted using mouse lines that expressed GFP with a minimal Pdx1 promoter. No MARIS sorting. After sorting, cells were pelleted by centrifugation at 3000 g for 5min at 4C. The supernatant was discarded. Total RNA was isolated from the pellet using the RecoverAll Total Nucleic Acid Isolation kit (Ambion), starting at the protease digestion stage of manufacturer-recommended protocol. The following modification to the isolation procedure was made: instead of incubating cells in digestion buffer for 15 minutes at 50C and 15 minutes at 80C, we carried out the incubation for 3 hours at 50C. Cell lysates were frozen at -80C overnight before continuing the RNA isolation by the manufacturer's instructions. NA	Illumina HiSeq 2000	Alias;;E-MTAB-3417:E18.5 pancreas islets|Broker name;;ArrayExpress|Description;;Protocols: Isolated islets were GFP sorted using mouse lines that expressed GFP with a minimal Pdx1 promoter. No MARIS sorting. After sorting, cells were pelleted by centrifugation at 3000 g for 5min at 4C. The supernatant was discarded. Total RNA was isolated from the pellet using the RecoverAll Total Nucleic Acid Isolation kit (Ambion), starting at the protease digestion stage of manufacturer-recommended protocol. The following modification to the isolation procedure was made: instead of incubating cells in digestion buffer for 15 minutes at 50C and 15 minutes at 80C, we carried out the incubation for 3 hours at 50C. Cell lysates were frozen at -80C overnight before continuing the RNA isolation by the manufacturer's instructions. NA|developmental stage;;E18.5|ENA checklist;;ERC000011|INSDC center alias;;Massachusetts Institute of Technology|INSDC center name;;Massachusetts Institute of Technology|INSDC first public;;2015-03-17T16:40:38Z|INSDC last update;;2018-03-08T23:43:19Z|INSDC status;;public|organism part;;islet|organism;;Mus musculus|Sample Name;;ERS685123|SRA accession;;ERS685123|strain or line;;Pdx1 minimal promoter-GFP on mixed/outbred background|Title;;E18.5 pancreas islets	Experimental Factor: developmental stage;;E18.5	200	SAMEA3308494	E-MTAB-3417:E18.5 pancreas islets	12748842000	63744210	2015-03-18 05:46:07	8556444576	12748842000	63744210	2	63744210	index:0,count:63744210,average:100,stdev:0|index:1,count:63744210,average:100,stdev:0	E-MTAB-3417:RNAseq_Mouse_Islet_E18_5	Massachusetts Institute of Technology	ArrayExpress	MIT BioMicroCenter			2.96	3.41	0.09	8201917178	8205999714	7751274974	7790372221	100.05	100.5	49745350	47225761	185.122	506.502	157	532373	87.32	92.47	54060547	43439787	54060547	43439787	88.42	88.79	54060547	43982872	54060547	41708942	551510621	6.72	0.38	0	4.35	0	0.19	0	0.06	0	0.00	0	21.71	0	49745350	0	200	0	197.22	0	2.12	0	0.01	0	1.84	0	0.01	0	356.89	0	0.80	0	243671	0	63744210	0	2770719	0	121727	0	38302	0	0	0	13838831	0	13410	0	0	0	126540	0	21311774	0	51344	0	21503068	0	73.69	0	46974631	0	164537	20008404	121.604283535010	63744210.0	49745350.0	243671.0	2770719.0	121727.0	38302.0	0.0	13838831.0	46974631.0	78.0	0.4	4.3	0.2	0.1	0.0	21.7	73.7	100	100	100.00	38	6374421000	24.4	25.5	25.1	24.8	0.2	34.8	18.4	bulk
208652	ERR1121786	ERP013145	ERS957184	ERX1201128	ERA532290		European Nucleotide Archive	RNA-Seq analysis of LT-HSC isolated from fetal liver and adult bone marrow.	Hematopoietic stem cells (HSC) has unique characteristic to self-renew and replenish the entire blood system. During development, HSCs originate in the aorta-gonads-mesonephros (AGM), from where they migrate into the fetal liver at E11. Once resided in fetal liver HSC proliferate extensively to make sufficient stem pool for adult life. Around birth, HSC from FL migrate to bone marrow (BM) which is major site of hematopoiesis for whole adult life. In contrast to FL HSC, BM HSC remain quiescence state and give rise to different blood cell type under normal homeostatic condition. It has shown that FL HSCs display significantly faster expansion kinetics when transplanted into lethally irradiate mice, compared with HSCs from adult BM. However, detail molecular mechanism behind the difference in self-renewal potential is not fully understood. Here, we present the genome-wide transcriptome analysis of more proliferative FL HSC compared to quiescent BM HSC using RNA-Seq platform.	Hematopoietic stem cells (HSC) has unique characteristic to self-renew and replenish the entire blood system. During development, HSCs originate in the aorta-gonads-mesonephros (AGM), from where they migrate into the fetal liver at E11. Once resided in fetal liver HSC proliferate extensively to make sufficient stem pool for adult life. Around birth, HSC from FL migrate to bone marrow (BM) which is major site of hematopoiesis for whole adult life. In contrast to FL HSC, BM HSC remain quiescence state and give rise to different blood cell type under normal homeostatic condition. It has shown that FL HSCs display significantly faster expansion kinetics when transplanted into lethally irradiate mice, compared with HSCs from adult BM. However, detail molecular mechanism behind the difference in self-renewal potential is not fully understood. Here, we present the genome-wide transcriptome analysis of more proliferative FL HSC compared to quiescent BM HSC using RNA-Seq platform.	Illumina HiSeq 2000 paired end sequencing; RNA-Seq analysis of LT-HSC isolated from fetal liver and adult bone marrow.	RNA-Seq analysis of LT-HSC isolated from fetal liver and adult bone marrow.		BM_HSC_rep  1	RNA-Seq	TRANSCRIPTOMIC	cDNA	paired	170	20	Total adult bone marrow (ABM) cells were flushed from femurs and tibiae of male C57BL/6J mice, pooled, washed twice with phosphatebuffered saline (PBS; Gibco Invitrogen, CA) containing 0.1% bovine serum albumin (BSA; Sigma). Lineage negative cell isolation was performed using lineage cell depletion kit (Miltenyi Biotec, Germany). To isolate LT-HSCs from ABM, resulting Lin cells were stained with FITC conjugated antiSca1, PE conjugated antickit, APC conjugated antilineage antibody cocktail (BD Pharmingen, San Diego, CA), PerCP/Cy5.5 conjugated anti-CD150 and APC conjugated anti-CD48 antibodies. Cells were incubated on ice for 30 minutes. FL tissues were obtained from C57BL/6J embryos dissected at embryonic day (E) 14.5 (14 days after vaginal plug was observed). Ter-119 positive erythrocytes and erythrocyte progenitors were depleted using MACS columns (Miltenyi Biotec, Germany) and stained with Alexa Fluor 488 conjugated anti-lineage antibody cocktail (containing CD4, CD5, CD8a, CD45R, Ter-119, GR-1 antibodies), PE conjugated anti-CD11b, APC conjugated anti-Sca-1, PE-Cy7 conjugated anti-CD150 and Alexa Fluor 488 conjugated anti-CD48. Cells were incubated on ice for 30 minutes. After incubation of cells with antibodies, cells were washed once with PBS. HSCs were sorted by fluorescence-activated cell sorting (FACS), using a FACS ARIAIII (Becton Dickinson). HSCs were directly sorted in QIAzol lysis buffer from miRNeasy Micro Kit (QIAGEN) and stored at -80c until isolation. Fraction of cells were used to checked the purity which was >95 percent. Total RNA isolation was isolated from the indicated populations using miRNeasy Micro Kit (QIAGEN) according to the manufacturer's protocol. DNase treatment was performed using RNAse-free DNase Set (Qiagen). Total RNA from FL and BM HSC was amplified using Ovation RNA-seq V2 system (NuGen technologies, CA) as per manufacturers instructions. Amplified cDNA (1ug) was sheared using the Covaris system (Covaris, MA) and fragments of 200bp (180-220bp) selected to construct a cDNA library. The fragmented DNA is combined with End Repair Mix, incubate at 20C for 30 min. Purify the end-repaired DNA with QIAquick PCR Purification Kit(Qiagen),then add A-Tailing Mix, incubate at 37C for 30 min. Combine the purified Adenylate 3'Ends DNA, Adapter and Ligation Mix, incubate the ligation reaction at 20C for 15 min. Adapter-ligated DNA is selected by running a 2% agarose gel to recover the target fragments. Purify the gel with QIAquick Gel Extraction kit (QIAGEN). Several rounds of PCR amplification with PCR Primer Cocktail and PCR Master Mix are performed to enrich the Adapter-ligated DNA fragments. Then the PCR products are purified with Ampure XP Beads (AGENCOURT). The Qualified libraries will amplify on cBot to generate the cluster on the flowcell (TruSeq PE Cluster Kit V3cBotHS,Illumina). And the amplified flowcell will be subjected to 2*90 bp paired-end sequencing on the HiSeq 2000 System (TruSeq SBS KIT-HS V3,Illumina).	Illumina HiSeq 2000	age;;8 week|Alias;;E-MTAB-4034:BM_HSC_rep 1|Broker name;;ArrayExpress|cell type;;hematopoietic stem cell|Description;;Protocols: Total adult bone marrow (ABM) cells were flushed from femurs and tibiae of male C57BL/6J mice, pooled, washed twice with phosphatebuffered saline (PBS; Gibco Invitrogen, CA) containing 0.1% bovine serum albumin (BSA; Sigma). Lineage negative cell isolation was performed using lineage cell depletion kit (Miltenyi Biotec, Germany). To isolate LT-HSCs from ABM, resulting Lin cells were stained with FITC conjugated antiSca1, PE conjugated antickit, APC conjugated antilineage antibody cocktail (BD Pharmingen, San Diego, CA), PerCP/Cy5.5 conjugated anti-CD150 and APC conjugated anti-CD48 antibodies. Cells were incubated on ice for 30 minutes. FL tissues were obtained from C57BL/6J embryos dissected at embryonic day (E) 14.5 (14 days after vaginal plug was observed). Ter-119 positive erythrocytes and erythrocyte progenitors were depleted using MACS columns (Miltenyi Biotec, Germany) and stained with Alexa Fluor 488 conjugated anti-lineage antibody cocktail (containing CD4, CD5, CD8a, CD45R, Ter-119, GR-1 antibodies), PE conjugated anti-CD11b, APC conjugated anti-Sca-1, PE-Cy7 conjugated anti-CD150 and Alexa Fluor 488 conjugated anti-CD48. Cells were incubated on ice for 30 minutes. After incubation of cells with antibodies, cells were washed once with PBS. HSCs were sorted by fluorescence-activated cell sorting (FACS), using a FACS ARIAIII (Becton Dickinson). HSCs were directly sorted in QIAzol lysis buffer from miRNeasy Micro Kit (QIAGEN) and stored at -80c until isolation. Fraction of cells were used to checked the purity which was >95 percent. Total RNA isolation was isolated from the indicated populations using miRNeasy Micro Kit (QIAGEN) according to the manufacturer's protocol. DNAse treatment was performed using RNAse-free DNAse Set (Qiagen). Total RNA from FL and BM HSC was amplified using Ovation RNA-seq V2 system (NuGen technologies, CA) as per manufacturers instructions. Amplified cDNA (1ug) was sheared using the Covaris system (Covaris, MA) and fragments of 200bp (180-220bp) selected to construct a cDNA library. The fragmented DNA is combined with End Repair Mix, incubate at 20C for 30 min. Purify the end-repaired DNA with QIAquick PCR Purification Kit(Qiagen),then add A-Tailing Mix, incubate at 37C for 30 min. Combine the purified Adenylate 3'Ends DNA, Adapter and Ligation Mix, incubate the ligation reaction at 20C for 15 min. Adapter-ligated DNA is selected by running a 2% agarose gel to recover the target fragments. Purify the gel with QIAquick Gel Extraction kit (QIAGEN). Several rounds of PCR amplification with PCR Primer Cocktail and PCR Master Mix are performed to enrich the Adapter-ligated DNA fragments. Then the PCR products are purified with Ampure XP Beads (AGENCOURT). The Qualified libraries will amplify on cBot to generate the cluster on the flowcell (TruSeq PE Cluster Kit V3cBotHS,Illumina). And the amplified flowcell will be subjected to 2*90 bp paired-end sequencing on the HiSeq 2000 System (TruSeq SBS KIT-HS V3,Illumina).|ENA checklist;;ERC000011|genotype;;wild type genotype|INSDC center alias;;Inter-departmental Stem Cell Institute, KU Leuven, Belgium. Department of Development and Regeneration, Stem Cell Biology and Embryology, KU Leuven|INSDC center name;;Inter-departmental Stem Cell Institute, KU Leuven, Belgium. Department of Development and Regeneration, Stem Cell Biology and Embryology, KU Leuven|INSDC first public;;2015-11-29T17:01:16Z|INSDC last update;;2018-03-09T09:24:41Z|INSDC status;;public|organism part;;adult bone marrow|organism;;Mus musculus|phenotype;;lin- sca1+ ckit+ cd150+ cd48-|Sample Name;;ERS957184|SRA accession;;ERS957184|strain;;C57BL/6J|Title;;BM_HSC_rep 1	Experimental Factor: adult bone marrow;;organism part	180	SAMEA3650035	E-MTAB-4034:BM_HSC_rep 1	3520743480	19559686	2015-11-30 10:46:22	2543943719	3520743480	19559686	2	19559686	index:0,count:19559686,average:90,stdev:0|index:1,count:19559686,average:90,stdev:0	E-MTAB-4034:BM-LT-HSC_1_L1_	Inter-departmental Stem Cell Institute, KU Leuven, Belgium. Department of Development and Regeneration, Stem Cell Biology and Embryology, KU Leuven	ArrayExpress	Illumina HiSeq2000 	in_mesa	26599326	7.05	2.47	0.1	3063112999	3030660298	2982158738	2959973179	98.94	99.26	18759829	18591103	167.221	287.135	166	487294	45.33	46.59	19655978	8504078	19655978	8504078	43.11	42.88	19655978	8087975	19655978	7827022	1581789085	51.64	5.38	0	2.59	0	0.18	0	0.20	0	0.00	0	3.71	0	18759829	0	180	0	177.14	0	2.26	0	0.01	0	1.96	0	0.01	0	521.59	0	0.35	0	1052297	0	19559686	0	507091	0	34622	0	38757	0	0	0	726478	0	2313	0	0	0	16173	0	2101902	0	16459	0	2136847	0	93.32	0	18252738	0	124609	2134750	17.131587606032	19559686.0	18759829.0	1052297.0	507091.0	34622.0	38757.0	0.0	726478.0	18252738.0	95.9	5.4	2.6	0.2	0.2	0.0	3.7	93.3	90	90	90.00	38	1760371740	26.9	23.0	23.2	26.9	0.0	35.5	21.0	bulk
208654	ERR1121787	ERP013145	ERS957185	ERX1201129	ERA532290		European Nucleotide Archive	RNA-Seq analysis of LT-HSC isolated from fetal liver and adult bone marrow.	Hematopoietic stem cells (HSC) has unique characteristic to self-renew and replenish the entire blood system. During development, HSCs originate in the aorta-gonads-mesonephros (AGM), from where they migrate into the fetal liver at E11. Once resided in fetal liver HSC proliferate extensively to make sufficient stem pool for adult life. Around birth, HSC from FL migrate to bone marrow (BM) which is major site of hematopoiesis for whole adult life. In contrast to FL HSC, BM HSC remain quiescence state and give rise to different blood cell type under normal homeostatic condition. It has shown that FL HSCs display significantly faster expansion kinetics when transplanted into lethally irradiate mice, compared with HSCs from adult BM. However, detail molecular mechanism behind the difference in self-renewal potential is not fully understood. Here, we present the genome-wide transcriptome analysis of more proliferative FL HSC compared to quiescent BM HSC using RNA-Seq platform.	Hematopoietic stem cells (HSC) has unique characteristic to self-renew and replenish the entire blood system. During development, HSCs originate in the aorta-gonads-mesonephros (AGM), from where they migrate into the fetal liver at E11. Once resided in fetal liver HSC proliferate extensively to make sufficient stem pool for adult life. Around birth, HSC from FL migrate to bone marrow (BM) which is major site of hematopoiesis for whole adult life. In contrast to FL HSC, BM HSC remain quiescence state and give rise to different blood cell type under normal homeostatic condition. It has shown that FL HSCs display significantly faster expansion kinetics when transplanted into lethally irradiate mice, compared with HSCs from adult BM. However, detail molecular mechanism behind the difference in self-renewal potential is not fully understood. Here, we present the genome-wide transcriptome analysis of more proliferative FL HSC compared to quiescent BM HSC using RNA-Seq platform.	Illumina HiSeq 2000 paired end sequencing; RNA-Seq analysis of LT-HSC isolated from fetal liver and adult bone marrow.	RNA-Seq analysis of LT-HSC isolated from fetal liver and adult bone marrow.		BM_HSC_rep  2	RNA-Seq	TRANSCRIPTOMIC	cDNA	paired	170	20	Total adult bone marrow (ABM) cells were flushed from femurs and tibiae of male C57BL/6J mice, pooled, washed twice with phosphatebuffered saline (PBS; Gibco Invitrogen, CA) containing 0.1% bovine serum albumin (BSA; Sigma). Lineage negative cell isolation was performed using lineage cell depletion kit (Miltenyi Biotec, Germany). To isolate LT-HSCs from ABM, resulting Lin cells were stained with FITC conjugated antiSca1, PE conjugated antickit, APC conjugated antilineage antibody cocktail (BD Pharmingen, San Diego, CA), PerCP/Cy5.5 conjugated anti-CD150 and APC conjugated anti-CD48 antibodies. Cells were incubated on ice for 30 minutes. FL tissues were obtained from C57BL/6J embryos dissected at embryonic day (E) 14.5 (14 days after vaginal plug was observed). Ter-119 positive erythrocytes and erythrocyte progenitors were depleted using MACS columns (Miltenyi Biotec, Germany) and stained with Alexa Fluor 488 conjugated anti-lineage antibody cocktail (containing CD4, CD5, CD8a, CD45R, Ter-119, GR-1 antibodies), PE conjugated anti-CD11b, APC conjugated anti-Sca-1, PE-Cy7 conjugated anti-CD150 and Alexa Fluor 488 conjugated anti-CD48. Cells were incubated on ice for 30 minutes. After incubation of cells with antibodies, cells were washed once with PBS. HSCs were sorted by fluorescence-activated cell sorting (FACS), using a FACS ARIAIII (Becton Dickinson). HSCs were directly sorted in QIAzol lysis buffer from miRNeasy Micro Kit (QIAGEN) and stored at -80c until isolation. Fraction of cells were used to checked the purity which was >95 percent. Total RNA isolation was isolated from the indicated populations using miRNeasy Micro Kit (QIAGEN) according to the manufacturer's protocol. DNase treatment was performed using RNAse-free DNase Set (Qiagen). Total RNA from FL and BM HSC was amplified using Ovation RNA-seq V2 system (NuGen technologies, CA) as per manufacturers instructions. Amplified cDNA (1ug) was sheared using the Covaris system (Covaris, MA) and fragments of 200bp (180-220bp) selected to construct a cDNA library. The fragmented DNA is combined with End Repair Mix, incubate at 20C for 30 min. Purify the end-repaired DNA with QIAquick PCR Purification Kit(Qiagen),then add A-Tailing Mix, incubate at 37C for 30 min. Combine the purified Adenylate 3'Ends DNA, Adapter and Ligation Mix, incubate the ligation reaction at 20C for 15 min. Adapter-ligated DNA is selected by running a 2% agarose gel to recover the target fragments. Purify the gel with QIAquick Gel Extraction kit (QIAGEN). Several rounds of PCR amplification with PCR Primer Cocktail and PCR Master Mix are performed to enrich the Adapter-ligated DNA fragments. Then the PCR products are purified with Ampure XP Beads (AGENCOURT). The Qualified libraries will amplify on cBot to generate the cluster on the flowcell (TruSeq PE Cluster Kit V3cBotHS,Illumina). And the amplified flowcell will be subjected to 2*90 bp paired-end sequencing on the HiSeq 2000 System (TruSeq SBS KIT-HS V3,Illumina).	Illumina HiSeq 2000	age;;8 week|Alias;;E-MTAB-4034:BM_HSC_rep 2|Broker name;;ArrayExpress|cell type;;hematopoietic stem cell|Description;;Protocols: Total adult bone marrow (ABM) cells were flushed from femurs and tibiae of male C57BL/6J mice, pooled, washed twice with phosphatebuffered saline (PBS; Gibco Invitrogen, CA) containing 0.1% bovine serum albumin (BSA; Sigma). Lineage negative cell isolation was performed using lineage cell depletion kit (Miltenyi Biotec, Germany). To isolate LT-HSCs from ABM, resulting Lin cells were stained with FITC conjugated antiSca1, PE conjugated antickit, APC conjugated antilineage antibody cocktail (BD Pharmingen, San Diego, CA), PerCP/Cy5.5 conjugated anti-CD150 and APC conjugated anti-CD48 antibodies. Cells were incubated on ice for 30 minutes. FL tissues were obtained from C57BL/6J embryos dissected at embryonic day (E) 14.5 (14 days after vaginal plug was observed). Ter-119 positive erythrocytes and erythrocyte progenitors were depleted using MACS columns (Miltenyi Biotec, Germany) and stained with Alexa Fluor 488 conjugated anti-lineage antibody cocktail (containing CD4, CD5, CD8a, CD45R, Ter-119, GR-1 antibodies), PE conjugated anti-CD11b, APC conjugated anti-Sca-1, PE-Cy7 conjugated anti-CD150 and Alexa Fluor 488 conjugated anti-CD48. Cells were incubated on ice for 30 minutes. After incubation of cells with antibodies, cells were washed once with PBS. HSCs were sorted by fluorescence-activated cell sorting (FACS), using a FACS ARIAIII (Becton Dickinson). HSCs were directly sorted in QIAzol lysis buffer from miRNeasy Micro Kit (QIAGEN) and stored at -80c until isolation. Fraction of cells were used to checked the purity which was >95 percent. Total RNA isolation was isolated from the indicated populations using miRNeasy Micro Kit (QIAGEN) according to the manufacturer's protocol. DNAse treatment was performed using RNAse-free DNAse Set (Qiagen). Total RNA from FL and BM HSC was amplified using Ovation RNA-seq V2 system (NuGen technologies, CA) as per manufacturers instructions. Amplified cDNA (1ug) was sheared using the Covaris system (Covaris, MA) and fragments of 200bp (180-220bp) selected to construct a cDNA library. The fragmented DNA is combined with End Repair Mix, incubate at 20C for 30 min. Purify the end-repaired DNA with QIAquick PCR Purification Kit(Qiagen),then add A-Tailing Mix, incubate at 37C for 30 min. Combine the purified Adenylate 3'Ends DNA, Adapter and Ligation Mix, incubate the ligation reaction at 20C for 15 min. Adapter-ligated DNA is selected by running a 2% agarose gel to recover the target fragments. Purify the gel with QIAquick Gel Extraction kit (QIAGEN). Several rounds of PCR amplification with PCR Primer Cocktail and PCR Master Mix are performed to enrich the Adapter-ligated DNA fragments. Then the PCR products are purified with Ampure XP Beads (AGENCOURT). The Qualified libraries will amplify on cBot to generate the cluster on the flowcell (TruSeq PE Cluster Kit V3cBotHS,Illumina). And the amplified flowcell will be subjected to 2*90 bp paired-end sequencing on the HiSeq 2000 System (TruSeq SBS KIT-HS V3,Illumina).|ENA checklist;;ERC000011|genotype;;wild type genotype|INSDC center alias;;Inter-departmental Stem Cell Institute, KU Leuven, Belgium. Department of Development and Regeneration, Stem Cell Biology and Embryology, KU Leuven|INSDC center name;;Inter-departmental Stem Cell Institute, KU Leuven, Belgium. Department of Development and Regeneration, Stem Cell Biology and Embryology, KU Leuven|INSDC first public;;2015-11-29T17:01:16Z|INSDC last update;;2018-03-09T09:24:45Z|INSDC status;;public|organism part;;adult bone marrow|organism;;Mus musculus|phenotype;;lin- sca1+ ckit+ cd150+ cd48-|Sample Name;;ERS957185|SRA accession;;ERS957185|strain;;C57BL/6J|Title;;BM_HSC_rep 2	Experimental Factor: adult bone marrow;;organism part	180	SAMEA3650036	E-MTAB-4034:BM_HSC_rep 2	3477643560	19320242	2015-11-30 10:46:22	2459057074	3477643560	19320242	2	19320242	index:0,count:19320242,average:90,stdev:0|index:1,count:19320242,average:90,stdev:0	E-MTAB-4034:BM-LT-HSC_2_L1_	Inter-departmental Stem Cell Institute, KU Leuven, Belgium. Department of Development and Regeneration, Stem Cell Biology and Embryology, KU Leuven	ArrayExpress	Illumina HiSeq2000 	in_mesa	26599326	7.88	2.31	0.09	3036948120	3005523804	2953276902	2932904487	98.97	99.31	18529076	18386513	166.780	280.417	166	597469	47.98	49.37	19440583	8890647	19440583	8890647	45.33	45.22	19440583	8399621	19440583	8144371	1481767768	48.79	5.11	0	2.69	0	0.16	0	0.18	0	0.00	0	3.76	0	18529076	0	180	0	177.03	0	2.56	0	0.01	0	2.22	0	0.01	0	336.00	0	0.39	0	987718	0	19320242	0	520462	0	31793	0	33826	0	0	0	725547	0	1925	0	0	0	15994	0	2094290	0	15309	0	2127518	0	93.21	0	18008614	0	122160	2145607	17.563907989522	19320242.0	18529076.0	987718.0	520462.0	31793.0	33826.0	0.0	725547.0	18008614.0	95.9	5.1	2.7	0.2	0.2	0.0	3.8	93.2	90	90	90.00	38	1738821780	26.9	23.0	23.3	26.8	0.0	35.7	20.7	bulk
208656	ERR1121788	ERP013145	ERS957186	ERX1201130	ERA532290		European Nucleotide Archive	RNA-Seq analysis of LT-HSC isolated from fetal liver and adult bone marrow.	Hematopoietic stem cells (HSC) has unique characteristic to self-renew and replenish the entire blood system. During development, HSCs originate in the aorta-gonads-mesonephros (AGM), from where they migrate into the fetal liver at E11. Once resided in fetal liver HSC proliferate extensively to make sufficient stem pool for adult life. Around birth, HSC from FL migrate to bone marrow (BM) which is major site of hematopoiesis for whole adult life. In contrast to FL HSC, BM HSC remain quiescence state and give rise to different blood cell type under normal homeostatic condition. It has shown that FL HSCs display significantly faster expansion kinetics when transplanted into lethally irradiate mice, compared with HSCs from adult BM. However, detail molecular mechanism behind the difference in self-renewal potential is not fully understood. Here, we present the genome-wide transcriptome analysis of more proliferative FL HSC compared to quiescent BM HSC using RNA-Seq platform.	Hematopoietic stem cells (HSC) has unique characteristic to self-renew and replenish the entire blood system. During development, HSCs originate in the aorta-gonads-mesonephros (AGM), from where they migrate into the fetal liver at E11. Once resided in fetal liver HSC proliferate extensively to make sufficient stem pool for adult life. Around birth, HSC from FL migrate to bone marrow (BM) which is major site of hematopoiesis for whole adult life. In contrast to FL HSC, BM HSC remain quiescence state and give rise to different blood cell type under normal homeostatic condition. It has shown that FL HSCs display significantly faster expansion kinetics when transplanted into lethally irradiate mice, compared with HSCs from adult BM. However, detail molecular mechanism behind the difference in self-renewal potential is not fully understood. Here, we present the genome-wide transcriptome analysis of more proliferative FL HSC compared to quiescent BM HSC using RNA-Seq platform.	Illumina HiSeq 2000 paired end sequencing; RNA-Seq analysis of LT-HSC isolated from fetal liver and adult bone marrow.	RNA-Seq analysis of LT-HSC isolated from fetal liver and adult bone marrow.		FL_HSC_E14.5_rep 1	RNA-Seq	TRANSCRIPTOMIC	cDNA	paired	170	20	Total adult bone marrow (ABM) cells were flushed from femurs and tibiae of male C57BL/6J mice, pooled, washed twice with phosphatebuffered saline (PBS; Gibco Invitrogen, CA) containing 0.1% bovine serum albumin (BSA; Sigma). Lineage negative cell isolation was performed using lineage cell depletion kit (Miltenyi Biotec, Germany). To isolate LT-HSCs from ABM, resulting Lin cells were stained with FITC conjugated antiSca1, PE conjugated antickit, APC conjugated antilineage antibody cocktail (BD Pharmingen, San Diego, CA), PerCP/Cy5.5 conjugated anti-CD150 and APC conjugated anti-CD48 antibodies. Cells were incubated on ice for 30 minutes. FL tissues were obtained from C57BL/6J embryos dissected at embryonic day (E) 14.5 (14 days after vaginal plug was observed). Ter-119 positive erythrocytes and erythrocyte progenitors were depleted using MACS columns (Miltenyi Biotec, Germany) and stained with Alexa Fluor 488 conjugated anti-lineage antibody cocktail (containing CD4, CD5, CD8a, CD45R, Ter-119, GR-1 antibodies), PE conjugated anti-CD11b, APC conjugated anti-Sca-1, PE-Cy7 conjugated anti-CD150 and Alexa Fluor 488 conjugated anti-CD48. Cells were incubated on ice for 30 minutes. After incubation of cells with antibodies, cells were washed once with PBS. HSCs were sorted by fluorescence-activated cell sorting (FACS), using a FACS ARIAIII (Becton Dickinson). HSCs were directly sorted in QIAzol lysis buffer from miRNeasy Micro Kit (QIAGEN) and stored at -80c until isolation. Fraction of cells were used to checked the purity which was >95 percent. Total RNA isolation was isolated from the indicated populations using miRNeasy Micro Kit (QIAGEN) according to the manufacturer's protocol. DNase treatment was performed using RNAse-free DNase Set (Qiagen). Total RNA from FL and BM HSC was amplified using Ovation RNA-seq V2 system (NuGen technologies, CA) as per manufacturers instructions. Amplified cDNA (1ug) was sheared using the Covaris system (Covaris, MA) and fragments of 200bp (180-220bp) selected to construct a cDNA library. The fragmented DNA is combined with End Repair Mix, incubate at 20C for 30 min. Purify the end-repaired DNA with QIAquick PCR Purification Kit(Qiagen),then add A-Tailing Mix, incubate at 37C for 30 min. Combine the purified Adenylate 3'Ends DNA, Adapter and Ligation Mix, incubate the ligation reaction at 20C for 15 min. Adapter-ligated DNA is selected by running a 2% agarose gel to recover the target fragments. Purify the gel with QIAquick Gel Extraction kit (QIAGEN). Several rounds of PCR amplification with PCR Primer Cocktail and PCR Master Mix are performed to enrich the Adapter-ligated DNA fragments. Then the PCR products are purified with Ampure XP Beads (AGENCOURT). The Qualified libraries will amplify on cBot to generate the cluster on the flowcell (TruSeq PE Cluster Kit V3cBotHS,Illumina). And the amplified flowcell will be subjected to 2*90 bp paired-end sequencing on the HiSeq 2000 System (TruSeq SBS KIT-HS V3,Illumina).	Illumina HiSeq 2000	age;;embryonic day 14.5|Alias;;E-MTAB-4034:FL_HSC_E14.5_rep 1|Broker name;;ArrayExpress|cell type;;hematopoietic stem cell|Description;;Protocols: Total adult bone marrow (ABM) cells were flushed from femurs and tibiae of male C57BL/6J mice, pooled, washed twice with phosphatebuffered saline (PBS; Gibco Invitrogen, CA) containing 0.1% bovine serum albumin (BSA; Sigma). Lineage negative cell isolation was performed using lineage cell depletion kit (Miltenyi Biotec, Germany). To isolate LT-HSCs from ABM, resulting Lin cells were stained with FITC conjugated antiSca1, PE conjugated antickit, APC conjugated antilineage antibody cocktail (BD Pharmingen, San Diego, CA), PerCP/Cy5.5 conjugated anti-CD150 and APC conjugated anti-CD48 antibodies. Cells were incubated on ice for 30 minutes. FL tissues were obtained from C57BL/6J embryos dissected at embryonic day (E) 14.5 (14 days after vaginal plug was observed). Ter-119 positive erythrocytes and erythrocyte progenitors were depleted using MACS columns (Miltenyi Biotec, Germany) and stained with Alexa Fluor 488 conjugated anti-lineage antibody cocktail (containing CD4, CD5, CD8a, CD45R, Ter-119, GR-1 antibodies), PE conjugated anti-CD11b, APC conjugated anti-Sca-1, PE-Cy7 conjugated anti-CD150 and Alexa Fluor 488 conjugated anti-CD48. Cells were incubated on ice for 30 minutes. After incubation of cells with antibodies, cells were washed once with PBS. HSCs were sorted by fluorescence-activated cell sorting (FACS), using a FACS ARIAIII (Becton Dickinson). HSCs were directly sorted in QIAzol lysis buffer from miRNeasy Micro Kit (QIAGEN) and stored at -80c until isolation. Fraction of cells were used to checked the purity which was >95 percent. Total RNA isolation was isolated from the indicated populations using miRNeasy Micro Kit (QIAGEN) according to the manufacturer's protocol. DNAse treatment was performed using RNAse-free DNAse Set (Qiagen). Total RNA from FL and BM HSC was amplified using Ovation RNA-seq V2 system (NuGen technologies, CA) as per manufacturers instructions. Amplified cDNA (1ug) was sheared using the Covaris system (Covaris, MA) and fragments of 200bp (180-220bp) selected to construct a cDNA library. The fragmented DNA is combined with End Repair Mix, incubate at 20C for 30 min. Purify the end-repaired DNA with QIAquick PCR Purification Kit(Qiagen),then add A-Tailing Mix, incubate at 37C for 30 min. Combine the purified Adenylate 3'Ends DNA, Adapter and Ligation Mix, incubate the ligation reaction at 20C for 15 min. Adapter-ligated DNA is selected by running a 2% agarose gel to recover the target fragments. Purify the gel with QIAquick Gel Extraction kit (QIAGEN). Several rounds of PCR amplification with PCR Primer Cocktail and PCR Master Mix are performed to enrich the Adapter-ligated DNA fragments. Then the PCR products are purified with Ampure XP Beads (AGENCOURT). The Qualified libraries will amplify on cBot to generate the cluster on the flowcell (TruSeq PE Cluster Kit V3cBotHS,Illumina). And the amplified flowcell will be subjected to 2*90 bp paired-end sequencing on the HiSeq 2000 System (TruSeq SBS KIT-HS V3,Illumina).|ENA checklist;;ERC000011|genotype;;wild type genotype|INSDC center alias;;Inter-departmental Stem Cell Institute, KU Leuven, Belgium. Department of Development and Regeneration, Stem Cell Biology and Embryology, KU Leuven|INSDC center name;;Inter-departmental Stem Cell Institute, KU Leuven, Belgium. Department of Development and Regeneration, Stem Cell Biology and Embryology, KU Leuven|INSDC first public;;2015-11-29T17:01:16Z|INSDC last update;;2018-03-09T09:24:45Z|INSDC status;;public|organism part;;fetus|organism;;Mus musculus|phenotype;;lin- sca1+ cd11b+ cd150+ cd48-|Sample Name;;ERS957186|SRA accession;;ERS957186|strain;;C57BL/6J|Title;;FL_HSC_E14.5_rep 1	Experimental Factor: fetus;;organism part	180	SAMEA3650037	E-MTAB-4034:FL_HSC_E14.5_rep 1	3558704220	19770579	2015-11-30 10:46:22	2456954434	3558704220	19770579	2	19770579	index:0,count:19770579,average:90,stdev:0|index:1,count:19770579,average:90,stdev:0	E-MTAB-4034:FL14.5_1_L1_	Inter-departmental Stem Cell Institute, KU Leuven, Belgium. Department of Development and Regeneration, Stem Cell Biology and Embryology, KU Leuven	ArrayExpress	Illumina HiSeq2000 	in_mesa	26599326	7.87	2.28	0.1	3116867649	3108185862	3006873003	3013566490	99.72	100.22	18628905	18410422	173.335	311.369	172	518115	51.25	53.17	19803880	9547173	19803880	9547173	47.9	47.84	19803880	8922349	19803880	8590315	1393420214	44.71	6.68	0	3.40	0	0.20	0	0.15	0	0.00	0	5.42	0	18628905	0	180	0	176.21	0	3.08	0	0.02	0	2.64	0	0.02	0	352.35	0	0.38	0	1321442	0	19770579	0	672588	0	40357	0	30295	0	0	0	1071022	0	2251	0	0	0	18770	0	2437388	0	20860	0	2479269	0	90.82	0	17956317	0	132355	2510305	18.966453855162	19770579.0	18628905.0	1321442.0	672588.0	40357.0	30295.0	0.0	1071022.0	17956317.0	94.2	6.7	3.4	0.2	0.2	0.0	5.4	90.8	90	90	90.00	38	1779352110	26.3	23.5	23.8	26.4	0.0	36.1	22.0	bulk
208658	ERR1121789	ERP013145	ERS957187	ERX1201131	ERA532290		European Nucleotide Archive	RNA-Seq analysis of LT-HSC isolated from fetal liver and adult bone marrow.	Hematopoietic stem cells (HSC) has unique characteristic to self-renew and replenish the entire blood system. During development, HSCs originate in the aorta-gonads-mesonephros (AGM), from where they migrate into the fetal liver at E11. Once resided in fetal liver HSC proliferate extensively to make sufficient stem pool for adult life. Around birth, HSC from FL migrate to bone marrow (BM) which is major site of hematopoiesis for whole adult life. In contrast to FL HSC, BM HSC remain quiescence state and give rise to different blood cell type under normal homeostatic condition. It has shown that FL HSCs display significantly faster expansion kinetics when transplanted into lethally irradiate mice, compared with HSCs from adult BM. However, detail molecular mechanism behind the difference in self-renewal potential is not fully understood. Here, we present the genome-wide transcriptome analysis of more proliferative FL HSC compared to quiescent BM HSC using RNA-Seq platform.	Hematopoietic stem cells (HSC) has unique characteristic to self-renew and replenish the entire blood system. During development, HSCs originate in the aorta-gonads-mesonephros (AGM), from where they migrate into the fetal liver at E11. Once resided in fetal liver HSC proliferate extensively to make sufficient stem pool for adult life. Around birth, HSC from FL migrate to bone marrow (BM) which is major site of hematopoiesis for whole adult life. In contrast to FL HSC, BM HSC remain quiescence state and give rise to different blood cell type under normal homeostatic condition. It has shown that FL HSCs display significantly faster expansion kinetics when transplanted into lethally irradiate mice, compared with HSCs from adult BM. However, detail molecular mechanism behind the difference in self-renewal potential is not fully understood. Here, we present the genome-wide transcriptome analysis of more proliferative FL HSC compared to quiescent BM HSC using RNA-Seq platform.	Illumina HiSeq 2000 paired end sequencing; RNA-Seq analysis of LT-HSC isolated from fetal liver and adult bone marrow.	RNA-Seq analysis of LT-HSC isolated from fetal liver and adult bone marrow.		FL_HSC_E14.5_rep 2	RNA-Seq	TRANSCRIPTOMIC	cDNA	paired	170	20	Total adult bone marrow (ABM) cells were flushed from femurs and tibiae of male C57BL/6J mice, pooled, washed twice with phosphatebuffered saline (PBS; Gibco Invitrogen, CA) containing 0.1% bovine serum albumin (BSA; Sigma). Lineage negative cell isolation was performed using lineage cell depletion kit (Miltenyi Biotec, Germany). To isolate LT-HSCs from ABM, resulting Lin cells were stained with FITC conjugated antiSca1, PE conjugated antickit, APC conjugated antilineage antibody cocktail (BD Pharmingen, San Diego, CA), PerCP/Cy5.5 conjugated anti-CD150 and APC conjugated anti-CD48 antibodies. Cells were incubated on ice for 30 minutes. FL tissues were obtained from C57BL/6J embryos dissected at embryonic day (E) 14.5 (14 days after vaginal plug was observed). Ter-119 positive erythrocytes and erythrocyte progenitors were depleted using MACS columns (Miltenyi Biotec, Germany) and stained with Alexa Fluor 488 conjugated anti-lineage antibody cocktail (containing CD4, CD5, CD8a, CD45R, Ter-119, GR-1 antibodies), PE conjugated anti-CD11b, APC conjugated anti-Sca-1, PE-Cy7 conjugated anti-CD150 and Alexa Fluor 488 conjugated anti-CD48. Cells were incubated on ice for 30 minutes. After incubation of cells with antibodies, cells were washed once with PBS. HSCs were sorted by fluorescence-activated cell sorting (FACS), using a FACS ARIAIII (Becton Dickinson). HSCs were directly sorted in QIAzol lysis buffer from miRNeasy Micro Kit (QIAGEN) and stored at -80c until isolation. Fraction of cells were used to checked the purity which was >95 percent. Total RNA isolation was isolated from the indicated populations using miRNeasy Micro Kit (QIAGEN) according to the manufacturer's protocol. DNase treatment was performed using RNAse-free DNase Set (Qiagen). Total RNA from FL and BM HSC was amplified using Ovation RNA-seq V2 system (NuGen technologies, CA) as per manufacturers instructions. Amplified cDNA (1ug) was sheared using the Covaris system (Covaris, MA) and fragments of 200bp (180-220bp) selected to construct a cDNA library. The fragmented DNA is combined with End Repair Mix, incubate at 20C for 30 min. Purify the end-repaired DNA with QIAquick PCR Purification Kit(Qiagen),then add A-Tailing Mix, incubate at 37C for 30 min. Combine the purified Adenylate 3'Ends DNA, Adapter and Ligation Mix, incubate the ligation reaction at 20C for 15 min. Adapter-ligated DNA is selected by running a 2% agarose gel to recover the target fragments. Purify the gel with QIAquick Gel Extraction kit (QIAGEN). Several rounds of PCR amplification with PCR Primer Cocktail and PCR Master Mix are performed to enrich the Adapter-ligated DNA fragments. Then the PCR products are purified with Ampure XP Beads (AGENCOURT). The Qualified libraries will amplify on cBot to generate the cluster on the flowcell (TruSeq PE Cluster Kit V3cBotHS,Illumina). And the amplified flowcell will be subjected to 2*90 bp paired-end sequencing on the HiSeq 2000 System (TruSeq SBS KIT-HS V3,Illumina).	Illumina HiSeq 2000	age;;embryonic day 14.5|Alias;;E-MTAB-4034:FL_HSC_E14.5_rep 2|Broker name;;ArrayExpress|cell type;;hematopoietic stem cell|Description;;Protocols: Total adult bone marrow (ABM) cells were flushed from femurs and tibiae of male C57BL/6J mice, pooled, washed twice with phosphatebuffered saline (PBS; Gibco Invitrogen, CA) containing 0.1% bovine serum albumin (BSA; Sigma). Lineage negative cell isolation was performed using lineage cell depletion kit (Miltenyi Biotec, Germany). To isolate LT-HSCs from ABM, resulting Lin cells were stained with FITC conjugated antiSca1, PE conjugated antickit, APC conjugated antilineage antibody cocktail (BD Pharmingen, San Diego, CA), PerCP/Cy5.5 conjugated anti-CD150 and APC conjugated anti-CD48 antibodies. Cells were incubated on ice for 30 minutes. FL tissues were obtained from C57BL/6J embryos dissected at embryonic day (E) 14.5 (14 days after vaginal plug was observed). Ter-119 positive erythrocytes and erythrocyte progenitors were depleted using MACS columns (Miltenyi Biotec, Germany) and stained with Alexa Fluor 488 conjugated anti-lineage antibody cocktail (containing CD4, CD5, CD8a, CD45R, Ter-119, GR-1 antibodies), PE conjugated anti-CD11b, APC conjugated anti-Sca-1, PE-Cy7 conjugated anti-CD150 and Alexa Fluor 488 conjugated anti-CD48. Cells were incubated on ice for 30 minutes. After incubation of cells with antibodies, cells were washed once with PBS. HSCs were sorted by fluorescence-activated cell sorting (FACS), using a FACS ARIAIII (Becton Dickinson). HSCs were directly sorted in QIAzol lysis buffer from miRNeasy Micro Kit (QIAGEN) and stored at -80c until isolation. Fraction of cells were used to checked the purity which was >95 percent. Total RNA isolation was isolated from the indicated populations using miRNeasy Micro Kit (QIAGEN) according to the manufacturer's protocol. DNAse treatment was performed using RNAse-free DNAse Set (Qiagen). Total RNA from FL and BM HSC was amplified using Ovation RNA-seq V2 system (NuGen technologies, CA) as per manufacturers instructions. Amplified cDNA (1ug) was sheared using the Covaris system (Covaris, MA) and fragments of 200bp (180-220bp) selected to construct a cDNA library. The fragmented DNA is combined with End Repair Mix, incubate at 20C for 30 min. Purify the end-repaired DNA with QIAquick PCR Purification Kit(Qiagen),then add A-Tailing Mix, incubate at 37C for 30 min. Combine the purified Adenylate 3'Ends DNA, Adapter and Ligation Mix, incubate the ligation reaction at 20C for 15 min. Adapter-ligated DNA is selected by running a 2% agarose gel to recover the target fragments. Purify the gel with QIAquick Gel Extraction kit (QIAGEN). Several rounds of PCR amplification with PCR Primer Cocktail and PCR Master Mix are performed to enrich the Adapter-ligated DNA fragments. Then the PCR products are purified with Ampure XP Beads (AGENCOURT). The Qualified libraries will amplify on cBot to generate the cluster on the flowcell (TruSeq PE Cluster Kit V3cBotHS,Illumina). And the amplified flowcell will be subjected to 2*90 bp paired-end sequencing on the HiSeq 2000 System (TruSeq SBS KIT-HS V3,Illumina).|ENA checklist;;ERC000011|genotype;;wild type genotype|INSDC center alias;;Inter-departmental Stem Cell Institute, KU Leuven, Belgium. Department of Development and Regeneration, Stem Cell Biology and Embryology, KU Leuven|INSDC center name;;Inter-departmental Stem Cell Institute, KU Leuven, Belgium. Department of Development and Regeneration, Stem Cell Biology and Embryology, KU Leuven|INSDC first public;;2015-11-29T17:01:16Z|INSDC last update;;2018-03-09T09:24:45Z|INSDC status;;public|organism part;;fetus|organism;;Mus musculus|phenotype;;lin- sca1+ cd11b+ cd150+ cd48-|Sample Name;;ERS957187|SRA accession;;ERS957187|strain;;C57BL/6J|Title;;FL_HSC_E14.5_rep 2	Experimental Factor: fetus;;organism part	180	SAMEA3650038	E-MTAB-4034:FL_HSC_E14.5_rep 2	3450886200	19171590	2015-11-30 10:46:22	2390862852	3450886200	19171590	2	19171590	index:0,count:19171590,average:90,stdev:0|index:1,count:19171590,average:90,stdev:0	E-MTAB-4034:FL14.5_2_L1_	Inter-departmental Stem Cell Institute, KU Leuven, Belgium. Department of Development and Regeneration, Stem Cell Biology and Embryology, KU Leuven	ArrayExpress	Illumina HiSeq2000 	in_mesa	26599326	6.91	2.4	0.09	2997463905	2979111106	2894836106	2889730778	99.39	99.82	18303987	18124503	167.790	281.110	164	552860	51.94	53.82	19418820	9506830	19418820	9506830	49.11	49.04	19418820	8989619	19418820	8662530	1322423307	44.12	5.46	0	3.33	0	0.23	0	0.16	0	0.00	0	4.13	0	18303987	0	180	0	176.74	0	2.99	0	0.02	0	2.58	0	0.02	0	439.60	0	0.35	0	1047137	0	19171590	0	639311	0	44318	0	30966	0	0	0	792319	0	2501	0	0	0	20555	0	2688615	0	17950	0	2729621	0	92.14	0	17664676	0	137175	2753591	20.073562967013	19171590.0	18303987.0	1047137.0	639311.0	44318.0	30966.0	0.0	792319.0	17664676.0	95.5	5.5	3.3	0.2	0.2	0.0	4.1	92.1	90	90	90.00	38	1725443100	26.3	23.6	23.9	26.3	0.0	36.1	22.0	bulk
200203	ERR1197705	ERP013684	ERS1025905	ERX1269964	ERA549726	UMR 1170 INSERM Institut Gustave Roussy	European Nucleotide Archive	RNA-sequencing of murine T-cell acute lymphoblastic leukemia (T-ALL) cells to investigate expression profiling of lymphocyte deficient for Tet2 and mutated for DNMT3A	T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive proliferation of T-lymphocytes usually associated with oncogenic activation of NOTCH1 signaling. Using a bone marrow transplantation approach, we have modeled murine CD4+ CD8+ T-ALL by overexpressing DNMT3A R882H in Tet2-/- multipotent progenitors. T-ALL derived from NOTCH1 L1601PdelP Tet2-/-, NOTCH1 L1601PdelP Tet2+/+ or TCL1A progenitors were used for comparison, as well as normal Tet2+/+  and Tet2-/- CD4+ CD8+ double positive (DP) thymocytes.	T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive proliferation of T-lymphocytes usually associated with oncogenic activation of NOTCH1 signaling. Using a bone marrow transplantation approach, we have modeled murine CD4+ CD8+ T-ALL by overexpressing DNMT3A R882H in Tet2-/- multipotent progenitors. T-ALL derived from NOTCH1 L1601PdelP Tet2-/-, NOTCH1 L1601PdelP Tet2+/+ or TCL1A progenitors were used for comparison, as well as normal Tet2+/+  and Tet2-/- CD4+ CD8+ double positive (DP) thymocytes.	Illumina HiSeq 2000 paired end sequencing; RNA-sequencing of murine T-cell acute lymphoblastic leukemia (T-ALL) cells to investigate expression profiling of lymphocyte deficient for Tet2 and mutated for DNMT3A	RNA-sequencing of murine T-cell acute lymphoblastic leukemia (T-ALL) cells to investigate expression profiling of lymphocyte deficient for Tet2 and mutated for DNMT3A		PC14	RNA-Seq	TRANSCRIPTOMIC	cDNA	paired	150	37.5	Cells were sorted using flow cytometry based on the expression of GFP and CD4/CD8 markers Allprep Kit (QIAGEN) according to manufacturer's protocol SureSelect Automated Strand Specific RNA library Preparation according to manufacturer's protocol	Illumina HiSeq 2000	Alias;;E-MTAB-4157:PC14|Broker name;;ArrayExpress|cell_type;;T cell|Description;;Protocols: Cells were sorted using flow cytometry based on the expression of GFP and CD4/CD8 markers Allprep Kit (QIAGEN) according to manufacturer's protocol SureSelect Automated Strand Specific RNA library Preparation according to manufacturer's protocol|disease;;normal|ENA checklist;;ERC000011|genotype;;Tet2+/+|INSDC center name;;UMR 1170 INSERM Institut Gustave Roussy|INSDC first public;;2016-02-24T17:02:27Z|INSDC last update;;2015-12-21T18:35:27Z|INSDC status;;public|organism;;Mus musculus|phenotype;;DP (CD4+/CD8+) T-cells|Sample Name;;ERS1025905|SRA accession;;ERS1025905|strain;;C57BL/6|Title;;PC14	Experimental Factor: Tet2+/+;;genotype	200	SAMEA3718756	E-MTAB-4157:PC14	17974243302	89764869	2016-02-25 05:20:35	10789768162	17974243302	89764869				E-MTAB-4157:PC14.R	UMR 1170 INSERM Institut Gustave Roussy	ArrayExpress	UMR 1170 INSERM, Institut Gustave Roussy, 94805 Villejuif, France	in_mesa	26876596	4.31	3.07	0.07	12481213523	12360602819	11678763301	11638237769	99.03	99.65	79034173	72241184	201.972	941.897	124	613375	83.67	89.67	88423485	66129069	88423485	66129069	85.33	85.88	88423485	67443680	88423485	63339016	1205463236	9.66	2.47	0	5.89	0	0.35	0	0.04	0	0.00	0	11.56	0	79034173	0	200	0	196.94	0	1.35	0	0.02	0	1.76	0	0.01	0	358.66	0	0.38	0	2218878	0	89764869	0	5285514	0	310582	0	39137	0	0	0	10380977	0	30429	0	0	0	243207	0	35381093	0	85464	0	35740193	0	82.16	0	73748659	0	291120	31001111	106.489114454520	89764869.0	79034173.0	2218878.0	5285514.0	310582.0	39137.0	0.0	10380977.0	73748659.0	88.0	2.5	5.9	0.3	0.0	0.0	11.6	82.2	101	101	101.00	38	9066251769	23.8	25.2	24.9	26.0	0.0	36.5	21.2	bulk
200205	ERR1197706	ERP013684	ERS1025906	ERX1269965	ERA549726	UMR 1170 INSERM Institut Gustave Roussy	European Nucleotide Archive	RNA-sequencing of murine T-cell acute lymphoblastic leukemia (T-ALL) cells to investigate expression profiling of lymphocyte deficient for Tet2 and mutated for DNMT3A	T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive proliferation of T-lymphocytes usually associated with oncogenic activation of NOTCH1 signaling. Using a bone marrow transplantation approach, we have modeled murine CD4+ CD8+ T-ALL by overexpressing DNMT3A R882H in Tet2-/- multipotent progenitors. T-ALL derived from NOTCH1 L1601PdelP Tet2-/-, NOTCH1 L1601PdelP Tet2+/+ or TCL1A progenitors were used for comparison, as well as normal Tet2+/+  and Tet2-/- CD4+ CD8+ double positive (DP) thymocytes.	T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive proliferation of T-lymphocytes usually associated with oncogenic activation of NOTCH1 signaling. Using a bone marrow transplantation approach, we have modeled murine CD4+ CD8+ T-ALL by overexpressing DNMT3A R882H in Tet2-/- multipotent progenitors. T-ALL derived from NOTCH1 L1601PdelP Tet2-/-, NOTCH1 L1601PdelP Tet2+/+ or TCL1A progenitors were used for comparison, as well as normal Tet2+/+  and Tet2-/- CD4+ CD8+ double positive (DP) thymocytes.	Illumina HiSeq 2000 paired end sequencing; RNA-sequencing of murine T-cell acute lymphoblastic leukemia (T-ALL) cells to investigate expression profiling of lymphocyte deficient for Tet2 and mutated for DNMT3A	RNA-sequencing of murine T-cell acute lymphoblastic leukemia (T-ALL) cells to investigate expression profiling of lymphocyte deficient for Tet2 and mutated for DNMT3A		PC15	RNA-Seq	TRANSCRIPTOMIC	cDNA	paired	150	37.5	Cells were sorted using flow cytometry based on the expression of GFP and CD4/CD8 markers Allprep Kit (QIAGEN) according to manufacturer's protocol SureSelect Automated Strand Specific RNA library Preparation according to manufacturer's protocol	Illumina HiSeq 2000	Alias;;E-MTAB-4157:PC15|Broker name;;ArrayExpress|cell_type;;T cell|Description;;Protocols: Cells were sorted using flow cytometry based on the expression of GFP and CD4/CD8 markers Allprep Kit (QIAGEN) according to manufacturer's protocol SureSelect Automated Strand Specific RNA library Preparation according to manufacturer's protocol|disease;;normal|ENA checklist;;ERC000011|genotype;;Tet2+/+|INSDC center name;;UMR 1170 INSERM Institut Gustave Roussy|INSDC first public;;2016-02-24T17:02:27Z|INSDC last update;;2015-12-21T18:35:27Z|INSDC status;;public|organism;;Mus musculus|phenotype;;DP (CD4+/CD8+) T-cells|Sample Name;;ERS1025906|SRA accession;;ERS1025906|strain;;C57BL/6|Title;;PC15	Experimental Factor: Tet2+/+;;genotype	202	SAMEA3718757	E-MTAB-4157:PC15	34820335396	172377898	2016-02-25 05:20:35	22169353824	34820335396	172377898	2	172377898	index:0,count:172377898,average:101,stdev:0|index:1,count:172377898,average:101,stdev:0	E-MTAB-4157:PC15.R	UMR 1170 INSERM Institut Gustave Roussy	ArrayExpress	UMR 1170 INSERM, Institut Gustave Roussy, 94805 Villejuif, France	in_mesa	26876596	1.47	3.21	0.06	26951986556	26396030025	24965581589	24489882834	97.94	98.09	143531146	120803594	305.472	1521.755	217	826808	68.74	74.5	162482029	98666837	162482029	98666837	72.19	71.55	162482029	103611887	162482029	94751971	6256594948	23.21	0.88	0	6.44	0	0.21	0	0.07	0	0.00	0	16.46	0	143531146	0	202	0	195.51	0	1.36	0	0.01	0	2.69	0	0.01	0	267.94	0	1.35	0	1511049	0	172377898	0	11101179	0	365242	0	113910	0	0	0	28367600	0	37049	0	0	0	291724	0	42326640	0	121793	0	42777206	0	76.83	0	132429967	0	173144	43944591	253.803718292288	172377898.0	143531146.0	1511049.0	11101179.0	365242.0	113910.0	0.0	28367600.0	132429967.0	83.3	0.9	6.4	0.2	0.1	0.0	16.5	76.8	101	101	101.00	38	17410167698	26.6	23.0	25.0	25.4	0.0	34.7	15.9	bulk
1930040	SRR528733	SRP014599	SRS348125	SRX171237	SRA055349	The Jackson Laboratory		CELF4 wt and knockout transcriptome by polysome fractions	CELF4 wildtype and mutant polysome; 129S1/SvImJ inbred mouse strai.n		Mouse 129S1 (WT) CELF4_polysome		Paired end RNA sequencing of pooled polysome fractions from mouse strain 129S1< / > (WT) and 129S1-Celf4<tm1Frk/tm1Frk> (KO) female adult cerebral cortex   hippocampus combined.  Tissue extracts from 3 biological replicates from each strain were subjected to sucrose gradient fractionation.  Individual fractions from each replicate were pooled into three groups ("monosomes," "polysomes," "RNA granules"), and then split again into 5 technical replicates each for sequencing (R1, R2 forward and reverse paired ends, respectively	WT_polysome	RNA-Seq	TRANSCRIPTOMIC	Hybrid Selection	paired				Illumina HiSeq 2000	genotype;;tm1Frk/tm1Frk (KO)|strain;;129S1		200	CELF4_polysomes	Mus musculus 129S1 CELF4_polysomes	4023603800	20118019	2015-07-22 17:07:41	2523427699	4023603800	20118019	2	20118019	index:0,count:20118019,average:100,stdev:0|index:1,count:20118019,average:100,stdev:0	WT_polysome_2	JAX					2.48	3.55	0.01	2877387621	2860466573	2730104342	2730571757	99.41	100.02	19041008	17975650	174.105	583.251	125	198929	90.74	95.74	20541303	17277373	20541303	17277373	91.31	91.97	20541303	17385604	20541303	16597647	77107593	2.68	1.55	0	4.95	0	0.22	0	0.05	0	0.00	0	5.08	0	19041008	0	200	0	196.91	0	2.19	0	0.02	0	1.64	0	0.02	0	198.97	0	0.66	0	312141	0	20118019	0	995082	0	44633	0	9397	0	0	0	1022981	0	5409	0	0	0	41839	0	6327669	0	36236	0	6411153	0	89.70	0	18045926	0	181878	5434764	29.881371028931	20118019.0	19041008.0	312141.0	995082.0	44633.0	9397.0	0.0	1022981.0	18045926.0	94.6	1.6	4.9	0.2	0.0	0.0	5.1	89.7	100	100	100.00	38	2011801900	25.4	24.7	24.5	25.4	0.0	33.3	14.7	bulk
1930072	SRR528735	SRP014599	SRS348125	SRX171237	SRA055349	The Jackson Laboratory		CELF4 wt and knockout transcriptome by polysome fractions	CELF4 wildtype and mutant polysome; 129S1/SvImJ inbred mouse strai.n		Mouse 129S1 (WT) CELF4_polysome		Paired end RNA sequencing of pooled polysome fractions from mouse strain 129S1< / > (WT) and 129S1-Celf4<tm1Frk/tm1Frk> (KO) female adult cerebral cortex   hippocampus combined.  Tissue extracts from 3 biological replicates from each strain were subjected to sucrose gradient fractionation.  Individual fractions from each replicate were pooled into three groups ("monosomes," "polysomes," "RNA granules"), and then split again into 5 technical replicates each for sequencing (R1, R2 forward and reverse paired ends, respectively	WT_polysome	RNA-Seq	TRANSCRIPTOMIC	Hybrid Selection	paired				Illumina HiSeq 2000	genotype;;tm1Frk/tm1Frk (KO)|strain;;129S1		200	CELF4_polysomes	Mus musculus 129S1 CELF4_polysomes	3934413200	19672066	2015-07-22 17:07:41	2480294660	3934413200	19672066	2	19672066	index:0,count:19672066,average:100,stdev:0|index:1,count:19672066,average:100,stdev:0	WT_polysome_7	JAX					2.49	3.56	0.01	2807766774	2790806886	2663906106	2664003961	99.4	100.0	18586085	17548822	173.983	584.173	125	194331	90.72	95.72	20052620	16860738	20052620	16860738	91.3	91.97	20052620	16969032	20052620	16200165	75747999	2.70	1.54	0	4.94	0	0.22	0	0.05	0	0.00	0	5.25	0	18586085	0	200	0	196.80	0	2.19	0	0.02	0	1.63	0	0.02	0	95.83	0	0.70	0	303926	0	19672066	0	971937	0	43280	0	9116	0	0	0	1033585	0	5322	0	0	0	40832	0	6141390	0	34878	0	6222422	0	89.54	0	17614148	0	180455	5283551	29.279050178715	19672066.0	18586085.0	303926.0	971937.0	43280.0	9116.0	0.0	1033585.0	17614148.0	94.5	1.5	4.9	0.2	0.0	0.0	5.3	89.5	100	100	100.00	38	1967206600	25.4	24.6	24.5	25.4	0.1	33.0	14.3	bulk
1930120	SRR528738	SRP014599	SRS348125	SRX171238	SRA055349	The Jackson Laboratory		CELF4 wt and knockout transcriptome by polysome fractions	CELF4 wildtype and mutant polysome; 129S1/SvImJ inbred mouse strai.n		Mouse 129S1 (WT) CELF4_RNAgranule		Paired end RNA sequencing of pooled polysome fractions from mouse strain 129S1< / > (WT) and 129S1-Celf4<tm1Frk/tm1Frk> (KO) female adult cerebral cortex   hippocampus combined.  Tissue extracts from 3 biological replicates from each strain were subjected to sucrose gradient fractionation.  Individual fractions from each replicate were pooled into three groups ("monosomes," "polysomes," "RNA granules"), and then split again into 5 technical replicates each for sequencing (R1, R2 forward and reverse paired ends, respectively	WT_RNAgranule	RNA-Seq	TRANSCRIPTOMIC	Hybrid Selection	paired				Illumina HiSeq 2000	genotype;;tm1Frk/tm1Frk (KO)|strain;;129S1		200	CELF4_polysomes	Mus musculus 129S1 CELF4_polysomes	3816785200	19083926	2015-07-22 17:07:41	2397874038	3816785200	19083926	2	19083926	index:0,count:19083926,average:100,stdev:0|index:1,count:19083926,average:100,stdev:0	WT_RNAgranule_2	JAX					3.44	3.57	0.01	2751375965	2742128366	2602906134	2608440748	99.66	100.21	18094512	16997150	176.553	612.042	125	185614	91.12	96.42	19568601	16487602	19568601	16487602	92.22	92.76	19568601	16685884	19568601	15861035	57235413	2.08	1.49	0	5.21	0	0.31	0	0.04	0	0.00	0	4.84	0	18094512	0	200	0	196.90	0	2.19	0	0.02	0	1.66	0	0.02	0	118.04	0	0.67	0	283779	0	19083926	0	995087	0	58350	0	6746	0	0	0	924318	0	5085	0	0	0	46523	0	6560473	0	35176	0	6647257	0	89.60	0	17099425	0	171212	5618735	32.817413499054	19083926.0	18094512.0	283779.0	995087.0	58350.0	6746.0	0.0	924318.0	17099425.0	94.8	1.5	5.2	0.3	0.0	0.0	4.8	89.6	100	100	100.00	38	1908392600	25.1	25.0	24.7	25.1	0.0	33.3	14.7	bulk
1930136	SRR528739	SRP014599	SRS348125	SRX171238	SRA055349	The Jackson Laboratory		CELF4 wt and knockout transcriptome by polysome fractions	CELF4 wildtype and mutant polysome; 129S1/SvImJ inbred mouse strai.n		Mouse 129S1 (WT) CELF4_RNAgranule		Paired end RNA sequencing of pooled polysome fractions from mouse strain 129S1< / > (WT) and 129S1-Celf4<tm1Frk/tm1Frk> (KO) female adult cerebral cortex   hippocampus combined.  Tissue extracts from 3 biological replicates from each strain were subjected to sucrose gradient fractionation.  Individual fractions from each replicate were pooled into three groups ("monosomes," "polysomes," "RNA granules"), and then split again into 5 technical replicates each for sequencing (R1, R2 forward and reverse paired ends, respectively	WT_RNAgranule	RNA-Seq	TRANSCRIPTOMIC	Hybrid Selection	paired				Illumina HiSeq 2000	genotype;;tm1Frk/tm1Frk (KO)|strain;;129S1		200	CELF4_polysomes	Mus musculus 129S1 CELF4_polysomes	3784992400	18924962	2015-07-22 17:07:41	2383068274	3784992400	18924962	2	18924962	index:0,count:18924962,average:100,stdev:0|index:1,count:18924962,average:100,stdev:0	WT_RNAgranule_6	JAX					3.45	3.57	0.01	2724402243	2715577581	2577243804	2582929586	99.68	100.22	17926669	16837696	176.419	611.827	125	184702	91.11	96.42	19389164	16333063	19389164	16333063	92.2	92.75	19389164	16529142	19389164	15711193	56911539	2.09	1.48	0	5.22	0	0.31	0	0.03	0	0.00	0	4.94	0	17926669	0	200	0	196.83	0	2.18	0	0.02	0	1.66	0	0.02	0	251.40	0	0.69	0	280424	0	18924962	0	987101	0	57795	0	6539	0	0	0	933959	0	4941	0	0	0	46046	0	6486627	0	35118	0	6572732	0	89.51	0	16939568	0	171221	5560012	32.472722388025	18924962.0	17926669.0	280424.0	987101.0	57795.0	6539.0	0.0	933959.0	16939568.0	94.7	1.5	5.2	0.3	0.0	0.0	4.9	89.5	100	100	100.00	38	1892496200	25.2	24.9	24.8	25.1	0.0	33.0	14.4	bulk
1930248	SRR528740	SRP014599	SRS348125	SRX171238	SRA055349	The Jackson Laboratory		CELF4 wt and knockout transcriptome by polysome fractions	CELF4 wildtype and mutant polysome; 129S1/SvImJ inbred mouse strai.n		Mouse 129S1 (WT) CELF4_RNAgranule		Paired end RNA sequencing of pooled polysome fractions from mouse strain 129S1< / > (WT) and 129S1-Celf4<tm1Frk/tm1Frk> (KO) female adult cerebral cortex   hippocampus combined.  Tissue extracts from 3 biological replicates from each strain were subjected to sucrose gradient fractionation.  Individual fractions from each replicate were pooled into three groups ("monosomes," "polysomes," "RNA granules"), and then split again into 5 technical replicates each for sequencing (R1, R2 forward and reverse paired ends, respectively	WT_RNAgranule	RNA-Seq	TRANSCRIPTOMIC	Hybrid Selection	paired				Illumina HiSeq 2000	genotype;;tm1Frk/tm1Frk (KO)|strain;;129S1		200	CELF4_polysomes	Mus musculus 129S1 CELF4_polysomes	3694907800	18474539	2015-07-22 17:07:41	2334481621	3694907800	18474539	2	18474539	index:0,count:18474539,average:100,stdev:0|index:1,count:18474539,average:100,stdev:0	WT_RNAgranule_7	JAX					3.45	3.58	0.01	2657650625	2648699078	2514203467	2519496305	99.66	100.21	17484054	16424237	176.439	611.121	125	180233	91.12	96.42	18908424	15931201	18908424	15931201	92.21	92.75	18908424	16121614	18908424	15325304	55277956	2.08	1.49	0	5.20	0	0.30	0	0.03	0	0.00	0	5.02	0	17484054	0	200	0	196.77	0	2.18	0	0.02	0	1.66	0	0.02	0	118.34	0	0.71	0	274427	0	18474539	0	961527	0	55773	0	6436	0	0	0	928276	0	4699	0	0	0	44713	0	6306217	0	34238	0	6389867	0	89.43	0	16522527	0	170180	5412254	31.803114349512	18474539.0	17484054.0	274427.0	961527.0	55773.0	6436.0	0.0	928276.0	16522527.0	94.6	1.5	5.2	0.3	0.0	0.0	5.0	89.4	100	100	100.00	38	1847453900	25.2	24.9	24.7	25.1	0.1	32.9	14.3	bulk
1930264	SRR528741	SRP014599	SRS348125	SRX171238	SRA055349	The Jackson Laboratory		CELF4 wt and knockout transcriptome by polysome fractions	CELF4 wildtype and mutant polysome; 129S1/SvImJ inbred mouse strai.n		Mouse 129S1 (WT) CELF4_RNAgranule		Paired end RNA sequencing of pooled polysome fractions from mouse strain 129S1< / > (WT) and 129S1-Celf4<tm1Frk/tm1Frk> (KO) female adult cerebral cortex   hippocampus combined.  Tissue extracts from 3 biological replicates from each strain were subjected to sucrose gradient fractionation.  Individual fractions from each replicate were pooled into three groups ("monosomes," "polysomes," "RNA granules"), and then split again into 5 technical replicates each for sequencing (R1, R2 forward and reverse paired ends, respectively	WT_RNAgranule	RNA-Seq	TRANSCRIPTOMIC	Hybrid Selection	paired				Illumina HiSeq 2000	genotype;;tm1Frk/tm1Frk (KO)|strain;;129S1		200	CELF4_polysomes	Mus musculus 129S1 CELF4_polysomes	3727535600	18637678	2015-07-22 17:07:41	2348449003	3727535600	18637678	2	18637678	index:0,count:18637678,average:100,stdev:0|index:1,count:18637678,average:100,stdev:0	WT_RNAgranule_8	JAX					3.45	3.57	0.01	2683467999	2674922056	2538916221	2544683126	99.68	100.23	17651724	16580448	176.490	610.125	125	181535	91.13	96.42	19086249	16086197	19086249	16086197	92.22	92.76	19086249	16277589	19086249	15474590	55884072	2.08	1.49	0	5.20	0	0.30	0	0.03	0	0.00	0	4.95	0	17651724	0	200	0	196.82	0	2.19	0	0.02	0	1.66	0	0.02	0	244.87	0	0.69	0	277289	0	18637678	0	969063	0	56768	0	6438	0	0	0	922748	0	4931	0	0	0	45323	0	6384325	0	34647	0	6469226	0	89.51	0	16682661	0	170272	5474044	32.148820710393	18637678.0	17651724.0	277289.0	969063.0	56768.0	6438.0	0.0	922748.0	16682661.0	94.7	1.5	5.2	0.3	0.0	0.0	5.0	89.5	100	100	100.00	38	1863767800	25.2	25.0	24.7	25.1	0.0	33.1	14.5	bulk
1930280	SRR528742	SRP014599	SRS348126	SRX171525	SRA055349	The Jackson Laboratory		CELF4 wt and knockout transcriptome by polysome fractions	CELF4 wildtype and mutant polysome; 129S1/SvImJ inbred mouse strai.n		Mouse 129S1 (KO) CELF4_polysome		Paired end RNA sequencing of the CA1 region of the hippocampus from mouse strain 129S1< / > (WT) and 129S1-Celf4<tm1Frk/tm1Frk> (DEL) male adult, dissected into cell body (cb) and neuropil (np) components. 3 biological replicates (A,B,C or A,B,D) from each strain-genotype were carried through to sequencing (R1, R2 forward and reverse paired ends, respectively).	KO_RNAgranule	RNA-Seq	TRANSCRIPTOMIC	Hybrid Selection	paired				Illumina HiSeq 2000	dev_stage;;adult|sex;;male|strain;;129S1|tissue;;hippocampus CA1 region		200	CELF4_hippocampal_CA1_dissection	Mus musculus 129S1 (WT) hippocampus CA1 region	3107898200	15539491	2015-07-22 17:07:41	1959098122	3107898200	15539491	2	15539491	index:0,count:15539491,average:100,stdev:0|index:1,count:15539491,average:100,stdev:0	KO_RNAgranule_1	JAX					4.9	3.57	0.01	2255682116	2249338306	2116317236	2121593933	99.72	100.25	14768872	13825542	178.466	624.705	126	146825	90.27	96.32	16140967	13331683	16140967	13331683	92.23	92.66	16140967	13621321	16140967	12825436	47854760	2.12	1.45	0	5.97	0	0.42	0	0.03	0	0.00	0	4.51	0	14768872	0	200	0	196.91	0	2.24	0	0.02	0	1.72	0	0.01	0	109.69	0	0.66	0	224740	0	15539491	0	927340	0	65182	0	4819	0	0	0	700618	0	3790	0	0	0	41844	0	5651981	0	22219	0	5719834	0	89.07	0	13841532	0	160684	4858708	30.237659007742	15539491.0	14768872.0	224740.0	927340.0	65182.0	4819.0	0.0	700618.0	13841532.0	95.0	1.4	6.0	0.4	0.0	0.0	4.5	89.1	100	100	100.00	38	1553949100	25.0	25.1	24.8	25.1	0.0	33.5	15.0	bulk
1930296	SRR528743	SRP014599	SRS348126	SRX171525	SRA055349	The Jackson Laboratory		CELF4 wt and knockout transcriptome by polysome fractions	CELF4 wildtype and mutant polysome; 129S1/SvImJ inbred mouse strai.n		Mouse 129S1 (KO) CELF4_polysome		Paired end RNA sequencing of the CA1 region of the hippocampus from mouse strain 129S1< / > (WT) and 129S1-Celf4<tm1Frk/tm1Frk> (DEL) male adult, dissected into cell body (cb) and neuropil (np) components. 3 biological replicates (A,B,C or A,B,D) from each strain-genotype were carried through to sequencing (R1, R2 forward and reverse paired ends, respectively).	KO_RNAgranule	RNA-Seq	TRANSCRIPTOMIC	Hybrid Selection	paired				Illumina HiSeq 2000	dev_stage;;adult|sex;;male|strain;;129S1|tissue;;hippocampus CA1 region		200	CELF4_hippocampal_CA1_dissection	Mus musculus 129S1 (WT) hippocampus CA1 region	3120067600	15600338	2015-07-22 17:07:41	1973675521	3120067600	15600338	2	15600338	index:0,count:15600338,average:100,stdev:0|index:1,count:15600338,average:100,stdev:0	KO_RNAgranule_2	JAX					4.92	3.57	0.01	2263951290	2257373159	2124239278	2129406314	99.71	100.24	14823624	13875520	178.402	626.343	127	147698	90.27	96.31	16196989	13381138	16196989	13381138	92.23	92.66	16196989	13671173	16196989	12873292	48197966	2.13	1.44	0	5.96	0	0.42	0	0.03	0	0.00	0	4.53	0	14823624	0	200	0	196.88	0	2.24	0	0.02	0	1.72	0	0.01	0	216.00	0	0.66	0	224874	0	15600338	0	929841	0	65589	0	5008	0	0	0	706117	0	3845	0	0	0	42198	0	5662783	0	22448	0	5731274	0	89.06	0	13893783	0	160895	4868792	30.260679325026	15600338.0	14823624.0	224874.0	929841.0	65589.0	5008.0	0.0	706117.0	13893783.0	95.0	1.4	6.0	0.4	0.0	0.0	4.5	89.1	100	100	100.00	38	1560033800	25.0	25.1	24.8	25.1	0.0	33.4	14.9	bulk
1930313	SRR528744	SRP014599	SRS348126	SRX171525	SRA055349	The Jackson Laboratory		CELF4 wt and knockout transcriptome by polysome fractions	CELF4 wildtype and mutant polysome; 129S1/SvImJ inbred mouse strai.n		Mouse 129S1 (KO) CELF4_polysome		Paired end RNA sequencing of the CA1 region of the hippocampus from mouse strain 129S1< / > (WT) and 129S1-Celf4<tm1Frk/tm1Frk> (DEL) male adult, dissected into cell body (cb) and neuropil (np) components. 3 biological replicates (A,B,C or A,B,D) from each strain-genotype were carried through to sequencing (R1, R2 forward and reverse paired ends, respectively).	KO_RNAgranule	RNA-Seq	TRANSCRIPTOMIC	Hybrid Selection	paired				Illumina HiSeq 2000	dev_stage;;adult|sex;;male|strain;;129S1|tissue;;hippocampus CA1 region		200	CELF4_hippocampal_CA1_dissection	Mus musculus 129S1 (WT) hippocampus CA1 region	3085239400	15426197	2015-07-22 17:07:41	1953236046	3085239400	15426197	2	15426197	index:0,count:15426197,average:100,stdev:0|index:1,count:15426197,average:100,stdev:0	KO_RNAgranule_6	JAX					4.91	3.57	0.01	2236580574	2230014732	2098600047	2103546491	99.71	100.24	14649822	13713134	178.371	623.991	127	146223	90.27	96.31	16009293	13224794	16009293	13224794	92.24	92.67	16009293	13512814	16009293	12724410	47495316	2.12	1.45	0	5.95	0	0.42	0	0.03	0	0.00	0	4.58	0	14649822	0	200	0	196.85	0	2.23	0	0.02	0	1.72	0	0.01	0	217.78	0	0.68	0	222985	0	15426197	0	918557	0	64637	0	4887	0	0	0	706851	0	3779	0	0	0	41531	0	5592316	0	21923	0	5659549	0	89.01	0	13731265	0	160267	4806694	29.991788702603	15426197.0	14649822.0	222985.0	918557.0	64637.0	4887.0	0.0	706851.0	13731265.0	95.0	1.4	6.0	0.4	0.0	0.0	4.6	89.0	100	100	100.00	38	1542619700	25.0	25.0	24.8	25.1	0.0	33.2	14.7	bulk
1930329	SRR528745	SRP014599	SRS348126	SRX171525	SRA055349	The Jackson Laboratory		CELF4 wt and knockout transcriptome by polysome fractions	CELF4 wildtype and mutant polysome; 129S1/SvImJ inbred mouse strai.n		Mouse 129S1 (KO) CELF4_polysome		Paired end RNA sequencing of the CA1 region of the hippocampus from mouse strain 129S1< / > (WT) and 129S1-Celf4<tm1Frk/tm1Frk> (DEL) male adult, dissected into cell body (cb) and neuropil (np) components. 3 biological replicates (A,B,C or A,B,D) from each strain-genotype were carried through to sequencing (R1, R2 forward and reverse paired ends, respectively).	KO_RNAgranule	RNA-Seq	TRANSCRIPTOMIC	Hybrid Selection	paired				Illumina HiSeq 2000	dev_stage;;adult|sex;;male|strain;;129S1|tissue;;hippocampus CA1 region		200	CELF4_hippocampal_CA1_dissection	Mus musculus 129S1 (WT) hippocampus CA1 region	3034090600	15170453	2015-07-22 17:07:41	1927457291	3034090600	15170453	2	15170453	index:0,count:15170453,average:100,stdev:0|index:1,count:15170453,average:100,stdev:0	KO_RNAgranule_7	JAX					4.91	3.56	0.01	2198375684	2192180097	2062804674	2067844454	99.72	100.24	14396225	13476401	178.415	627.004	125	143370	90.28	96.32	15730582	12997474	15730582	12997474	92.24	92.66	15730582	13278847	15730582	12504146	46472411	2.11	1.43	0	5.95	0	0.42	0	0.03	0	0.00	0	4.65	0	14396225	0	200	0	196.80	0	2.24	0	0.02	0	1.71	0	0.01	0	212.50	0	0.69	0	217547	0	15170453	0	902268	0	63401	0	4840	0	0	0	705987	0	3853	0	0	0	40799	0	5475744	0	21322	0	5541718	0	88.95	0	13493957	0	159528	4716010	29.562271200040	15170453.0	14396225.0	217547.0	902268.0	63401.0	4840.0	0.0	705987.0	13493957.0	94.9	1.4	5.9	0.4	0.0	0.0	4.7	88.9	100	100	100.00	38	1517045300	25.0	25.0	24.8	25.1	0.1	33.1	14.6	bulk
1930344	SRR528746	SRP014599	SRS348126	SRX171525	SRA055349	The Jackson Laboratory		CELF4 wt and knockout transcriptome by polysome fractions	CELF4 wildtype and mutant polysome; 129S1/SvImJ inbred mouse strai.n		Mouse 129S1 (KO) CELF4_polysome		Paired end RNA sequencing of the CA1 region of the hippocampus from mouse strain 129S1< / > (WT) and 129S1-Celf4<tm1Frk/tm1Frk> (DEL) male adult, dissected into cell body (cb) and neuropil (np) components. 3 biological replicates (A,B,C or A,B,D) from each strain-genotype were carried through to sequencing (R1, R2 forward and reverse paired ends, respectively).	KO_RNAgranule	RNA-Seq	TRANSCRIPTOMIC	Hybrid Selection	paired				Illumina HiSeq 2000	dev_stage;;adult|sex;;male|strain;;129S1|tissue;;hippocampus CA1 region		200	CELF4_hippocampal_CA1_dissection	Mus musculus 129S1 (WT) hippocampus CA1 region	3049473400	15247367	2015-07-22 17:07:41	1931140676	3049473400	15247367	2	15247367	index:0,count:15247367,average:100,stdev:0|index:1,count:15247367,average:100,stdev:0	KO_RNAgranule_8	JAX					4.91	3.57	0.01	2210939986	2204917081	2074593302	2079919115	99.73	100.26	14478518	13552424	178.487	627.626	127	144190	90.29	96.33	15820628	13072476	15820628	13072476	92.25	92.68	15820628	13356335	15820628	12576858	46721120	2.11	1.45	0	5.95	0	0.41	0	0.03	0	0.00	0	4.60	0	14478518	0	200	0	196.84	0	2.23	0	0.02	0	1.71	0	0.01	0	200.33	0	0.67	0	221194	0	15247367	0	907593	0	62995	0	4972	0	0	0	700882	0	3827	0	0	0	41069	0	5524952	0	21822	0	5591670	0	89.01	0	13570925	0	159980	4753258	29.711576447056	15247367.0	14478518.0	221194.0	907593.0	62995.0	4972.0	0.0	700882.0	13570925.0	95.0	1.5	6.0	0.4	0.0	0.0	4.6	89.0	100	100	100.00	38	1524736700	25.0	25.1	24.8	25.1	0.0	33.3	14.8	bulk
1930361	SRR528747	SRP014599	SRS348126	SRX171524	SRA055349	The Jackson Laboratory		CELF4 wt and knockout transcriptome by polysome fractions	CELF4 wildtype and mutant polysome; 129S1/SvImJ inbred mouse strai.n		Mouse 129S1 (KO) CELF4_polysome		Paired end RNA sequencing of the CA1 region of the hippocampus from mouse strain 129S1< / > (WT) and 129S1-Celf4<tm1Frk/tm1Frk> (DEL) male adult, dissected into cell body (cb) and neuropil (np) components. 3 biological replicates (A,B,C or A,B,D) from each strain-genotype were carried through to sequencing (R1, R2 forward and reverse paired ends, respectively).	KO_monosome	RNA-Seq	TRANSCRIPTOMIC	Hybrid Selection	paired				Illumina HiSeq 2000	dev_stage;;adult|sex;;male|strain;;129S1|tissue;;hippocampus CA1 region		200	CELF4_hippocampal_CA1_dissection	Mus musculus 129S1 (WT) hippocampus CA1 region	2849387200	14246936	2015-07-22 17:07:41	1740787033	2849387200	14246936	2	14246936	index:0,count:14246936,average:100,stdev:0|index:1,count:14246936,average:100,stdev:0	KO_monosome_1	JAX					5.39	3.4	0.01	1458831389	1432433586	1318779916	1307197590	98.19	99.12	9964522	9522810	166.752	509.273	124	118047	82.4	91.35	11447990	8210367	11447990	8210367	85.25	85.94	11447990	8495069	11447990	7724204	70678950	4.84	1.16	0	6.86	0	0.13	0	0.07	0	0.00	0	29.86	0	9964522	0	200	0	196.39	0	2.45	0	0.03	0	1.84	0	0.03	0	104.03	0	0.74	0	164763	0	14246936	0	977018	0	18464	0	9829	0	0	0	4254121	0	2193	0	0	0	17397	0	2666626	0	21166	0	2707382	0	63.08	0	8987504	0	147891	2303804	15.577716020583	14246936.0	9964522.0	164763.0	977018.0	18464.0	9829.0	0.0	4254121.0	8987504.0	69.9	1.2	6.9	0.1	0.1	0.0	29.9	63.1	100	100	100.00	38	1424693600	25.8	25.5	24.9	23.8	0.0	30.8	11.7	bulk
1930377	SRR528748	SRP014599	SRS348126	SRX171524	SRA055349	The Jackson Laboratory		CELF4 wt and knockout transcriptome by polysome fractions	CELF4 wildtype and mutant polysome; 129S1/SvImJ inbred mouse strai.n		Mouse 129S1 (KO) CELF4_polysome		Paired end RNA sequencing of the CA1 region of the hippocampus from mouse strain 129S1< / > (WT) and 129S1-Celf4<tm1Frk/tm1Frk> (DEL) male adult, dissected into cell body (cb) and neuropil (np) components. 3 biological replicates (A,B,C or A,B,D) from each strain-genotype were carried through to sequencing (R1, R2 forward and reverse paired ends, respectively).	KO_monosome	RNA-Seq	TRANSCRIPTOMIC	Hybrid Selection	paired				Illumina HiSeq 2000	dev_stage;;adult|sex;;male|strain;;129S1|tissue;;hippocampus CA1 region		200	CELF4_hippocampal_CA1_dissection	Mus musculus 129S1 (WT) hippocampus CA1 region	2925062800	14625314	2015-07-22 17:07:41	1793564365	2925062800	14625314	2	14625314	index:0,count:14625314,average:100,stdev:0|index:1,count:14625314,average:100,stdev:0	KO_monosome_2	JAX					5.4	3.39	0.01	1493743337	1466580413	1350296785	1338383917	98.18	99.12	10203986	9752117	166.652	506.183	124	120481	82.39	91.35	11725216	8406914	11725216	8406914	85.24	85.93	11725216	8698249	11725216	7908482	72285592	4.84	1.15	0	6.84	0	0.13	0	0.07	0	0.00	0	30.03	0	10203986	0	200	0	196.35	0	2.45	0	0.03	0	1.84	0	0.03	0	50.67	0	0.75	0	168581	0	14625314	0	1000740	0	18961	0	10026	0	0	0	4392341	0	2303	0	0	0	17700	0	2725365	0	21255	0	2766623	0	62.93	0	9203246	0	148756	2356247	15.839677055043	14625314.0	10203986.0	168581.0	1000740.0	18961.0	10026.0	0.0	4392341.0	9203246.0	69.8	1.2	6.8	0.1	0.1	0.0	30.0	62.9	100	100	100.00	38	1462531400	25.8	25.5	24.9	23.8	0.0	30.7	11.6	bulk
1930392	SRR528749	SRP014599	SRS348126	SRX171524	SRA055349	The Jackson Laboratory		CELF4 wt and knockout transcriptome by polysome fractions	CELF4 wildtype and mutant polysome; 129S1/SvImJ inbred mouse strai.n		Mouse 129S1 (KO) CELF4_polysome		Paired end RNA sequencing of the CA1 region of the hippocampus from mouse strain 129S1< / > (WT) and 129S1-Celf4<tm1Frk/tm1Frk> (DEL) male adult, dissected into cell body (cb) and neuropil (np) components. 3 biological replicates (A,B,C or A,B,D) from each strain-genotype were carried through to sequencing (R1, R2 forward and reverse paired ends, respectively).	KO_monosome	RNA-Seq	TRANSCRIPTOMIC	Hybrid Selection	paired				Illumina HiSeq 2000	dev_stage;;adult|sex;;male|strain;;129S1|tissue;;hippocampus CA1 region		200	CELF4_hippocampal_CA1_dissection	Mus musculus 129S1 (WT) hippocampus CA1 region	2869225200	14346126	2015-07-22 17:07:41	1762894492	2869225200	14346126	2	14346126	index:0,count:14346126,average:100,stdev:0|index:1,count:14346126,average:100,stdev:0	KO_monosome_6	JAX					5.39	3.4	0.01	1464678568	1438117002	1324106639	1312392670	98.19	99.12	10011123	9567938	166.507	506.067	124	118173	82.4	91.36	11501903	8249647	11501903	8249647	85.25	85.94	11501903	8534071	11501903	7760209	70863349	4.84	1.15	0	6.84	0	0.13	0	0.07	0	0.00	0	30.02	0	10011123	0	200	0	196.30	0	2.44	0	0.03	0	1.83	0	0.03	0	54.59	0	0.77	0	164570	0	14346126	0	981043	0	18384	0	9963	0	0	0	4306656	0	2204	0	0	0	17289	0	2670261	0	20882	0	2710636	0	62.94	0	9030080	0	148099	2310310	15.599767722942	14346126.0	10011123.0	164570.0	981043.0	18384.0	9963.0	0.0	4306656.0	9030080.0	69.8	1.1	6.8	0.1	0.1	0.0	30.0	62.9	100	100	100.00	38	1434612600	25.9	25.4	25.0	23.7	0.0	30.5	11.5	bulk
1930504	SRR528750	SRP014599	SRS348126	SRX171524	SRA055349	The Jackson Laboratory		CELF4 wt and knockout transcriptome by polysome fractions	CELF4 wildtype and mutant polysome; 129S1/SvImJ inbred mouse strai.n		Mouse 129S1 (KO) CELF4_polysome		Paired end RNA sequencing of the CA1 region of the hippocampus from mouse strain 129S1< / > (WT) and 129S1-Celf4<tm1Frk/tm1Frk> (DEL) male adult, dissected into cell body (cb) and neuropil (np) components. 3 biological replicates (A,B,C or A,B,D) from each strain-genotype were carried through to sequencing (R1, R2 forward and reverse paired ends, respectively).	KO_monosome	RNA-Seq	TRANSCRIPTOMIC	Hybrid Selection	paired				Illumina HiSeq 2000	dev_stage;;adult|sex;;male|strain;;129S1|tissue;;hippocampus CA1 region		200	CELF4_hippocampal_CA1_dissection	Mus musculus 129S1 (WT) hippocampus CA1 region	2792117000	13960585	2015-07-22 17:07:41	1722230937	2792117000	13960585	2	13960585	index:0,count:13960585,average:100,stdev:0|index:1,count:13960585,average:100,stdev:0	KO_monosome_7	JAX					5.39	3.4	0.01	1424845254	1398914658	1288283264	1276795279	98.18	99.11	9738276	9308288	166.532	503.506	124	115027	82.44	91.38	11185790	8027811	11185790	8027811	85.29	85.99	11185790	8305873	11185790	7553945	68656054	4.82	1.15	0	6.83	0	0.13	0	0.07	0	0.00	0	30.05	0	9738276	0	200	0	196.25	0	2.45	0	0.03	0	1.83	0	0.03	0	97.59	0	0.79	0	159904	0	13960585	0	953368	0	18167	0	9555	0	0	0	4194587	0	2165	0	0	0	16559	0	2589051	0	20235	0	2628010	0	62.93	0	8784908	0	147152	2242159	15.237027019680	13960585.0	9738276.0	159904.0	953368.0	18167.0	9555.0	0.0	4194587.0	8784908.0	69.8	1.1	6.8	0.1	0.1	0.0	30.0	62.9	100	100	100.00	38	1396058500	25.9	25.4	24.9	23.7	0.1	30.4	11.5	bulk
1933852	SRR527821	SRP014599	SRS348125	SRX171211	SRA055349	The Jackson Laboratory		CELF4 wt and knockout transcriptome by polysome fractions	CELF4 wildtype and mutant polysome; 129S1/SvImJ inbred mouse strai.n		Mouse 129S1 (WT) CELF4_monosome		Paired end RNA sequencing of pooled polysome fractions from mouse strain 129S1< / > (WT) and 129S1-Celf4<tm1Frk/tm1Frk> (KO) female adult cerebral cortex   hippocampus combined.  Tissue extracts from 3 biological replicates from each strain were subjected to sucrose gradient fractionation.  Individual fractions from each replicate were pooled into three groups ("monosomes," "polysomes," "RNA granules"), and then split again into 5 technical replicates each for sequencing (R1, R2 forward and reverse paired ends, respectively	WT_monosome	RNA-Seq	TRANSCRIPTOMIC	Hybrid Selection	paired				Illumina HiSeq 2000	genotype;;tm1Frk/tm1Frk (KO)|strain;;129S1		200	CELF4_polysomes	Mus musculus 129S1 CELF4_polysomes	3190590600	15952953	2015-07-22 17:07:41	2002003755	3190590600	15952953	2	15952953	index:0,count:15952953,average:100,stdev:0|index:1,count:15952953,average:100,stdev:0	WT_monosome_6	JAX					7.28	3.37	0.01	2239958774	2207952591	2029156163	2017878723	98.57	99.44	14674952	14103201	172.353	452.418	134	172771	84.84	93.78	16624434	12450548	16624434	12450548	88.99	89.5	16624434	13059192	16624434	11881262	79239839	3.54	1.03	0	8.77	0	0.16	0	0.07	0	0.00	0	7.79	0	14674952	0	200	0	197.12	0	2.34	0	0.03	0	1.68	0	0.02	0	182.32	0	0.71	0	164938	0	15952953	0	1399179	0	24853	0	11005	0	0	0	1242143	0	3531	0	0	0	25098	0	3741978	0	41457	0	3812064	0	83.22	0	13275773	0	166754	3316382	19.887870755724	15952953.0	14674952.0	164938.0	1399179.0	24853.0	11005.0	0.0	1242143.0	13275773.0	92.0	1.0	8.8	0.2	0.1	0.0	7.8	83.2	100	100	100.00	38	1595295300	25.4	24.6	24.5	25.4	0.0	32.9	14.2	bulk
1934600	SRR527850	SRP014599	SRS348125	SRX171211	SRA055349	The Jackson Laboratory		CELF4 wt and knockout transcriptome by polysome fractions	CELF4 wildtype and mutant polysome; 129S1/SvImJ inbred mouse strai.n		Mouse 129S1 (WT) CELF4_monosome		Paired end RNA sequencing of pooled polysome fractions from mouse strain 129S1< / > (WT) and 129S1-Celf4<tm1Frk/tm1Frk> (KO) female adult cerebral cortex   hippocampus combined.  Tissue extracts from 3 biological replicates from each strain were subjected to sucrose gradient fractionation.  Individual fractions from each replicate were pooled into three groups ("monosomes," "polysomes," "RNA granules"), and then split again into 5 technical replicates each for sequencing (R1, R2 forward and reverse paired ends, respectively	WT_monosome	RNA-Seq	TRANSCRIPTOMIC	Hybrid Selection	paired				Illumina HiSeq 2000	genotype;;tm1Frk/tm1Frk (KO)|strain;;129S1		200	CELF4_polysomes	Mus musculus 129S1 CELF4_polysomes	3115922000	15579610	2015-07-22 17:07:41	1961638992	3115922000	15579610	2	15579610	index:0,count:15579610,average:100,stdev:0|index:1,count:15579610,average:100,stdev:0	WT_monosome_7	JAX					7.27	3.37	0.01	2186896462	2155678689	1981267451	1970250336	98.57	99.44	14325077	13767232	172.326	450.918	134	168765	84.85	93.78	16223409	12154711	16223409	12154711	88.99	89.5	16223409	12747390	16223409	11599471	77557281	3.55	1.03	0	8.76	0	0.16	0	0.07	0	0.00	0	7.83	0	14325077	0	200	0	197.07	0	2.33	0	0.03	0	1.68	0	0.02	0	165.45	0	0.73	0	160542	0	15579610	0	1364799	0	24684	0	10592	0	0	0	1219257	0	3336	0	0	0	24595	0	3646553	0	40335	0	3714819	0	83.19	0	12960278	0	165804	3235764	19.515596728668	15579610.0	14325077.0	160542.0	1364799.0	24684.0	10592.0	0.0	1219257.0	12960278.0	91.9	1.0	8.8	0.2	0.1	0.0	7.8	83.2	100	100	100.00	38	1557961000	25.4	24.6	24.5	25.4	0.1	32.8	14.1	bulk
1934616	SRR527851	SRP014599	SRS348125	SRX171211	SRA055349	The Jackson Laboratory		CELF4 wt and knockout transcriptome by polysome fractions	CELF4 wildtype and mutant polysome; 129S1/SvImJ inbred mouse strai.n		Mouse 129S1 (WT) CELF4_monosome		Paired end RNA sequencing of pooled polysome fractions from mouse strain 129S1< / > (WT) and 129S1-Celf4<tm1Frk/tm1Frk> (KO) female adult cerebral cortex   hippocampus combined.  Tissue extracts from 3 biological replicates from each strain were subjected to sucrose gradient fractionation.  Individual fractions from each replicate were pooled into three groups ("monosomes," "polysomes," "RNA granules"), and then split again into 5 technical replicates each for sequencing (R1, R2 forward and reverse paired ends, respectively	WT_monosome	RNA-Seq	TRANSCRIPTOMIC	Hybrid Selection	paired				Illumina HiSeq 2000	genotype;;tm1Frk/tm1Frk (KO)|strain;;129S1		200	CELF4_polysomes	Mus musculus 129S1 CELF4_polysomes	3171127400	15855637	2015-07-22 17:07:41	1990957656	3171127400	15855637	2	15855637	index:0,count:15855637,average:100,stdev:0|index:1,count:15855637,average:100,stdev:0	WT_monosome_8	JAX					7.26	3.37	0.01	2226243424	2194192734	2017117161	2005640345	98.56	99.43	14581511	14013086	172.401	454.098	135	170929	84.83	93.76	16513574	12369756	16513574	12369756	88.95	89.45	16513574	12970054	16513574	11802106	78917678	3.54	1.03	0	8.75	0	0.16	0	0.07	0	0.00	0	7.81	0	14581511	0	200	0	197.11	0	2.32	0	0.03	0	1.68	0	0.02	0	208.32	0	0.71	0	163535	0	15855637	0	1388027	0	25009	0	10871	0	0	0	1238246	0	3319	0	0	0	25029	0	3719321	0	41402	0	3789071	0	83.21	0	13193484	0	166235	3297283	19.835070833459	15855637.0	14581511.0	163535.0	1388027.0	25009.0	10871.0	0.0	1238246.0	13193484.0	92.0	1.0	8.8	0.2	0.1	0.0	7.8	83.2	100	100	100.00	38	1585563700	25.4	24.7	24.5	25.4	0.0	33.0	14.3	bulk
965015	SRR528732	SRP014599	SRS348125	SRX171237	SRA055349	The Jackson Laboratory		CELF4 wt and knockout transcriptome by polysome fractions	CELF4 wildtype and mutant polysome; 129S1/SvImJ inbred mouse strai.n		Mouse 129S1 (WT) CELF4_polysome		Paired end RNA sequencing of pooled polysome fractions from mouse strain 129S1< / > (WT) and 129S1-Celf4<tm1Frk/tm1Frk> (KO) female adult cerebral cortex   hippocampus combined.  Tissue extracts from 3 biological replicates from each strain were subjected to sucrose gradient fractionation.  Individual fractions from each replicate were pooled into three groups ("monosomes," "polysomes," "RNA granules"), and then split again into 5 technical replicates each for sequencing (R1, R2 forward and reverse paired ends, respectively	WT_polysome	RNA-Seq	TRANSCRIPTOMIC	Hybrid Selection	paired				Illumina HiSeq 2000	genotype;;tm1Frk/tm1Frk (KO)|strain;;129S1		200	CELF4_polysomes	Mus musculus 129S1 CELF4_polysomes	3934177200	19670886	2015-07-22 17:07:41	2456184167	3934177200	19670886	2	19670886	index:0,count:19670886,average:100,stdev:0|index:1,count:19670886,average:100,stdev:0	WT_polysome_1	JAX					2.48	3.56	0.01	2814726593	2798037611	2670586906	2670936790	99.41	100.01	18626205	17583100	174.087	583.628	125	194756	90.74	95.74	20096507	16900672	20096507	16900672	91.31	91.98	20096507	17007070	20096507	16236215	75430952	2.68	1.56	0	4.95	0	0.22	0	0.05	0	0.00	0	5.04	0	18626205	0	200	0	196.95	0	2.18	0	0.02	0	1.64	0	0.02	0	230.67	0	0.65	0	306723	0	19670886	0	973438	0	43368	0	9156	0	0	0	992157	0	5310	0	0	0	41214	0	6197698	0	35496	0	6279718	0	89.74	0	17652767	0	180721	5323318	29.456001239480	19670886.0	18626205.0	306723.0	973438.0	43368.0	9156.0	0.0	992157.0	17652767.0	94.7	1.6	4.9	0.2	0.0	0.0	5.0	89.7	100	100	100.00	38	1967088600	25.4	24.7	24.5	25.4	0.0	33.4	14.8	bulk
965030	SRR528734	SRP014599	SRS348125	SRX171237	SRA055349	The Jackson Laboratory		CELF4 wt and knockout transcriptome by polysome fractions	CELF4 wildtype and mutant polysome; 129S1/SvImJ inbred mouse strai.n		Mouse 129S1 (WT) CELF4_polysome		Paired end RNA sequencing of pooled polysome fractions from mouse strain 129S1< / > (WT) and 129S1-Celf4<tm1Frk/tm1Frk> (KO) female adult cerebral cortex   hippocampus combined.  Tissue extracts from 3 biological replicates from each strain were subjected to sucrose gradient fractionation.  Individual fractions from each replicate were pooled into three groups ("monosomes," "polysomes," "RNA granules"), and then split again into 5 technical replicates each for sequencing (R1, R2 forward and reverse paired ends, respectively	WT_polysome	RNA-Seq	TRANSCRIPTOMIC	Hybrid Selection	paired				Illumina HiSeq 2000	genotype;;tm1Frk/tm1Frk (KO)|strain;;129S1		200	CELF4_polysomes	Mus musculus 129S1 CELF4_polysomes	4014176200	20070881	2015-07-22 17:07:41	2522269219	4014176200	20070881	2	20070881	index:0,count:20070881,average:100,stdev:0|index:1,count:20070881,average:100,stdev:0	WT_polysome_6	JAX					2.49	3.56	0.01	2865999730	2848878464	2719117028	2719329069	99.4	100.01	18974261	17913834	173.968	583.737	125	199376	90.73	95.74	20470625	17215332	20470625	17215332	91.31	91.98	20470625	17324459	20470625	16539411	76909197	2.68	1.55	0	4.94	0	0.22	0	0.05	0	0.00	0	5.20	0	18974261	0	200	0	196.84	0	2.18	0	0.02	0	1.63	0	0.02	0	104.41	0	0.69	0	311371	0	20070881	0	992364	0	44273	0	9422	0	0	0	1042925	0	5366	0	0	0	41546	0	6283861	0	35580	0	6366353	0	89.59	0	17981897	0	181560	5403420	29.761070720423	20070881.0	18974261.0	311371.0	992364.0	44273.0	9422.0	0.0	1042925.0	17981897.0	94.5	1.6	4.9	0.2	0.0	0.0	5.2	89.6	100	100	100.00	38	2007088100	25.4	24.7	24.5	25.4	0.0	33.1	14.4	bulk
965047	SRR528736	SRP014599	SRS348125	SRX171237	SRA055349	The Jackson Laboratory		CELF4 wt and knockout transcriptome by polysome fractions	CELF4 wildtype and mutant polysome; 129S1/SvImJ inbred mouse strai.n		Mouse 129S1 (WT) CELF4_polysome		Paired end RNA sequencing of pooled polysome fractions from mouse strain 129S1< / > (WT) and 129S1-Celf4<tm1Frk/tm1Frk> (KO) female adult cerebral cortex   hippocampus combined.  Tissue extracts from 3 biological replicates from each strain were subjected to sucrose gradient fractionation.  Individual fractions from each replicate were pooled into three groups ("monosomes," "polysomes," "RNA granules"), and then split again into 5 technical replicates each for sequencing (R1, R2 forward and reverse paired ends, respectively	WT_polysome	RNA-Seq	TRANSCRIPTOMIC	Hybrid Selection	paired				Illumina HiSeq 2000	genotype;;tm1Frk/tm1Frk (KO)|strain;;129S1		200	CELF4_polysomes	Mus musculus 129S1 CELF4_polysomes	3979243200	19896216	2015-07-22 17:07:41	2501122770	3979243200	19896216	2	19896216	index:0,count:19896216,average:100,stdev:0|index:1,count:19896216,average:100,stdev:0	WT_polysome_8	JAX					2.49	3.55	0.01	2841872430	2824858253	2696196435	2696385578	99.4	100.01	18808189	17757966	174.073	585.533	125	196840	90.72	95.73	20292976	17062682	20292976	17062682	91.3	91.97	20292976	17171885	20292976	16393313	76489627	2.69	1.55	0	4.94	0	0.22	0	0.05	0	0.00	0	5.20	0	18808189	0	200	0	196.84	0	2.19	0	0.02	0	1.64	0	0.02	0	223.14	0	0.68	0	308434	0	19896216	0	983859	0	43742	0	9315	0	0	0	1034970	0	5470	0	0	0	41923	0	6229340	0	35557	0	6312290	0	89.59	0	17824330	0	181344	5356091	29.535529160049	19896216.0	18808189.0	308434.0	983859.0	43742.0	9315.0	0.0	1034970.0	17824330.0	94.5	1.6	4.9	0.2	0.0	0.0	5.2	89.6	100	100	100.00	38	1989621600	25.4	24.7	24.5	25.4	0.0	33.2	14.5	bulk
965055	SRR528737	SRP014599	SRS348125	SRX171238	SRA055349	The Jackson Laboratory		CELF4 wt and knockout transcriptome by polysome fractions	CELF4 wildtype and mutant polysome; 129S1/SvImJ inbred mouse strai.n		Mouse 129S1 (WT) CELF4_RNAgranule		Paired end RNA sequencing of pooled polysome fractions from mouse strain 129S1< / > (WT) and 129S1-Celf4<tm1Frk/tm1Frk> (KO) female adult cerebral cortex   hippocampus combined.  Tissue extracts from 3 biological replicates from each strain were subjected to sucrose gradient fractionation.  Individual fractions from each replicate were pooled into three groups ("monosomes," "polysomes," "RNA granules"), and then split again into 5 technical replicates each for sequencing (R1, R2 forward and reverse paired ends, respectively	WT_RNAgranule	RNA-Seq	TRANSCRIPTOMIC	Hybrid Selection	paired				Illumina HiSeq 2000	genotype;;tm1Frk/tm1Frk (KO)|strain;;129S1		200	CELF4_polysomes	Mus musculus 129S1 CELF4_polysomes	3756832800	18784164	2015-07-22 17:07:41	2350571665	3756832800	18784164	2	18784164	index:0,count:18784164,average:100,stdev:0|index:1,count:18784164,average:100,stdev:0	WT_RNAgranule_1	JAX					3.44	3.57	0.01	2709856589	2701118438	2563523519	2569193065	99.68	100.22	17817957	16733571	176.526	614.412	125	183337	91.12	96.43	19271266	16236378	19271266	16236378	92.21	92.76	19271266	16430670	19271266	15618556	56343639	2.08	1.50	0	5.22	0	0.30	0	0.04	0	0.00	0	4.80	0	17817957	0	200	0	196.93	0	2.19	0	0.02	0	1.66	0	0.02	0	210.66	0	0.66	0	281941	0	18784164	0	980455	0	57089	0	6607	0	0	0	902511	0	4793	0	0	0	45728	0	6472861	0	34917	0	6558299	0	89.64	0	16837502	0	171006	5541450	32.405003333216	18784164.0	17817957.0	281941.0	980455.0	57089.0	6607.0	0.0	902511.0	16837502.0	94.9	1.5	5.2	0.3	0.0	0.0	4.8	89.6	100	100	100.00	38	1878416400	25.1	25.0	24.7	25.1	0.0	33.4	14.8	bulk
965263	SRR528751	SRP014599	SRS348126	SRX171524	SRA055349	The Jackson Laboratory		CELF4 wt and knockout transcriptome by polysome fractions	CELF4 wildtype and mutant polysome; 129S1/SvImJ inbred mouse strai.n		Mouse 129S1 (KO) CELF4_polysome		Paired end RNA sequencing of the CA1 region of the hippocampus from mouse strain 129S1< / > (WT) and 129S1-Celf4<tm1Frk/tm1Frk> (DEL) male adult, dissected into cell body (cb) and neuropil (np) components. 3 biological replicates (A,B,C or A,B,D) from each strain-genotype were carried through to sequencing (R1, R2 forward and reverse paired ends, respectively).	KO_monosome	RNA-Seq	TRANSCRIPTOMIC	Hybrid Selection	paired				Illumina HiSeq 2000	dev_stage;;adult|sex;;male|strain;;129S1|tissue;;hippocampus CA1 region		200	CELF4_hippocampal_CA1_dissection	Mus musculus 129S1 (WT) hippocampus CA1 region	2839090800	14195454	2015-07-22 17:07:41	1746367895	2839090800	14195454	2	14195454	index:0,count:14195454,average:100,stdev:0|index:1,count:14195454,average:100,stdev:0	KO_monosome_8	JAX					5.39	3.4	0.01	1447952207	1421693953	1308873546	1297388264	98.19	99.12	9890968	9453744	166.645	509.908	124	116937	82.39	91.35	11367076	8148842	11367076	8148842	85.24	85.94	11367076	8431399	11367076	7666508	70317014	4.86	1.15	0	6.83	0	0.13	0	0.07	0	0.00	0	30.12	0	9890968	0	200	0	196.29	0	2.44	0	0.03	0	1.84	0	0.03	0	49.66	0	0.77	0	163880	0	14195454	0	970213	0	18503	0	9841	0	0	0	4276142	0	2289	0	0	0	16893	0	2634087	0	21007	0	2674276	0	62.84	0	8920755	0	147904	2277473	15.398319180009	14195454.0	9890968.0	163880.0	970213.0	18503.0	9841.0	0.0	4276142.0	8920755.0	69.7	1.2	6.8	0.1	0.1	0.0	30.1	62.8	100	100	100.00	38	1419545400	25.9	25.4	25.0	23.7	0.0	30.6	11.6	bulk
965271	SRR528752	SRP014599	SRS348126	SRX171523	SRA055349	The Jackson Laboratory		CELF4 wt and knockout transcriptome by polysome fractions	CELF4 wildtype and mutant polysome; 129S1/SvImJ inbred mouse strai.n		Mouse 129S1 (KO) CELF4_polysome		Paired end RNA sequencing of the CA1 region of the hippocampus from mouse strain 129S1< / > (WT) and 129S1-Celf4<tm1Frk/tm1Frk> (DEL) male adult, dissected into cell body (cb) and neuropil (np) components. 3 biological replicates (A,B,C or A,B,D) from each strain-genotype were carried through to sequencing (R1, R2 forward and reverse paired ends, respectively).	KO_polysome	RNA-Seq	TRANSCRIPTOMIC	Hybrid Selection	paired				Illumina HiSeq 2000	dev_stage;;adult|sex;;male|strain;;129S1|tissue;;hippocampus CA1 region		200	CELF4_hippocampal_CA1_dissection	Mus musculus 129S1 (WT) hippocampus CA1 region	3629993000	18149965	2015-07-22 17:07:41	2270815153	3629993000	18149965	2	18149965	index:0,count:18149965,average:100,stdev:0|index:1,count:18149965,average:100,stdev:0	KO_polysome_1	JAX					1.87	3.5	0.01	2589136125	2578183975	2464376313	2468254621	99.58	100.16	17175252	16123228	174.632	636.861	125	176087	91.15	95.88	18484640	15655015	18484640	15655015	91.28	91.97	18484640	15678359	18484640	15015480	66151096	2.55	1.62	0	4.67	0	0.23	0	0.04	0	0.00	0	5.10	0	17175252	0	200	0	196.79	0	2.23	0	0.02	0	1.69	0	0.02	0	231.70	0	0.66	0	294054	0	18149965	0	848325	0	40947	0	7740	0	0	0	926026	0	5537	0	0	0	40964	0	6191170	0	29598	0	6267269	0	89.96	0	16326927	0	172817	5300218	30.669540612324	18149965.0	17175252.0	294054.0	848325.0	40947.0	7740.0	0.0	926026.0	16326927.0	94.6	1.6	4.7	0.2	0.0	0.0	5.1	90.0	100	100	100.00	38	1814996500	25.1	25.0	24.9	25.0	0.0	33.3	14.8	bulk
965279	SRR528753	SRP014599	SRS348126	SRX171523	SRA055349	The Jackson Laboratory		CELF4 wt and knockout transcriptome by polysome fractions	CELF4 wildtype and mutant polysome; 129S1/SvImJ inbred mouse strai.n		Mouse 129S1 (KO) CELF4_polysome		Paired end RNA sequencing of the CA1 region of the hippocampus from mouse strain 129S1< / > (WT) and 129S1-Celf4<tm1Frk/tm1Frk> (DEL) male adult, dissected into cell body (cb) and neuropil (np) components. 3 biological replicates (A,B,C or A,B,D) from each strain-genotype were carried through to sequencing (R1, R2 forward and reverse paired ends, respectively).	KO_polysome	RNA-Seq	TRANSCRIPTOMIC	Hybrid Selection	paired				Illumina HiSeq 2000	dev_stage;;adult|sex;;male|strain;;129S1|tissue;;hippocampus CA1 region		200	CELF4_hippocampal_CA1_dissection	Mus musculus 129S1 (WT) hippocampus CA1 region	3684223800	18421119	2015-07-22 17:07:41	2319160330	3684223800	18421119	2	18421119	index:0,count:18421119,average:100,stdev:0|index:1,count:18421119,average:100,stdev:0	KO_polysome_6	JAX					1.87	3.51	0.01	2622884073	2611874616	2496292667	2500338985	99.58	100.16	17409593	16344567	174.495	632.292	125	178695	91.14	95.88	18740529	15866428	18740529	15866428	91.26	91.95	18740529	15887958	18740529	15215935	67217510	2.56	1.61	0	4.67	0	0.22	0	0.04	0	0.00	0	5.23	0	17409593	0	200	0	196.69	0	2.22	0	0.02	0	1.69	0	0.02	0	193.91	0	0.69	0	295753	0	18421119	0	861002	0	41215	0	7778	0	0	0	962533	0	5330	0	0	0	41192	0	6244095	0	29478	0	6320095	0	89.83	0	16548591	0	173750	5346278	30.769945323741	18421119.0	17409593.0	295753.0	861002.0	41215.0	7778.0	0.0	962533.0	16548591.0	94.5	1.6	4.7	0.2	0.0	0.0	5.2	89.8	100	100	100.00	38	1842111900	25.1	25.0	24.9	25.0	0.0	33.0	14.4	bulk
965287	SRR528754	SRP014599	SRS348126	SRX171523	SRA055349	The Jackson Laboratory		CELF4 wt and knockout transcriptome by polysome fractions	CELF4 wildtype and mutant polysome; 129S1/SvImJ inbred mouse strai.n		Mouse 129S1 (KO) CELF4_polysome		Paired end RNA sequencing of the CA1 region of the hippocampus from mouse strain 129S1< / > (WT) and 129S1-Celf4<tm1Frk/tm1Frk> (DEL) male adult, dissected into cell body (cb) and neuropil (np) components. 3 biological replicates (A,B,C or A,B,D) from each strain-genotype were carried through to sequencing (R1, R2 forward and reverse paired ends, respectively).	KO_polysome	RNA-Seq	TRANSCRIPTOMIC	Hybrid Selection	paired				Illumina HiSeq 2000	dev_stage;;adult|sex;;male|strain;;129S1|tissue;;hippocampus CA1 region		200	CELF4_hippocampal_CA1_dissection	Mus musculus 129S1 (WT) hippocampus CA1 region	3646340000	18231700	2015-07-22 17:07:41	2296019439	3646340000	18231700	2	18231700	index:0,count:18231700,average:100,stdev:0|index:1,count:18231700,average:100,stdev:0	KO_polysome_8	JAX					1.87	3.51	0.01	2596779440	2585914070	2471505548	2475523023	99.58	100.16	17229698	16174789	174.566	635.989	125	176142	91.14	95.88	18543689	15702872	18543689	15702872	91.27	91.95	18543689	15725385	18543689	15059783	66616472	2.57	1.60	0	4.67	0	0.22	0	0.04	0	0.00	0	5.23	0	17229698	0	200	0	196.69	0	2.22	0	0.02	0	1.69	0	0.02	0	236.09	0	0.69	0	292563	0	18231700	0	851438	0	40780	0	7893	0	0	0	953329	0	5509	0	0	0	40599	0	6182351	0	29501	0	6257960	0	89.83	0	16378260	0	173242	5296713	30.574069798317	18231700.0	17229698.0	292563.0	851438.0	40780.0	7893.0	0.0	953329.0	16378260.0	94.5	1.6	4.7	0.2	0.0	0.0	5.2	89.8	100	100	100.00	38	1823170000	25.1	25.0	24.9	25.0	0.0	33.1	14.5	bulk
965294	SRR528755	SRP014599	SRS348126	SRX171523	SRA055349	The Jackson Laboratory		CELF4 wt and knockout transcriptome by polysome fractions	CELF4 wildtype and mutant polysome; 129S1/SvImJ inbred mouse strai.n		Mouse 129S1 (KO) CELF4_polysome		Paired end RNA sequencing of the CA1 region of the hippocampus from mouse strain 129S1< / > (WT) and 129S1-Celf4<tm1Frk/tm1Frk> (DEL) male adult, dissected into cell body (cb) and neuropil (np) components. 3 biological replicates (A,B,C or A,B,D) from each strain-genotype were carried through to sequencing (R1, R2 forward and reverse paired ends, respectively).	KO_polysome	RNA-Seq	TRANSCRIPTOMIC	Hybrid Selection	paired				Illumina HiSeq 2000	dev_stage;;adult|sex;;male|strain;;129S1|tissue;;hippocampus CA1 region		200	CELF4_hippocampal_CA1_dissection	Mus musculus 129S1 (WT) hippocampus CA1 region	3710080800	18550404	2015-07-22 17:07:41	2330597136	3710080800	18550404	2	18550404	index:0,count:18550404,average:100,stdev:0|index:1,count:18550404,average:100,stdev:0	KO_polysome_2	JAX					1.87	3.51	0.01	2644597589	2633639718	2517063611	2521180774	99.59	100.16	17544776	16469961	174.577	634.197	125	180217	91.15	95.89	18881835	15991742	18881835	15991742	91.28	91.96	18881835	16014284	18881835	15336476	67579766	2.56	1.61	0	4.67	0	0.22	0	0.04	0	0.00	0	5.16	0	17544776	0	200	0	196.76	0	2.23	0	0.02	0	1.69	0	0.02	0	235.98	0	0.67	0	298185	0	18550404	0	867175	0	41313	0	7948	0	0	0	956367	0	5469	0	0	0	41397	0	6313715	0	30045	0	6390626	0	89.90	0	16677601	0	174120	5404957	31.041563289685	18550404.0	17544776.0	298185.0	867175.0	41313.0	7948.0	0.0	956367.0	16677601.0	94.6	1.6	4.7	0.2	0.0	0.0	5.2	89.9	100	100	100.00	38	1855040400	25.1	25.0	24.9	25.0	0.0	33.3	14.7	bulk
965303	SRR528756	SRP014599	SRS348126	SRX171523	SRA055349	The Jackson Laboratory		CELF4 wt and knockout transcriptome by polysome fractions	CELF4 wildtype and mutant polysome; 129S1/SvImJ inbred mouse strai.n		Mouse 129S1 (KO) CELF4_polysome		Paired end RNA sequencing of the CA1 region of the hippocampus from mouse strain 129S1< / > (WT) and 129S1-Celf4<tm1Frk/tm1Frk> (DEL) male adult, dissected into cell body (cb) and neuropil (np) components. 3 biological replicates (A,B,C or A,B,D) from each strain-genotype were carried through to sequencing (R1, R2 forward and reverse paired ends, respectively).	KO_polysome	RNA-Seq	TRANSCRIPTOMIC	Hybrid Selection	paired				Illumina HiSeq 2000	dev_stage;;adult|sex;;male|strain;;129S1|tissue;;hippocampus CA1 region		200	CELF4_hippocampal_CA1_dissection	Mus musculus 129S1 (WT) hippocampus CA1 region	3593846600	17969233	2015-07-22 17:07:41	2269452487	3593846600	17969233	2	17969233	index:0,count:17969233,average:100,stdev:0|index:1,count:17969233,average:100,stdev:0	KO_polysome_7	JAX					1.87	3.52	0.01	2557415782	2546605615	2434031474	2437859802	99.58	100.16	16971492	15932408	174.544	633.991	125	173759	91.14	95.88	18267094	15468406	18267094	15468406	91.28	91.97	18267094	15491455	18267094	14836422	65551445	2.56	1.61	0	4.67	0	0.22	0	0.04	0	0.00	0	5.29	0	16971492	0	200	0	196.65	0	2.22	0	0.02	0	1.69	0	0.02	0	199.04	0	0.71	0	288556	0	17969233	0	838859	0	39946	0	7575	0	0	0	950220	0	5399	0	0	0	40237	0	6077052	0	28942	0	6151630	0	89.78	0	16132633	0	172537	5211014	30.202298637394	17969233.0	16971492.0	288556.0	838859.0	39946.0	7575.0	0.0	950220.0	16132633.0	94.4	1.6	4.7	0.2	0.0	0.0	5.3	89.8	100	100	100.00	38	1796923300	25.1	25.0	24.9	25.0	0.1	32.9	14.3	bulk
1844873	SRR540268	SRP014858	SRS356268	SRX176917	SRA055284	JAX		CELF4 wt and knockout transcriptome by localization to hippocampal CA1 cell body or neuropil	CELF wildtype and mutant transcriptome by subcellular localization; 129S1/SvImJ.C57BL/6J-Celf4 congenic mouse strain.		wt mouse hippocampal cell body transcriptome		CELF4 wt and knockout transcriptome by localization to hippocampal CA1 cell body or neuropil	wt 129S1 cell body A	RNA-Seq	TRANSCRIPTOMIC	RANDOM	paired				Illumina HiSeq 2000	cellular region;;body|strain;;129S1/SvImJ|tissue;;hippocampal CA1		200	129S1_hippocampus_cb	Mus musculus 129S1 hippocampus cell body	6677611000	33388055	2012-08-15 10:32:11	5004929631	6677611000	33388055	2	33388055	index:0,count:33388055,average:100,stdev:0|index:1,count:33388055,average:100,stdev:0	wt_A_cb_GES11_4836_ATCACG_L007	JAX					17.6	2.46	0.05	4934304507	4898591079	4763021987	4747777791	99.28	99.68	30417683	29434966	178.419	572.781	150	290459	66.58	69.11	32195466	20253015	32195466	20253015	64.46	64.72	32195466	19607442	32195466	18966395	1383859312	28.05	4.52	0	3.33	0	0.22	0	0.18	0	0.00	0	8.50	0	30417683	0	200	0	195.49	0	2.40	0	0.02	0	2.46	0	0.02	0	207.95	0	0.77	0	1510615	0	33388055	0	1111861	0	72434	0	59630	0	0	0	2838308	0	5972	0	0	0	42094	0	5661028	0	37127	0	5746221	0	87.77	0	29305822	0	181522	5264491	29.001944667864	33388055.0	30417683.0	1510615.0	1111861.0	72434.0	59630.0	0.0	2838308.0	29305822.0	91.1	4.5	3.3	0.2	0.2	0.0	8.5	87.8	100	100	100.00	38	3338805500	26.9	22.6	22.9	26.7	0.8	33.0	16.1	bulk
1845000	SRR540270	SRP014858	SRS356268	SRX176917	SRA055284	JAX		CELF4 wt and knockout transcriptome by localization to hippocampal CA1 cell body or neuropil	CELF wildtype and mutant transcriptome by subcellular localization; 129S1/SvImJ.C57BL/6J-Celf4 congenic mouse strain.		wt mouse hippocampal cell body transcriptome		CELF4 wt and knockout transcriptome by localization to hippocampal CA1 cell body or neuropil	wt 129S1 cell body A	RNA-Seq	TRANSCRIPTOMIC	RANDOM	paired				Illumina HiSeq 2000	cellular region;;body|strain;;129S1/SvImJ|tissue;;hippocampal CA1		200	129S1_hippocampus_cb	Mus musculus 129S1 hippocampus cell body	5856469400	29282347	2012-08-15 10:53:10	4388343255	5856469400	29282347	2	29282347	index:0,count:29282347,average:100,stdev:0|index:1,count:29282347,average:100,stdev:0	wt_B_cb_GES11_4838_TTAGGC_L007	JAX					15.76	2.34	0.04	4237274891	4201658669	4066890784	4051025271	99.16	99.61	25722788	24747223	185.230	634.000	158	226769	68.34	71.39	27416298	17579259	27416298	17579259	65.51	66.06	27416298	16851092	27416298	16268289	1085243013	25.61	6.30	0	3.75	0	0.19	0	0.15	0	0.00	0	11.81	0	25722788	0	200	0	194.03	0	2.75	0	0.02	0	2.17	0	0.02	0	306.44	0	0.84	0	1845553	0	29282347	0	1096946	0	55599	0	44604	0	0	0	3459356	0	5378	0	0	0	37067	0	5137439	0	34212	0	5214096	0	84.10	0	24625842	0	168390	4853459	28.822727002791	29282347.0	25722788.0	1845553.0	1096946.0	55599.0	44604.0	0.0	3459356.0	24625842.0	87.8	6.3	3.7	0.2	0.2	0.0	11.8	84.1	100	100	100.00	38	2928234700	25.9	23.6	23.9	25.8	0.8	32.6	15.5	bulk
1845016	SRR540271	SRP014858	SRS356269	SRX176918	SRA055284	JAX		CELF4 wt and knockout transcriptome by localization to hippocampal CA1 cell body or neuropil	CELF wildtype and mutant transcriptome by subcellular localization; 129S1/SvImJ.C57BL/6J-Celf4 congenic mouse strain.		wt mouse hippocampal neuropil transcriptome		CELF4 wt and knockout transcriptome by localization to hippocampal CA1 cell body or neuropil	wt 129S1 neuropil A	RNA-Seq	TRANSCRIPTOMIC	RANDOM	paired				Illumina HiSeq 2000	cellular region;;neuropil|strain;;129S1/SvImJ|tissue;;hippocampal CA1		200	129S1_hippocampus_np	Mus musculus 129S1 hippocampus neuropil	5838180800	29190904	2012-08-15 11:00:23	4356954667	5838180800	29190904	2	29190904	index:0,count:29190904,average:100,stdev:0|index:1,count:29190904,average:100,stdev:0	wt_B_np_GES11_4839_TTAGGC_L008	JAX					29.81	1.95	0.03	4411162261	4381384775	4251540935	4236958536	99.32	99.66	26493126	25629564	187.591	567.618	155	229235	73.77	76.71	27976092	19544894	27976092	19544894	72.28	72.66	27976092	19149340	27976092	18513794	932185644	21.13	5.60	0	3.47	0	0.17	0	0.12	0	0.00	0	8.96	0	26493126	0	200	0	195.33	0	2.49	0	0.02	0	2.41	0	0.02	0	275.10	0	0.76	0	1635542	0	29190904	0	1012808	0	48665	0	34974	0	0	0	2614139	0	4348	0	0	0	31261	0	4367524	0	27435	0	4430568	0	87.29	0	25480318	0	161991	4132021	25.507719564667	29190904.0	26493126.0	1635542.0	1012808.0	48665.0	34974.0	0.0	2614139.0	25480318.0	90.8	5.6	3.5	0.2	0.1	0.0	9.0	87.3	100	100	100.00	38	2919090400	27.4	22.6	22.8	27.2	0.0	33.6	17.3	bulk
1845048	SRR540273	SRP014858	SRS356269	SRX176918	SRA055284	JAX		CELF4 wt and knockout transcriptome by localization to hippocampal CA1 cell body or neuropil	CELF wildtype and mutant transcriptome by subcellular localization; 129S1/SvImJ.C57BL/6J-Celf4 congenic mouse strain.		wt mouse hippocampal neuropil transcriptome		CELF4 wt and knockout transcriptome by localization to hippocampal CA1 cell body or neuropil	wt 129S1 neuropil A	RNA-Seq	TRANSCRIPTOMIC	RANDOM	paired				Illumina HiSeq 2000	cellular region;;neuropil|strain;;129S1/SvImJ|tissue;;hippocampal CA1		200	129S1_hippocampus_np	Mus musculus 129S1 hippocampus neuropil	6784252600	33921263	2012-08-15 11:18:18	5052318495	6784252600	33921263	2	33921263	index:0,count:33921263,average:100,stdev:0|index:1,count:33921263,average:100,stdev:0	wt_C_np_GES11_4841_ACTTGA_L008	JAX					25.52	2.12	0.04	5134113451	5078707048	4956481234	4920250159	98.92	99.27	31125844	30089928	184.205	553.230	154	278332	72.25	75.0	32857385	22489868	32857385	22489868	70.99	71.35	32857385	22096164	32857385	21397477	1172233285	22.83	4.62	0	3.35	0	0.18	0	0.14	0	0.00	0	7.92	0	31125844	0	200	0	195.85	0	2.37	0	0.02	0	2.56	0	0.02	0	288.01	0	0.74	0	1566462	0	33921263	0	1137603	0	60617	0	46768	0	0	0	2688034	0	6148	0	0	0	41091	0	5571886	0	32627	0	5651752	0	88.41	0	29988241	0	173705	5223124	30.068932961055	33921263.0	31125844.0	1566462.0	1137603.0	60617.0	46768.0	0.0	2688034.0	29988241.0	91.8	4.6	3.4	0.2	0.1	0.0	7.9	88.4	100	100	100.00	38	3392126300	27.3	22.7	22.9	27.1	0.0	33.7	17.4	bulk
1845064	SRR540274	SRP014858	SRS356275	SRX176920	SRA055284	JAX		CELF4 wt and knockout transcriptome by localization to hippocampal CA1 cell body or neuropil	CELF wildtype and mutant transcriptome by subcellular localization; 129S1/SvImJ.C57BL/6J-Celf4 congenic mouse strain.		Celf4 knock out mouse hippocampal cell body transcriptome		Paired end RNA sequencing of the CA1 region of the hippocampus from mouse strain 129S1( / ) (WT) and 129S1-Celf4 (tm1Frk/tm1Frk) (DEL) male adult, dissected into cell body (cb) and neuropil (np) components. 3 biological replicates (A,B,C or A,B,D) from each strain-genotype were carried through to sequencing (R1, R2 forward and reverse paired ends, respectively)	129S1 Celf4 cell body	RNA-Seq	TRANSCRIPTOMIC	RANDOM	paired				Illumina HiSeq 2000	cellular region;;cell body|strain;;129S1-Celf4 tm1Frk/tm1Frk (DEL)|tissue;;hippocampal CA1		200	129S1-Celf4_hippocampus_cb	Mus musculus 129S1-Celf4(tm1Frk/tm1Frk) (DEL) cell body	6337074600	31685373	2012-08-15 11:28:11	4748772609	6337074600	31685373	2	31685373	index:0,count:31685373,average:100,stdev:0|index:1,count:31685373,average:100,stdev:0	del_A_cb_GES11_4842_GATCAG_L007	JAX					18.71	2.54	0.05	4733364194	4692111254	4587977139	4564103943	99.13	99.48	28849395	27781805	183.669	625.167	151	259859	70.76	73.11	30311930	20415242	30311930	20415242	69.04	69.21	30311930	19918978	30311930	19326055	1147365994	24.24	4.69	0	2.92	0	0.21	0	0.16	0	0.00	0	8.57	0	28849395	0	200	0	195.52	0	2.23	0	0.02	0	2.82	0	0.02	0	162.95	0	0.77	0	1486886	0	31685373	0	925945	0	67302	0	51976	0	0	0	2716700	0	5130	0	0	0	41477	0	5816221	0	37747	0	5900575	0	88.13	0	27923450	0	176052	5441753	30.909918660396	31685373.0	28849395.0	1486886.0	925945.0	67302.0	51976.0	0.0	2716700.0	27923450.0	91.0	4.7	2.9	0.2	0.2	0.0	8.6	88.1	100	100	100.00	38	3168537300	26.8	22.6	23.0	26.7	0.8	33.0	16.1	bulk
1845083	SRR540275	SRP014858	SRS356275	SRX176920	SRA055284	JAX		CELF4 wt and knockout transcriptome by localization to hippocampal CA1 cell body or neuropil	CELF wildtype and mutant transcriptome by subcellular localization; 129S1/SvImJ.C57BL/6J-Celf4 congenic mouse strain.		Celf4 knock out mouse hippocampal cell body transcriptome		Paired end RNA sequencing of the CA1 region of the hippocampus from mouse strain 129S1( / ) (WT) and 129S1-Celf4 (tm1Frk/tm1Frk) (DEL) male adult, dissected into cell body (cb) and neuropil (np) components. 3 biological replicates (A,B,C or A,B,D) from each strain-genotype were carried through to sequencing (R1, R2 forward and reverse paired ends, respectively)	129S1 Celf4 cell body	RNA-Seq	TRANSCRIPTOMIC	RANDOM	paired				Illumina HiSeq 2000	cellular region;;cell body|strain;;129S1-Celf4 tm1Frk/tm1Frk (DEL)|tissue;;hippocampal CA1		200	129S1-Celf4_hippocampus_cb	Mus musculus 129S1-Celf4(tm1Frk/tm1Frk) (DEL) cell body	5851692000	29258460	2012-08-15 11:34:10	4381121091	5851692000	29258460	2	29258460	index:0,count:29258460,average:100,stdev:0|index:1,count:29258460,average:100,stdev:0	del_B_cb_GES11_4844_TAGCTT_L007	JAX					19.68	2.48	0.04	4354203039	4334549857	4214063191	4210314795	99.55	99.91	26318418	25322791	186.258	638.920	154	230008	71.58	74.07	27707738	18838382	27707738	18838382	69.67	69.87	27707738	18337051	27707738	17769444	1019923858	23.42	5.21	0	3.03	0	0.22	0	0.15	0	0.00	0	9.68	0	26318418	0	200	0	195.15	0	2.27	0	0.02	0	2.69	0	0.02	0	208.58	0	0.78	0	1523043	0	29258460	0	885513	0	64864	0	44260	0	0	0	2830918	0	4745	0	0	0	37786	0	5274359	0	36800	0	5353690	0	86.92	0	25432905	0	169647	4979063	29.349549358374	29258460.0	26318418.0	1523043.0	885513.0	64864.0	44260.0	0.0	2830918.0	25432905.0	90.0	5.2	3.0	0.2	0.2	0.0	9.7	86.9	100	100	100.00	38	2925846000	26.8	22.7	23.1	26.7	0.8	33.0	16.0	bulk
1845099	SRR540276	SRP014858	SRS356274	SRX176919	SRA055284	JAX		CELF4 wt and knockout transcriptome by localization to hippocampal CA1 cell body or neuropil	CELF wildtype and mutant transcriptome by subcellular localization; 129S1/SvImJ.C57BL/6J-Celf4 congenic mouse strain.		Celf4 knock out mouse hippocampal neuropil transcriptome		Paired end RNA sequencing of the CA1 region of the hippocampus from mouse strain 129S1( / ) (WT) and 129S1-Celf4 (tm1Frk/tm1Frk) (DEL) male adult, dissected into cell body (cb) and neuropil (np) components. 3 biological replicates (A,B,C or A,B,D) from each strain-genotype were carried through to sequencing (R1, R2 forward and reverse paired ends, respectively)	129S1 Celf4 neuropil	RNA-Seq	TRANSCRIPTOMIC	RANDOM	paired				Illumina HiSeq 2000	cellular region;;neuropil|strain;;129S1-Celf4 tm1Frk/tm1Frk (DEL)|tissue;;hippocampal CA1		200	129S1-Celf4_hippocampus_np	Mus musculus 129S1-Celf4(tm1Frk/tm1Frk) (DEL) hippocampus neuropil	5171659800	25858299	2012-08-15 11:38:13	3851413688	5171659800	25858299	2	25858299	index:0,count:25858299,average:100,stdev:0|index:1,count:25858299,average:100,stdev:0	del_B_np_GES11_4845_GATCAG_L008	JAX					22.82	2.3	0.04	3879677639	3849806274	3746008108	3730641055	99.23	99.59	23379108	22540282	187.331	609.961	153	202516	70.81	73.48	24691658	16555595	24691658	16555595	69.08	69.4	24691658	16150345	24691658	15636770	935672909	24.12	5.92	0	3.28	0	0.20	0	0.15	0	0.00	0	9.24	0	23379108	0	200	0	195.20	0	2.44	0	0.02	0	2.42	0	0.02	0	181.11	0	0.76	0	1532008	0	25858299	0	848719	0	51559	0	38737	0	0	0	2388895	0	4517	0	0	0	31441	0	4270849	0	29211	0	4336018	0	87.13	0	22530389	0	161844	4023795	24.862182101283	25858299.0	23379108.0	1532008.0	848719.0	51559.0	38737.0	0.0	2388895.0	22530389.0	90.4	5.9	3.3	0.2	0.1	0.0	9.2	87.1	100	100	100.00	38	2585829900	27.2	22.8	23.0	27.0	0.0	33.6	17.3	bulk
1845117	SRR540277	SRP014858	SRS356274	SRX176919	SRA055284	JAX		CELF4 wt and knockout transcriptome by localization to hippocampal CA1 cell body or neuropil	CELF wildtype and mutant transcriptome by subcellular localization; 129S1/SvImJ.C57BL/6J-Celf4 congenic mouse strain.		Celf4 knock out mouse hippocampal neuropil transcriptome		Paired end RNA sequencing of the CA1 region of the hippocampus from mouse strain 129S1( / ) (WT) and 129S1-Celf4 (tm1Frk/tm1Frk) (DEL) male adult, dissected into cell body (cb) and neuropil (np) components. 3 biological replicates (A,B,C or A,B,D) from each strain-genotype were carried through to sequencing (R1, R2 forward and reverse paired ends, respectively)	129S1 Celf4 neuropil	RNA-Seq	TRANSCRIPTOMIC	RANDOM	paired				Illumina HiSeq 2000	cellular region;;neuropil|strain;;129S1-Celf4 tm1Frk/tm1Frk (DEL)|tissue;;hippocampal CA1		200	129S1-Celf4_hippocampus_np	Mus musculus 129S1-Celf4(tm1Frk/tm1Frk) (DEL) hippocampus neuropil	6658322800	33291614	2012-08-15 11:48:14	4955536832	6658322800	33291614	2	33291614	index:0,count:33291614,average:100,stdev:0|index:1,count:33291614,average:100,stdev:0	del_C_np_GES11_4847_TAGCTT_L008	JAX					21.36	2.32	0.04	4996522562	4957371982	4829988551	4809381099	99.22	99.57	30234183	29199050	184.316	602.775	154	269899	69.87	72.41	31878053	21124906	31878053	21124906	67.98	68.21	31878053	20551879	31878053	19899027	1244404239	24.91	5.54	0	3.18	0	0.21	0	0.17	0	0.00	0	8.80	0	30234183	0	200	0	195.43	0	2.37	0	0.02	0	2.53	0	0.02	0	286.72	0	0.75	0	1845003	0	33291614	0	1059826	0	70989	0	58108	0	0	0	2928334	0	5724	0	0	0	41468	0	5576688	0	36425	0	5660305	0	87.63	0	29174357	0	170154	5235853	30.771260152568	33291614.0	30234183.0	1845003.0	1059826.0	70989.0	58108.0	0.0	2928334.0	29174357.0	90.8	5.5	3.2	0.2	0.2	0.0	8.8	87.6	100	100	100.00	38	3329161400	27.2	22.7	23.0	27.1	0.0	33.7	17.3	bulk
1845133	SRR540278	SRP014858	SRS356275	SRX176920	SRA055284	JAX		CELF4 wt and knockout transcriptome by localization to hippocampal CA1 cell body or neuropil	CELF wildtype and mutant transcriptome by subcellular localization; 129S1/SvImJ.C57BL/6J-Celf4 congenic mouse strain.		Celf4 knock out mouse hippocampal cell body transcriptome		Paired end RNA sequencing of the CA1 region of the hippocampus from mouse strain 129S1( / ) (WT) and 129S1-Celf4 (tm1Frk/tm1Frk) (DEL) male adult, dissected into cell body (cb) and neuropil (np) components. 3 biological replicates (A,B,C or A,B,D) from each strain-genotype were carried through to sequencing (R1, R2 forward and reverse paired ends, respectively)	129S1 Celf4 cell body	RNA-Seq	TRANSCRIPTOMIC	RANDOM	paired				Illumina HiSeq 2000	cellular region;;cell body|strain;;129S1-Celf4 tm1Frk/tm1Frk (DEL)|tissue;;hippocampal CA1		200	129S1-Celf4_hippocampus_cb	Mus musculus 129S1-Celf4(tm1Frk/tm1Frk) (DEL) cell body	5974831000	29874155	2012-08-15 11:55:14	4473698052	5974831000	29874155	2	29874155	index:0,count:29874155,average:100,stdev:0|index:1,count:29874155,average:100,stdev:0	del_D_cb_GES11_4848_GGCTAC_L007	JAX					29.4	2.27	0.03	4455619842	4470351699	4274601293	4304173435	100.33	100.69	27107607	26156195	182.180	557.875	154	252291	80.7	84.29	28837179	21874757	28837179	21874757	78.87	79.5	28837179	21379430	28837179	20630598	622137372	13.96	4.46	0	3.87	0	0.23	0	0.09	0	0.00	0	8.94	0	27107607	0	200	0	195.43	0	2.44	0	0.02	0	2.55	0	0.02	0	259.78	0	0.77	0	1331761	0	29874155	0	1156974	0	67602	0	26905	0	0	0	2672041	0	6000	0	0	0	38861	0	5389510	0	29230	0	5463601	0	86.87	0	25950633	0	170851	5089934	29.791654716683	29874155.0	27107607.0	1331761.0	1156974.0	67602.0	26905.0	0.0	2672041.0	25950633.0	90.7	4.5	3.9	0.2	0.1	0.0	8.9	86.9	100	100	100.00	38	2987415500	26.8	22.7	23.0	26.7	0.8	32.9	15.8	bulk
1845148	SRR540279	SRP014858	SRS356274	SRX176919	SRA055284	JAX		CELF4 wt and knockout transcriptome by localization to hippocampal CA1 cell body or neuropil	CELF wildtype and mutant transcriptome by subcellular localization; 129S1/SvImJ.C57BL/6J-Celf4 congenic mouse strain.		Celf4 knock out mouse hippocampal neuropil transcriptome		Paired end RNA sequencing of the CA1 region of the hippocampus from mouse strain 129S1( / ) (WT) and 129S1-Celf4 (tm1Frk/tm1Frk) (DEL) male adult, dissected into cell body (cb) and neuropil (np) components. 3 biological replicates (A,B,C or A,B,D) from each strain-genotype were carried through to sequencing (R1, R2 forward and reverse paired ends, respectively)	129S1 Celf4 neuropil	RNA-Seq	TRANSCRIPTOMIC	RANDOM	paired				Illumina HiSeq 2000	cellular region;;neuropil|strain;;129S1-Celf4 tm1Frk/tm1Frk (DEL)|tissue;;hippocampal CA1		200	129S1-Celf4_hippocampus_np	Mus musculus 129S1-Celf4(tm1Frk/tm1Frk) (DEL) hippocampus neuropil	5359184800	26795924	2012-08-15 12:03:01	3996078172	5359184800	26795924	2	26795924	index:0,count:26795924,average:100,stdev:0|index:1,count:26795924,average:100,stdev:0	del_D_np_GES11_4849_GGCTAC_L008	JAX					29.63	2.05	0.03	4038151270	4018058463	3890217925	3883199610	99.5	99.82	24459923	23639516	184.646	560.399	153	219712	76.81	79.88	25859807	18787172	25859807	18787172	75.59	75.96	25859807	18490450	25859807	17864776	730921116	18.10	5.50	0	3.51	0	0.21	0	0.12	0	0.00	0	8.39	0	24459923	0	200	0	195.47	0	2.35	0	0.02	0	2.68	0	0.02	0	259.32	0	0.74	0	1473320	0	26795924	0	941600	0	56032	0	32994	0	0	0	2246975	0	4547	0	0	0	32758	0	4438314	0	27512	0	4503131	0	87.77	0	23518323	0	165519	4182654	25.269932756964	26795924.0	24459923.0	1473320.0	941600.0	56032.0	32994.0	0.0	2246975.0	23518323.0	91.3	5.5	3.5	0.2	0.1	0.0	8.4	87.8	100	100	100.00	38	2679592400	27.3	22.6	22.9	27.2	0.0	33.6	17.3	bulk
922447	SRR540269	SRP014858	SRS356269	SRX176918	SRA055284	JAX		CELF4 wt and knockout transcriptome by localization to hippocampal CA1 cell body or neuropil	CELF wildtype and mutant transcriptome by subcellular localization; 129S1/SvImJ.C57BL/6J-Celf4 congenic mouse strain.		wt mouse hippocampal neuropil transcriptome		CELF4 wt and knockout transcriptome by localization to hippocampal CA1 cell body or neuropil	wt 129S1 neuropil A	RNA-Seq	TRANSCRIPTOMIC	RANDOM	paired				Illumina HiSeq 2000	cellular region;;neuropil|strain;;129S1/SvImJ|tissue;;hippocampal CA1		200	129S1_hippocampus_np	Mus musculus 129S1 hippocampus neuropil	7351510400	36757552	2012-08-15 10:45:11	5480225485	7351510400	36757552	2	36757552	index:0,count:36757552,average:100,stdev:0|index:1,count:36757552,average:100,stdev:0	wt_A_np_GES11_4837_ATCACG_L008	JAX					20.83	2.29	0.05	5464852520	5409418132	5279531357	5245204941	98.99	99.35	33738402	32663389	178.332	563.706	147	317083	68.11	70.64	35633516	22980793	35633516	22980793	66.53	66.76	35633516	22444700	35633516	21716272	1461885266	26.75	4.98	0	3.29	0	0.21	0	0.17	0	0.00	0	7.84	0	33738402	0	200	0	195.67	0	2.34	0	0.02	0	2.58	0	0.02	0	263.08	0	0.74	0	1830573	0	36757552	0	1208162	0	75435	0	63195	0	0	0	2880520	0	6571	0	0	0	46240	0	6118722	0	39629	0	6211162	0	88.50	0	32530240	0	176680	5650579	31.981995698438	36757552.0	33738402.0	1830573.0	1208162.0	75435.0	63195.0	0.0	2880520.0	32530240.0	91.8	5.0	3.3	0.2	0.2	0.0	7.8	88.5	100	100	100.00	38	3675755200	27.3	22.7	22.9	27.1	0.0	33.7	17.5	bulk
922518	SRR540272	SRP014858	SRS356268	SRX176917	SRA055284	JAX		CELF4 wt and knockout transcriptome by localization to hippocampal CA1 cell body or neuropil	CELF wildtype and mutant transcriptome by subcellular localization; 129S1/SvImJ.C57BL/6J-Celf4 congenic mouse strain.		wt mouse hippocampal cell body transcriptome		CELF4 wt and knockout transcriptome by localization to hippocampal CA1 cell body or neuropil	wt 129S1 cell body A	RNA-Seq	TRANSCRIPTOMIC	RANDOM	paired				Illumina HiSeq 2000	cellular region;;body|strain;;129S1/SvImJ|tissue;;hippocampal CA1		200	129S1_hippocampus_cb	Mus musculus 129S1 hippocampus cell body	6060090400	30300452	2012-08-15 11:13:12	4534213094	6060090400	30300452	2	30300452	index:0,count:30300452,average:100,stdev:0|index:1,count:30300452,average:100,stdev:0	wt_C_cb_GES11_4840_ACTTGA_L007	JAX					15.48	2.39	0.04	4509798129	4459178875	4339842049	4310524390	98.88	99.32	27070194	26001306	188.431	653.455	160	233623	68.29	71.13	28767582	18485232	28767582	18485232	65.89	66.42	28767582	17835706	28767582	17260404	1184123595	26.26	4.74	0	3.57	0	0.20	0	0.17	0	0.00	0	10.28	0	27070194	0	200	0	195.10	0	2.55	0	0.02	0	2.29	0	0.02	0	269.34	0	0.82	0	1437431	0	30300452	0	1083080	0	61446	0	52438	0	0	0	3116374	0	5280	0	0	0	40004	0	5391516	0	34360	0	5471160	0	85.76	0	25987114	0	171902	5110889	29.731410920175	30300452.0	27070194.0	1437431.0	1083080.0	61446.0	52438.0	0.0	3116374.0	25987114.0	89.3	4.7	3.6	0.2	0.2	0.0	10.3	85.8	100	100	100.00	38	3030045200	26.2	23.3	23.6	26.1	0.8	32.8	15.7	bulk
3582135	SRR579545	SRP015997	SRS366858	SRX191149	SRA059267	GEO		The evolutionary landscape of alternative splicing in vertebrate species	How species with similar repertoires of protein coding genes differ so dramatically at the phenotypic level is poorly understood. From comparing the transcriptomes of multiple organs from vertebrate species spanning ~350 million years of evolution, we observe significant differences in alternative splicing complexity between the main vertebrate lineages, with the highest complexity in the primate lineage. Moreover, within as little as six million years, the splicing profiles of physiologically-equivalent organs have diverged to the extent that they are more strongly related to the identity of a species than they are to organ type. Most vertebrate species-specific splicing patterns are governed by the highly variable use of a largely conserved cis-regulatory code. However, a smaller number of pronounced species-dependent splicing changes are predicted to remodel interactions involving factors acting at multiple steps in gene regulation. These events are expected to further contribute to the dramatic diversification of alternative splicing as well as to other gene regulatory changes that contribute to phenotypic differences among vertebrate species. Overall design: mRNA profiles of several organs (brain, liver, kidney, heart, skeletal muscle) in multiple vertebrate species (mouse, chicken, lizard, frog, pufferfish) generated by deep sequencing using Illumina HiSeq		GSM1015150: Mouse brain rep1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired				Illumina HiSeq 2000	age;;adult|molecule subtype;;poly-A enriched RNA|sex;;mixed|source_name;;Mouse_brain_pooled|strain;;C57BL/6|tissue;;brain	GEO Accession;;GSM1015150		GSM1015150	Mouse brain rep1	11571398208	80356932	2012-12-24 12:04:54	7398264144	11571398208	80356932	2	80356932	index:0,count:80356932,average:72,stdev:0|index:1,count:80356932,average:72,stdev:0	GSM1015150_r1	GEO			in_mesa	23258890	2.5	2.52	0.05	7723626225	8024131739	7318247139	7671028639	103.89	104.82	67672240	65436959	130.607	422.520	98	729732	86.17	91.17	73468210	58311450	73468210	58311450	80.47	81.69	73468210	54452873	73468210	52244307	486021092	6.29	3.51	0	4.62	0	0.29	0	0.07	0	0.00	0	15.43	0	67672240	0	144	0	140.35	0	3.37	0	0.02	0	1.44	0	0.01	0	298.54	0	0.89	0	2821314	0	80356932	0	3716191	0	230090	0	57547	0	0	0	12397055	0	9155	0	0	0	97713	0	14273694	0	102439	0	14483001	0	79.59	0	63956049	0	146960	12978576	88.313663581927	80356932.0	67672240.0	2821314.0	3716191.0	230090.0	57547.0	0.0	12397055.0	63956049.0	84.2	3.5	4.6	0.3	0.1	0.0	15.4	79.6	72	72	72.00	39	5785699104	23.3	26.6	26.6	23.4	0.0	32.4	12.7	bulk
3582168	SRR579546	SRP015997	SRS366859	SRX191150	SRA059267	GEO		The evolutionary landscape of alternative splicing in vertebrate species	How species with similar repertoires of protein coding genes differ so dramatically at the phenotypic level is poorly understood. From comparing the transcriptomes of multiple organs from vertebrate species spanning ~350 million years of evolution, we observe significant differences in alternative splicing complexity between the main vertebrate lineages, with the highest complexity in the primate lineage. Moreover, within as little as six million years, the splicing profiles of physiologically-equivalent organs have diverged to the extent that they are more strongly related to the identity of a species than they are to organ type. Most vertebrate species-specific splicing patterns are governed by the highly variable use of a largely conserved cis-regulatory code. However, a smaller number of pronounced species-dependent splicing changes are predicted to remodel interactions involving factors acting at multiple steps in gene regulation. These events are expected to further contribute to the dramatic diversification of alternative splicing as well as to other gene regulatory changes that contribute to phenotypic differences among vertebrate species. Overall design: mRNA profiles of several organs (brain, liver, kidney, heart, skeletal muscle) in multiple vertebrate species (mouse, chicken, lizard, frog, pufferfish) generated by deep sequencing using Illumina HiSeq		GSM1015151: Mouse brain rep2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired				Illumina HiSeq 2000	age;;adult|molecule subtype;;poly-A enriched RNA|sex;;mixed|source_name;;Mouse_brain_pooled|strain;;C57BL/6|tissue;;brain	GEO Accession;;GSM1015151		GSM1015151	Mouse brain rep2	9234691448	60754549	2012-12-24 12:04:54	5866049594	9234691448	60754549	2	60754549	index:0,count:60754549,average:76,stdev:0|index:1,count:60754549,average:76,stdev:0	GSM1015151_r1	GEO			in_mesa	23258890	2.39	2.52	0.05	5898453848	6133532022	5598817618	5870643160	103.99	104.86	50602164	48960323	131.258	419.078	98	538137	86.33	91.2	54828840	43684457	54828840	43684457	80.41	81.58	54828840	40688139	54828840	39078754	368140339	6.24	3.46	0	4.45	0	0.28	0	0.06	0	0.00	0	16.38	0	50602164	0	152	0	147.52	0	3.47	0	0.02	0	1.50	0	0.01	0	218.72	0	1.03	0	2099213	0	60754549	0	2701056	0	167813	0	35077	0	0	0	9949495	0	7196	0	0	0	77221	0	11426593	0	82454	0	11593464	0	78.84	0	47901108	0	147368	10173318	69.033426524076	60754549.0	50602164.0	2099213.0	2701056.0	167813.0	35077.0	0.0	9949495.0	47901108.0	83.3	3.5	4.4	0.3	0.1	0.0	16.4	78.8	76	76	76.00	39	4617345724	23.1	26.8	26.9	23.2	0.0	32.7	13.1	bulk
3582198	SRR579547	SRP015997	SRS366860	SRX191151	SRA059267	GEO		The evolutionary landscape of alternative splicing in vertebrate species	How species with similar repertoires of protein coding genes differ so dramatically at the phenotypic level is poorly understood. From comparing the transcriptomes of multiple organs from vertebrate species spanning ~350 million years of evolution, we observe significant differences in alternative splicing complexity between the main vertebrate lineages, with the highest complexity in the primate lineage. Moreover, within as little as six million years, the splicing profiles of physiologically-equivalent organs have diverged to the extent that they are more strongly related to the identity of a species than they are to organ type. Most vertebrate species-specific splicing patterns are governed by the highly variable use of a largely conserved cis-regulatory code. However, a smaller number of pronounced species-dependent splicing changes are predicted to remodel interactions involving factors acting at multiple steps in gene regulation. These events are expected to further contribute to the dramatic diversification of alternative splicing as well as to other gene regulatory changes that contribute to phenotypic differences among vertebrate species. Overall design: mRNA profiles of several organs (brain, liver, kidney, heart, skeletal muscle) in multiple vertebrate species (mouse, chicken, lizard, frog, pufferfish) generated by deep sequencing using Illumina HiSeq		GSM1015152: Mouse liver; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired				Illumina HiSeq 2000	age;;adult|molecule subtype;;poly-A enriched RNA|sex;;mixed|source_name;;Mouse_liver_pooled|strain;;C57BL/6|tissue;;liver	GEO Accession;;GSM1015152		GSM1015152	Mouse liver	10370110168	68224409	2012-12-24 12:04:54	6689629593	10370110168	68224409	2	68224409	index:0,count:68224409,average:76,stdev:0|index:1,count:68224409,average:76,stdev:0	GSM1015152_r1	GEO			in_mesa	23258890	2.83	1.01	0.05	7296342269	7859013360	6683435794	7295701930	107.71	109.16	57317568	54062910	160.276	442.261	98	555409	82.58	90.38	66404839	47334966	66404839	47334966	74.6	75.61	66404839	42761088	66404839	39596186	429113529	5.88	2.94	0	7.25	0	0.71	0	0.62	0	0.00	0	14.66	0	57317568	0	152	0	147.93	0	4.48	0	0.03	0	1.63	0	0.02	0	186.07	0	1.03	0	2006453	0	68224409	0	4945970	0	483967	0	420988	0	0	0	10001886	0	6183	0	0	0	82496	0	15792091	0	96829	0	15977599	0	76.76	0	52371598	0	150710	16288835	108.080651582509	68224409.0	57317568.0	2006453.0	4945970.0	483967.0	420988.0	0.0	10001886.0	52371598.0	84.0	2.9	7.2	0.7	0.6	0.0	14.7	76.8	76	76	76.00	39	5185055084	23.5	26.2	26.4	23.8	0.0	32.4	12.9	bulk
3582232	SRR579548	SRP015997	SRS366861	SRX191152	SRA059267	GEO		The evolutionary landscape of alternative splicing in vertebrate species	How species with similar repertoires of protein coding genes differ so dramatically at the phenotypic level is poorly understood. From comparing the transcriptomes of multiple organs from vertebrate species spanning ~350 million years of evolution, we observe significant differences in alternative splicing complexity between the main vertebrate lineages, with the highest complexity in the primate lineage. Moreover, within as little as six million years, the splicing profiles of physiologically-equivalent organs have diverged to the extent that they are more strongly related to the identity of a species than they are to organ type. Most vertebrate species-specific splicing patterns are governed by the highly variable use of a largely conserved cis-regulatory code. However, a smaller number of pronounced species-dependent splicing changes are predicted to remodel interactions involving factors acting at multiple steps in gene regulation. These events are expected to further contribute to the dramatic diversification of alternative splicing as well as to other gene regulatory changes that contribute to phenotypic differences among vertebrate species. Overall design: mRNA profiles of several organs (brain, liver, kidney, heart, skeletal muscle) in multiple vertebrate species (mouse, chicken, lizard, frog, pufferfish) generated by deep sequencing using Illumina HiSeq		GSM1015153: Mouse kidney; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired				Illumina HiSeq 2000	age;;adult|molecule subtype;;poly-A enriched RNA|sex;;mixed|source_name;;Mouse_kidney_pooled|strain;;C57BL/6|tissue;;kidney	GEO Accession;;GSM1015153		GSM1015153	Mouse kidney	6327372150	42182481	2012-12-24 12:04:54	4286763614	6327372150	42182481	2	42182481	index:0,count:42182481,average:75,stdev:0|index:1,count:42182481,average:75,stdev:0	GSM1015153_r1	GEO			in_mesa	23258890	3.75	1.49	0.08	2483751357	2532815677	2281074094	2360224608	101.98	103.47	17960738	16925505	173.354	477.572	153	224456	75.21	82.05	20479060	13509020	20479060	13509020	69.94	70.91	20479060	12561256	20479060	11674985	306437609	12.34	0.47	0	3.55	0	0.17	0	0.03	0	0.00	0	57.22	0	17960738	0	150	0	147.70	0	3.78	0	0.02	0	2.02	0	0.02	0	120.62	0	0.77	0	200037	0	42182481	0	1496568	0	71264	0	12843	0	0	0	24137636	0	2801	0	0	0	29961	0	4129114	0	26076	0	4187952	0	39.03	0	16464170	0	107543	4225940	39.295351626791	42182481.0	17960738.0	200037.0	1496568.0	71264.0	12843.0	0.0	24137636.0	16464170.0	42.6	0.5	3.5	0.2	0.0	0.0	57.2	39.0	75	75	75.00	38	3163686075	23.8	25.7	30.5	19.9	0.0	33.9	15.0	bulk
3582262	SRR579549	SRP015997	SRS366862	SRX191153	SRA059267	GEO		The evolutionary landscape of alternative splicing in vertebrate species	How species with similar repertoires of protein coding genes differ so dramatically at the phenotypic level is poorly understood. From comparing the transcriptomes of multiple organs from vertebrate species spanning ~350 million years of evolution, we observe significant differences in alternative splicing complexity between the main vertebrate lineages, with the highest complexity in the primate lineage. Moreover, within as little as six million years, the splicing profiles of physiologically-equivalent organs have diverged to the extent that they are more strongly related to the identity of a species than they are to organ type. Most vertebrate species-specific splicing patterns are governed by the highly variable use of a largely conserved cis-regulatory code. However, a smaller number of pronounced species-dependent splicing changes are predicted to remodel interactions involving factors acting at multiple steps in gene regulation. These events are expected to further contribute to the dramatic diversification of alternative splicing as well as to other gene regulatory changes that contribute to phenotypic differences among vertebrate species. Overall design: mRNA profiles of several organs (brain, liver, kidney, heart, skeletal muscle) in multiple vertebrate species (mouse, chicken, lizard, frog, pufferfish) generated by deep sequencing using Illumina HiSeq		GSM1015154: Mouse heart; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired				Illumina HiSeq 2000	age;;adult|molecule subtype;;poly-A enriched RNA|sex;;mixed|source_name;;Mouse_heart_pooled|strain;;C57BL/6|tissue;;heart	GEO Accession;;GSM1015154		GSM1015154	Mouse heart	5882596232	38701291	2012-12-24 12:04:54	3686946783	5882596232	38701291	2	38701291	index:0,count:38701291,average:76,stdev:0|index:1,count:38701291,average:76,stdev:0	GSM1015154_r1	GEO			in_mesa	23258890	17.14	1.19	0.04	4263145035	4365695569	3766539876	3903719026	102.41	103.64	33495649	32350955	146.360	337.926	110	411787	79.67	90.29	38527272	26684400	38527272	26684400	81.11	81.16	38527272	27167532	38527272	23985263	251871895	5.91	2.49	0	10.19	0	0.33	0	0.04	0	0.00	0	13.08	0	33495649	0	152	0	148.46	0	3.33	0	0.02	0	1.78	0	0.01	0	258.01	0	0.88	0	963268	0	38701291	0	3942734	0	128315	0	13947	0	0	0	5063380	0	5182	0	0	0	61005	0	7902788	0	52953	0	8021928	0	76.36	0	29552915	0	163873	7720221	47.111000591922	38701291.0	33495649.0	963268.0	3942734.0	128315.0	13947.0	0.0	5063380.0	29552915.0	86.5	2.5	10.2	0.3	0.0	0.0	13.1	76.4	76	76	76.00	39	2941298116	24.4	24.8	25.7	25.1	0.0	33.6	13.9	bulk
3582485	SRR579550	SRP015997	SRS366863	SRX191154	SRA059267	GEO		The evolutionary landscape of alternative splicing in vertebrate species	How species with similar repertoires of protein coding genes differ so dramatically at the phenotypic level is poorly understood. From comparing the transcriptomes of multiple organs from vertebrate species spanning ~350 million years of evolution, we observe significant differences in alternative splicing complexity between the main vertebrate lineages, with the highest complexity in the primate lineage. Moreover, within as little as six million years, the splicing profiles of physiologically-equivalent organs have diverged to the extent that they are more strongly related to the identity of a species than they are to organ type. Most vertebrate species-specific splicing patterns are governed by the highly variable use of a largely conserved cis-regulatory code. However, a smaller number of pronounced species-dependent splicing changes are predicted to remodel interactions involving factors acting at multiple steps in gene regulation. These events are expected to further contribute to the dramatic diversification of alternative splicing as well as to other gene regulatory changes that contribute to phenotypic differences among vertebrate species. Overall design: mRNA profiles of several organs (brain, liver, kidney, heart, skeletal muscle) in multiple vertebrate species (mouse, chicken, lizard, frog, pufferfish) generated by deep sequencing using Illumina HiSeq		GSM1015155: Mouse skeletal muscle; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired				Illumina HiSeq 2000	age;;adult|molecule subtype;;poly-A enriched RNA|sex;;mixed|source_name;;Mouse_skeletal muscle_pooled|strain;;C57BL/6|tissue;;skeletal muscle	GEO Accession;;GSM1015155		GSM1015155	Mouse skeletal muscle	11853942750	79026285	2012-12-24 12:04:54	8130674059	11853942750	79026285	2	79026285	index:0,count:79026285,average:75,stdev:0|index:1,count:79026285,average:75,stdev:0	GSM1015155_r1	GEO			in_mesa	23258890	3.01	1.06	0.02	6092415926	6381954920	5579388744	5964191577	104.75	106.9	51281206	49461627	145.004	366.565	173	537376	73.7	81.21	58711535	37791736	58711535	37791736	61.8	63.81	58711535	31690258	58711535	29698381	655095415	10.75	1.81	0	6.00	0	0.51	0	0.03	0	0.00	0	34.57	0	51281206	0	150	0	145.96	0	4.76	0	0.04	0	1.93	0	0.02	0	165.79	0	0.84	0	1432807	0	79026285	0	4742833	0	400176	0	26653	0	0	0	27318250	0	4562	0	0	0	62983	0	11533725	0	64650	0	11665920	0	58.89	0	46538373	0	167298	10446018	62.439586845031	79026285.0	51281206.0	1432807.0	4742833.0	400176.0	26653.0	0.0	27318250.0	46538373.0	64.9	1.8	6.0	0.5	0.0	0.0	34.6	58.9	75	75	75.00	38	5926971375	23.4	26.6	28.4	21.6	0.0	34.0	14.9	bulk
2781820	SRR594393	SRP016501	SRS369701	SRX196264	SRA059960	GEO		Evolutionary dynamics of gene and isoform regulation in mammalian tissues	Most mammalian genes produce multiple distinct mRNAs through alternative splicing, but the extent of splicing conservation is not clear.  To assess tissue-specific transcriptome variation across mammals, we sequenced cDNA from 9 tissues from 4 mammals and one bird in biological triplicate, at unprecedented depth.  We find that while tissue-specific gene expression programs are largely conserved, alternative splicing is well conserved in only a subset of tissues and is frequently lineage-specific.  Thousands of novel, lineage-specific and conserved alternative exons were identified; widely conserved alternative exons had signatures of binding by MBNL, PTB, RBFOX, STAR and TIA family splicing factors, implicating them as ancestral mammalian splicing regulators.  Our data also indicates that alternative splicing is often used to alter protein phosphorylatability, delimiting the scope of kinase signaling. Overall design: Tissue transcriptomes from 9 tissues from 5 species, 3 individuals per species, were sequenced and compared (two samples for mouse_heart)		GSM1020640: mouse_a_brain; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired				Illumina HiSeq 2000	source_name;;mouse_brain|strain;;DBA/2J|tissue;;brain	GEO Accession;;GSM1020640		GSM1020640	mouse_a_brain	8726460400	87264604	2015-07-22 17:02:33	5927043102	8726460400	87264604	2	87264604	index:0,count:87264604,average:50,stdev:0|index:1,count:87264604,average:50,stdev:0	GSM1020640_r1	GEO			in_mesa	23258891	7.15	3.39	0.08	8133292805	7992722272	7532272484	7451243629	98.27	98.92	82311911	73929167	174.162	986.028	150	2326458	78.15	84.35	91278187	64323690	91278187	64323690	81.87	81.78	91278187	67389405	91278187	62364078	1067821988	13.13	0.93	0	6.94	0	0.38	0	0.25	0	0.00	0	5.05	0	82311911	0	100	0	98.88	0	1.78	0	0.01	0	1.52	0	0.01	0	423.96	0	0.67	0	810641	0	87264604	0	6055348	0	329177	0	218399	0	0	0	4405117	0	7082	0	0	0	71575	0	9439536	0	23402	0	9541595	0	87.39	0	76256563	0	207864	9652669	46.437425432013	87264604.0	82311911.0	810641.0	6055348.0	329177.0	218399.0	0.0	4405117.0	76256563.0	94.3	0.9	6.9	0.4	0.3	0.0	5.0	87.4	50	50	50.00	37	4363230200	24.6	23.9	24.4	27.1	0.0	31.6	15.5	bulk
2781850	SRR594394	SRP016501	SRS369702	SRX196265	SRA059960	GEO		Evolutionary dynamics of gene and isoform regulation in mammalian tissues	Most mammalian genes produce multiple distinct mRNAs through alternative splicing, but the extent of splicing conservation is not clear.  To assess tissue-specific transcriptome variation across mammals, we sequenced cDNA from 9 tissues from 4 mammals and one bird in biological triplicate, at unprecedented depth.  We find that while tissue-specific gene expression programs are largely conserved, alternative splicing is well conserved in only a subset of tissues and is frequently lineage-specific.  Thousands of novel, lineage-specific and conserved alternative exons were identified; widely conserved alternative exons had signatures of binding by MBNL, PTB, RBFOX, STAR and TIA family splicing factors, implicating them as ancestral mammalian splicing regulators.  Our data also indicates that alternative splicing is often used to alter protein phosphorylatability, delimiting the scope of kinase signaling. Overall design: Tissue transcriptomes from 9 tissues from 5 species, 3 individuals per species, were sequenced and compared (two samples for mouse_heart)		GSM1020641: mouse_a_colon; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired				Illumina HiSeq 2000	source_name;;mouse_colon|strain;;DBA/2J|tissue;;colon	GEO Accession;;GSM1020641		GSM1020641	mouse_a_colon	10181649100	101816491	2015-07-22 17:02:33	6835402318	10181649100	101816491	2	101816491	index:0,count:101816491,average:50,stdev:0|index:1,count:101816491,average:50,stdev:0	GSM1020641_r1	GEO			in_mesa	23258891	6.5	2.41	0.18	9391279961	9311298827	8441471055	8451209233	99.15	100.12	95080717	83141477	196.534	1006.665	158	2179347	79.28	88.15	110500766	75376965	110500766	75376965	84.28	84.55	110500766	80130804	110500766	72296092	926062360	9.86	1.39	0	9.40	0	0.53	0	0.16	0	0.00	0	5.92	0	95080717	0	100	0	98.77	0	1.97	0	0.01	0	1.55	0	0.00	0	415.11	0	0.65	0	1418447	0	101816491	0	9569733	0	543265	0	160543	0	0	0	6031966	0	6831	0	0	0	75976	0	13134767	0	26867	0	13244441	0	83.99	0	85510984	0	201333	14216649	70.612611941410	101816491.0	95080717.0	1418447.0	9569733.0	543265.0	160543.0	0.0	6031966.0	85510984.0	93.4	1.4	9.4	0.5	0.2	0.0	5.9	84.0	50	50	50.00	37	5090824550	24.1	24.4	24.8	26.6	0.1	32.0	15.8	bulk
2781913	SRR594396	SRP016501	SRS369704	SRX196267	SRA059960	GEO		Evolutionary dynamics of gene and isoform regulation in mammalian tissues	Most mammalian genes produce multiple distinct mRNAs through alternative splicing, but the extent of splicing conservation is not clear.  To assess tissue-specific transcriptome variation across mammals, we sequenced cDNA from 9 tissues from 4 mammals and one bird in biological triplicate, at unprecedented depth.  We find that while tissue-specific gene expression programs are largely conserved, alternative splicing is well conserved in only a subset of tissues and is frequently lineage-specific.  Thousands of novel, lineage-specific and conserved alternative exons were identified; widely conserved alternative exons had signatures of binding by MBNL, PTB, RBFOX, STAR and TIA family splicing factors, implicating them as ancestral mammalian splicing regulators.  Our data also indicates that alternative splicing is often used to alter protein phosphorylatability, delimiting the scope of kinase signaling. Overall design: Tissue transcriptomes from 9 tissues from 5 species, 3 individuals per species, were sequenced and compared (two samples for mouse_heart)		GSM1020643: mouse_a_kidney; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired				Illumina HiSeq 2000	source_name;;mouse_kidney|strain;;DBA/2J|tissue;;kidney	GEO Accession;;GSM1020643		GSM1020643	mouse_a_kidney	11927478600	119274786	2015-07-22 17:02:33	7555854784	11927478600	119274786	2	119274786	index:0,count:119274786,average:50,stdev:0|index:1,count:119274786,average:50,stdev:0	GSM1020643_r1	GEO			in_mesa	23258891	13.2	1.86	0.09	11178101370	11148357043	9928463004	9986854187	99.73	100.59	112915152	98759488	191.292	859.769	160	2785915	78.75	88.6	129755026	88919111	129755026	88919111	85.47	85.14	129755026	96503776	129755026	85443638	1046526892	9.36	1.06	0	10.52	0	0.47	0	0.16	0	0.00	0	4.70	0	112915152	0	100	0	99.00	0	2.34	0	0.01	0	1.46	0	0.00	0	483.55	0	0.46	0	1259766	0	119274786	0	12553610	0	559617	0	195038	0	0	0	5604979	0	8717	0	0	0	95379	0	15880637	0	27954	0	16012687	0	84.14	0	100361542	0	206534	16538657	80.077164050471	119274786.0	112915152.0	1259766.0	12553610.0	559617.0	195038.0	0.0	5604979.0	100361542.0	94.7	1.1	10.5	0.5	0.2	0.0	4.7	84.1	50	50	50.00	37	5963739300	24.8	23.6	24.6	26.9	0.0	33.6	17.3	bulk
2781944	SRR594397	SRP016501	SRS369705	SRX196268	SRA059960	GEO		Evolutionary dynamics of gene and isoform regulation in mammalian tissues	Most mammalian genes produce multiple distinct mRNAs through alternative splicing, but the extent of splicing conservation is not clear.  To assess tissue-specific transcriptome variation across mammals, we sequenced cDNA from 9 tissues from 4 mammals and one bird in biological triplicate, at unprecedented depth.  We find that while tissue-specific gene expression programs are largely conserved, alternative splicing is well conserved in only a subset of tissues and is frequently lineage-specific.  Thousands of novel, lineage-specific and conserved alternative exons were identified; widely conserved alternative exons had signatures of binding by MBNL, PTB, RBFOX, STAR and TIA family splicing factors, implicating them as ancestral mammalian splicing regulators.  Our data also indicates that alternative splicing is often used to alter protein phosphorylatability, delimiting the scope of kinase signaling. Overall design: Tissue transcriptomes from 9 tissues from 5 species, 3 individuals per species, were sequenced and compared (two samples for mouse_heart)		GSM1020644: mouse_a_liver; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired				Illumina HiSeq 2000	source_name;;mouse_liver|strain;;DBA/2J|tissue;;liver	GEO Accession;;GSM1020644		GSM1020644	mouse_a_liver	11629247800	116292478	2015-07-22 17:02:33	7481554926	11629247800	116292478	2	116292478	index:0,count:116292478,average:50,stdev:0|index:1,count:116292478,average:50,stdev:0	GSM1020644_r1	GEO			in_mesa	23258891	5.86	1.04	0.03	10045213332	10012706389	8226862556	8262799820	99.68	100.44	101641079	86815195	225.062	985.981	160	2147501	73.83	90.07	157640791	75042166	157640791	75042166	87.08	86.42	157640791	88513963	157640791	72001361	747254085	7.44	1.29	0	15.76	0	5.79	0	1.49	0	0.00	0	5.32	0	101641079	0	100	0	98.82	0	2.38	0	0.01	0	1.43	0	0.00	0	109.34	0	0.54	0	1504927	0	116292478	0	18328717	0	6734300	0	1732724	0	0	0	6184375	0	4609	0	0	0	73331	0	15100905	0	16903	0	15195748	0	71.64	0	83312362	0	165980	24081124	145.084492107483	116292478.0	101641079.0	1504927.0	18328717.0	6734300.0	1732724.0	0.0	6184375.0	83312362.0	87.4	1.3	15.8	5.8	1.5	0.0	5.3	71.6	50	50	50.00	37	5814623900	24.6	23.3	24.4	27.7	0.0	33.1	16.9	bulk
2782009	SRR594399	SRP016501	SRS369707	SRX196270	SRA059960	GEO		Evolutionary dynamics of gene and isoform regulation in mammalian tissues	Most mammalian genes produce multiple distinct mRNAs through alternative splicing, but the extent of splicing conservation is not clear.  To assess tissue-specific transcriptome variation across mammals, we sequenced cDNA from 9 tissues from 4 mammals and one bird in biological triplicate, at unprecedented depth.  We find that while tissue-specific gene expression programs are largely conserved, alternative splicing is well conserved in only a subset of tissues and is frequently lineage-specific.  Thousands of novel, lineage-specific and conserved alternative exons were identified; widely conserved alternative exons had signatures of binding by MBNL, PTB, RBFOX, STAR and TIA family splicing factors, implicating them as ancestral mammalian splicing regulators.  Our data also indicates that alternative splicing is often used to alter protein phosphorylatability, delimiting the scope of kinase signaling. Overall design: Tissue transcriptomes from 9 tissues from 5 species, 3 individuals per species, were sequenced and compared (two samples for mouse_heart)		GSM1020646: mouse_a_skm; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired				Illumina HiSeq 2000	source_name;;mouse_skm|strain;;DBA/2J|tissue;;skeletal muscle	GEO Accession;;GSM1020646		GSM1020646	mouse_a_skm	11311127700	113111277	2015-07-22 17:02:33	7426709775	11311127700	113111277	2	113111277	index:0,count:113111277,average:50,stdev:0|index:1,count:113111277,average:50,stdev:0	GSM1020646_r1	GEO			in_mesa	23258891	10.76	1.4	0.03	10535986613	10754654489	9533070351	9804117912	102.08	102.84	106790070	92777414	225.918	794.272	166	2176109	85.78	94.73	121172624	91604102	121172624	91604102	90.34	90.23	121172624	96478720	121172624	87250798	494659729	4.69	1.07	0	8.92	0	1.00	0	0.09	0	0.00	0	4.50	0	106790070	0	100	0	98.65	0	2.02	0	0.00	0	1.48	0	0.00	0	481.32	0	0.51	0	1212973	0	113111277	0	10094135	0	1126119	0	100754	0	0	0	5094334	0	7518	0	0	0	101057	0	21750990	0	24041	0	21883606	0	85.49	0	96695935	0	171670	22740609	132.466994815635	113111277.0	106790070.0	1212973.0	10094135.0	1126119.0	100754.0	0.0	5094334.0	96695935.0	94.4	1.1	8.9	1.0	0.1	0.0	4.5	85.5	50	50	50.00	37	5655563850	22.4	25.0	25.4	27.1	0.0	32.6	16.4	bulk
2785306	SRR594400	SRP016501	SRS369708	SRX196271	SRA059960	GEO		Evolutionary dynamics of gene and isoform regulation in mammalian tissues	Most mammalian genes produce multiple distinct mRNAs through alternative splicing, but the extent of splicing conservation is not clear.  To assess tissue-specific transcriptome variation across mammals, we sequenced cDNA from 9 tissues from 4 mammals and one bird in biological triplicate, at unprecedented depth.  We find that while tissue-specific gene expression programs are largely conserved, alternative splicing is well conserved in only a subset of tissues and is frequently lineage-specific.  Thousands of novel, lineage-specific and conserved alternative exons were identified; widely conserved alternative exons had signatures of binding by MBNL, PTB, RBFOX, STAR and TIA family splicing factors, implicating them as ancestral mammalian splicing regulators.  Our data also indicates that alternative splicing is often used to alter protein phosphorylatability, delimiting the scope of kinase signaling. Overall design: Tissue transcriptomes from 9 tissues from 5 species, 3 individuals per species, were sequenced and compared (two samples for mouse_heart)		GSM1020647: mouse_a_spleen; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired				Illumina HiSeq 2000	source_name;;mouse_spleen|strain;;DBA/2J|tissue;;spleen	GEO Accession;;GSM1020647		GSM1020647	mouse_a_spleen	11407225700	114072257	2015-07-22 17:02:37	7431230507	11407225700	114072257	2	114072257	index:0,count:114072257,average:50,stdev:0|index:1,count:114072257,average:50,stdev:0	GSM1020647_r1	GEO			in_mesa	23258891	3.41	3.02	0.23	10422380301	10191102508	9179363102	9081635436	97.78	98.94	105261400	96489646	198.506	768.374	171	2437236	68.15	77.36	128898699	71736242	128898699	71736242	74.19	73.56	128898699	78089378	128898699	68216720	1978022481	18.98	1.67	0	10.98	0	0.62	0	0.26	0	0.00	0	6.84	0	105261400	0	100	0	99.02	0	2.30	0	0.01	0	1.56	0	0.01	0	482.00	0	0.55	0	1909485	0	114072257	0	12529915	0	707534	0	300979	0	0	0	7802344	0	8497	0	0	0	60408	0	9610335	0	33917	0	9713157	0	81.29	0	92731485	0	200642	10809746	53.875788718215	114072257.0	105261400.0	1909485.0	12529915.0	707534.0	300979.0	0.0	7802344.0	92731485.0	92.3	1.7	11.0	0.6	0.3	0.0	6.8	81.3	50	50	50.00	37	5703612850	24.5	24.7	24.5	26.4	0.0	32.8	16.5	bulk
2785338	SRR594401	SRP016501	SRS369709	SRX196272	SRA059960	GEO		Evolutionary dynamics of gene and isoform regulation in mammalian tissues	Most mammalian genes produce multiple distinct mRNAs through alternative splicing, but the extent of splicing conservation is not clear.  To assess tissue-specific transcriptome variation across mammals, we sequenced cDNA from 9 tissues from 4 mammals and one bird in biological triplicate, at unprecedented depth.  We find that while tissue-specific gene expression programs are largely conserved, alternative splicing is well conserved in only a subset of tissues and is frequently lineage-specific.  Thousands of novel, lineage-specific and conserved alternative exons were identified; widely conserved alternative exons had signatures of binding by MBNL, PTB, RBFOX, STAR and TIA family splicing factors, implicating them as ancestral mammalian splicing regulators.  Our data also indicates that alternative splicing is often used to alter protein phosphorylatability, delimiting the scope of kinase signaling. Overall design: Tissue transcriptomes from 9 tissues from 5 species, 3 individuals per species, were sequenced and compared (two samples for mouse_heart)		GSM1020648: mouse_a_testes; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired				Illumina HiSeq 2000	source_name;;mouse_testes|strain;;DBA/2J|tissue;;testes	GEO Accession;;GSM1020648		GSM1020648	mouse_a_testes	10919993800	109199938	2015-07-22 17:02:37	7132204819	10919993800	109199938	2	109199938	index:0,count:109199938,average:50,stdev:0|index:1,count:109199938,average:50,stdev:0	GSM1020648_r1	GEO			in_mesa	23258891	1.2	1.68	0.19	10256877367	9842576814	9729033424	9386426261	95.96	96.48	103867369	86141357	209.813	1226.785	170	2331666	79.61	83.91	114230867	82687996	114230867	82687996	80.56	80.84	114230867	83680400	114230867	79654914	1212171383	11.82	0.87	0	4.88	0	0.45	0	0.36	0	0.00	0	4.07	0	103867369	0	100	0	98.84	0	1.95	0	0.01	0	1.53	0	0.00	0	527.68	0	0.51	0	947730	0	109199938	0	5328172	0	496150	0	391380	0	0	0	4445039	0	13436	0	0	0	156852	0	17886448	0	46413	0	18103149	0	90.24	0	98539197	0	334271	18797791	56.235183429014	109199938.0	103867369.0	947730.0	5328172.0	496150.0	391380.0	0.0	4445039.0	98539197.0	95.1	0.9	4.9	0.5	0.4	0.0	4.1	90.2	50	50	50.00	37	5459996900	23.3	25.0	24.6	27.2	0.0	33.0	16.8	bulk
2785371	SRR594402	SRP016501	SRS369710	SRX196273	SRA059960	GEO		Evolutionary dynamics of gene and isoform regulation in mammalian tissues	Most mammalian genes produce multiple distinct mRNAs through alternative splicing, but the extent of splicing conservation is not clear.  To assess tissue-specific transcriptome variation across mammals, we sequenced cDNA from 9 tissues from 4 mammals and one bird in biological triplicate, at unprecedented depth.  We find that while tissue-specific gene expression programs are largely conserved, alternative splicing is well conserved in only a subset of tissues and is frequently lineage-specific.  Thousands of novel, lineage-specific and conserved alternative exons were identified; widely conserved alternative exons had signatures of binding by MBNL, PTB, RBFOX, STAR and TIA family splicing factors, implicating them as ancestral mammalian splicing regulators.  Our data also indicates that alternative splicing is often used to alter protein phosphorylatability, delimiting the scope of kinase signaling. Overall design: Tissue transcriptomes from 9 tissues from 5 species, 3 individuals per species, were sequenced and compared (two samples for mouse_heart)		GSM1020649: mouse_b_brain; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired				Illumina HiSeq 2000	source_name;;mouse_brain|strain;;C57BL/6|tissue;;brain	GEO Accession;;GSM1020649		GSM1020649	mouse_b_brain	19011896480	118824353	2015-07-22 17:02:37	12230336069	19011896480	118824353	2	118824353	index:0,count:118824353,average:80,stdev:0|index:1,count:118824353,average:80,stdev:0	GSM1020649_r1	GEO			in_mesa	23258891	4.15	3.18	0.05	16898096538	16642073327	16084406046	15902975150	98.48	98.87	113905295	107049188	179.777	677.473	182	2648366	78.38	82.4	122471962	89282860	122471962	89282860	79.63	79.6	122471962	90702557	122471962	86246827	2656123811	15.72	0.26	0	4.67	0	0.30	0	0.18	0	0.00	0	3.67	0	113905295	0	160	0	158.01	0	1.75	0	0.00	0	1.36	0	0.00	0	308.19	0	0.81	0	303800	0	118824353	0	5549105	0	354031	0	208569	0	0	0	4356458	0	22325	0	0	0	208443	0	30162987	0	49121	0	30442876	0	91.19	0	108356190	0	291750	29959581	102.689223650386	118824353.0	113905295.0	303800.0	5549105.0	354031.0	208569.0	0.0	4356458.0	108356190.0	95.9	0.3	4.7	0.3	0.2	0.0	3.7	91.2	80	80	80.00	38	9505948240	23.9	25.5	24.5	25.8	0.2	32.3	13.7	bulk
2785402	SRR594403	SRP016501	SRS369711	SRX196274	SRA059960	GEO		Evolutionary dynamics of gene and isoform regulation in mammalian tissues	Most mammalian genes produce multiple distinct mRNAs through alternative splicing, but the extent of splicing conservation is not clear.  To assess tissue-specific transcriptome variation across mammals, we sequenced cDNA from 9 tissues from 4 mammals and one bird in biological triplicate, at unprecedented depth.  We find that while tissue-specific gene expression programs are largely conserved, alternative splicing is well conserved in only a subset of tissues and is frequently lineage-specific.  Thousands of novel, lineage-specific and conserved alternative exons were identified; widely conserved alternative exons had signatures of binding by MBNL, PTB, RBFOX, STAR and TIA family splicing factors, implicating them as ancestral mammalian splicing regulators.  Our data also indicates that alternative splicing is often used to alter protein phosphorylatability, delimiting the scope of kinase signaling. Overall design: Tissue transcriptomes from 9 tissues from 5 species, 3 individuals per species, were sequenced and compared (two samples for mouse_heart)		GSM1020650: mouse_b_colon; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired				Illumina HiSeq 2000	source_name;;mouse_colon|strain;;C57BL/6|tissue;;colon	GEO Accession;;GSM1020650		GSM1020650	mouse_b_colon	13991573440	87447334	2015-07-22 17:02:37	8957908853	13991573440	87447334	2	87447334	index:0,count:87447334,average:80,stdev:0|index:1,count:87447334,average:80,stdev:0	GSM1020650_r1	GEO			in_mesa	23258891	3.32	1.64	0.07	12103538075	12134298542	10896102359	11001447319	100.25	100.97	80005487	74986698	192.683	633.676	169	1430437	80.79	89.76	96845792	64632593	96845792	64632593	84.86	84.87	96845792	67891945	96845792	61109805	1017635063	8.41	0.20	0	9.15	0	2.13	0	0.07	0	0.00	0	6.32	0	80005487	0	160	0	155.90	0	2.48	0	0.01	0	1.57	0	0.00	0	226.65	0	1.21	0	177379	0	87447334	0	8002495	0	1859113	0	59998	0	0	0	5522736	0	8144	0	0	0	96910	0	23537100	0	24842	0	23666996	0	82.34	0	72002992	0	207292	28597900	137.959496748548	87447334.0	80005487.0	177379.0	8002495.0	1859113.0	59998.0	0.0	5522736.0	72002992.0	91.5	0.2	9.2	2.1	0.1	0.0	6.3	82.3	80	80	80.00	38	6995786720	23.6	25.6	25.0	25.7	0.1	31.1	12.5	bulk
2785434	SRR594404	SRP016501	SRS369712	SRX196275	SRA059960	GEO		Evolutionary dynamics of gene and isoform regulation in mammalian tissues	Most mammalian genes produce multiple distinct mRNAs through alternative splicing, but the extent of splicing conservation is not clear.  To assess tissue-specific transcriptome variation across mammals, we sequenced cDNA from 9 tissues from 4 mammals and one bird in biological triplicate, at unprecedented depth.  We find that while tissue-specific gene expression programs are largely conserved, alternative splicing is well conserved in only a subset of tissues and is frequently lineage-specific.  Thousands of novel, lineage-specific and conserved alternative exons were identified; widely conserved alternative exons had signatures of binding by MBNL, PTB, RBFOX, STAR and TIA family splicing factors, implicating them as ancestral mammalian splicing regulators.  Our data also indicates that alternative splicing is often used to alter protein phosphorylatability, delimiting the scope of kinase signaling. Overall design: Tissue transcriptomes from 9 tissues from 5 species, 3 individuals per species, were sequenced and compared (two samples for mouse_heart)		GSM1020651: mouse_b_kidney; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired				Illumina HiSeq 2000	source_name;;mouse_kidney|strain;;C57BL/6|tissue;;kidney	GEO Accession;;GSM1020651		GSM1020651	mouse_b_kidney	18427204450	118885190	2015-07-22 17:02:33	11992642384	18427204450	118885190	2	118885190	index:0,count:118885190,average:80,stdev:0|index:1,count:118885190,average:75,stdev:0	GSM1020651_r1	GEO			in_mesa	23258891	15.25	1.8	0.1	17254551267	17111102641	15282705020	15329443069	99.17	100.31	115788983	109674112	175.717	422.232	166	2235977	78.92	89.11	133146189	91382585	133146189	91382585	85.78	85.73	133146189	99327257	133146189	87915257	1532249658	8.88	0.12	0	11.14	0	0.40	0	0.09	0	0.00	0	2.12	0	115788983	0	155	0	153.69	0	2.04	0	0.00	0	1.19	0	0.00	0	309.46	0	0.51	0	145363	0	118885190	0	13240863	0	470012	0	106177	0	0	0	2520018	0	16156	0	0	0	178335	0	31548071	0	29975	0	31772537	0	86.26	0	102548120	0	248525	32522696	130.862874962277	118885190.0	115788983.0	145363.0	13240863.0	470012.0	106177.0	0.0	2520018.0	102548120.0	97.4	0.1	11.1	0.4	0.1	0.0	2.1	86.3	80	80	80.00	37	9510815200	25.3	23.2	24.3	27.2	0.0	32.5	15.7	bulk
2785468	SRR594405	SRP016501	SRS369713	SRX196276	SRA059960	GEO		Evolutionary dynamics of gene and isoform regulation in mammalian tissues	Most mammalian genes produce multiple distinct mRNAs through alternative splicing, but the extent of splicing conservation is not clear.  To assess tissue-specific transcriptome variation across mammals, we sequenced cDNA from 9 tissues from 4 mammals and one bird in biological triplicate, at unprecedented depth.  We find that while tissue-specific gene expression programs are largely conserved, alternative splicing is well conserved in only a subset of tissues and is frequently lineage-specific.  Thousands of novel, lineage-specific and conserved alternative exons were identified; widely conserved alternative exons had signatures of binding by MBNL, PTB, RBFOX, STAR and TIA family splicing factors, implicating them as ancestral mammalian splicing regulators.  Our data also indicates that alternative splicing is often used to alter protein phosphorylatability, delimiting the scope of kinase signaling. Overall design: Tissue transcriptomes from 9 tissues from 5 species, 3 individuals per species, were sequenced and compared (two samples for mouse_heart)		GSM1020652: mouse_b_liver; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired				Illumina HiSeq 2000	source_name;;mouse_liver|strain;;C57BL/6|tissue;;liver	GEO Accession;;GSM1020652		GSM1020652	mouse_b_liver	21447315360	134045721	2015-07-22 17:02:37	13711169304	21447315360	134045721	2	134045721	index:0,count:134045721,average:80,stdev:0|index:1,count:134045721,average:80,stdev:0	GSM1020652_r1	GEO			in_mesa	23258891	4.47	1.24	0.04	18452839735	18479012578	16831592649	16900203042	100.14	100.41	124226409	115416386	188.801	495.375	175	2561366	82.68	90.75	146149504	102711298	146149504	102711298	87.25	87.34	146149504	108382633	146149504	98842940	1481057955	8.03	0.19	0	8.24	0	1.55	0	2.49	0	0.00	0	3.28	0	124226409	0	160	0	157.68	0	2.04	0	0.00	0	1.64	0	0.00	0	126.79	0	0.60	0	254953	0	134045721	0	11051061	0	2073721	0	3343986	0	0	0	4401605	0	16524	0	0	0	236430	0	48039121	0	47121	0	48339196	0	84.43	0	113175348	0	231105	54471129	235.698617511521	134045721.0	124226409.0	254953.0	11051061.0	2073721.0	3343986.0	0.0	4401605.0	113175348.0	92.7	0.2	8.2	1.5	2.5	0.0	3.3	84.4	80	80	80.00	38	10723657680	23.4	25.6	25.0	26.0	0.0	34.2	16.7	bulk
2785500	SRR594406	SRP016501	SRS369714	SRX196277	SRA059960	GEO		Evolutionary dynamics of gene and isoform regulation in mammalian tissues	Most mammalian genes produce multiple distinct mRNAs through alternative splicing, but the extent of splicing conservation is not clear.  To assess tissue-specific transcriptome variation across mammals, we sequenced cDNA from 9 tissues from 4 mammals and one bird in biological triplicate, at unprecedented depth.  We find that while tissue-specific gene expression programs are largely conserved, alternative splicing is well conserved in only a subset of tissues and is frequently lineage-specific.  Thousands of novel, lineage-specific and conserved alternative exons were identified; widely conserved alternative exons had signatures of binding by MBNL, PTB, RBFOX, STAR and TIA family splicing factors, implicating them as ancestral mammalian splicing regulators.  Our data also indicates that alternative splicing is often used to alter protein phosphorylatability, delimiting the scope of kinase signaling. Overall design: Tissue transcriptomes from 9 tissues from 5 species, 3 individuals per species, were sequenced and compared (two samples for mouse_heart)		GSM1020653: mouse_b_lung; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired				Illumina HiSeq 2000	source_name;;mouse_lung|strain;;C57BL/6|tissue;;lung	GEO Accession;;GSM1020653		GSM1020653	mouse_b_lung	9978064160	62362901	2015-07-22 17:02:33	6787372787	9978064160	62362901	2	62362901	index:0,count:62362901,average:80,stdev:0|index:1,count:62362901,average:80,stdev:0	GSM1020653_r1	GEO			in_mesa	23258891	1.55	2.53	0.05	8945814203	8865413191	8344272536	8305479079	99.1	99.54	58551093	55363790	183.158	489.251	169	1995375	77.88	83.51	65766666	45597449	65766666	45597449	79.91	79.91	65766666	46787781	65766666	43629858	1288715713	14.41	0.26	0	6.34	0	0.18	0	0.07	0	0.00	0	5.86	0	58551093	0	160	0	156.56	0	1.86	0	0.01	0	1.27	0	0.00	0	248.35	0	1.38	0	164562	0	62362901	0	3950916	0	112921	0	41659	0	0	0	3657228	0	9371	0	0	0	82564	0	14615399	0	24212	0	14731546	0	87.55	0	54600177	0	213298	16031719	75.161131374884	62362901.0	58551093.0	164562.0	3950916.0	112921.0	41659.0	0.0	3657228.0	54600177.0	93.9	0.3	6.3	0.2	0.1	0.0	5.9	87.6	80	80	80.00	38	4989032080	24.2	26.4	23.8	25.4	0.2	28.7	11.4	bulk
2785531	SRR594407	SRP016501	SRS369715	SRX196278	SRA059960	GEO		Evolutionary dynamics of gene and isoform regulation in mammalian tissues	Most mammalian genes produce multiple distinct mRNAs through alternative splicing, but the extent of splicing conservation is not clear.  To assess tissue-specific transcriptome variation across mammals, we sequenced cDNA from 9 tissues from 4 mammals and one bird in biological triplicate, at unprecedented depth.  We find that while tissue-specific gene expression programs are largely conserved, alternative splicing is well conserved in only a subset of tissues and is frequently lineage-specific.  Thousands of novel, lineage-specific and conserved alternative exons were identified; widely conserved alternative exons had signatures of binding by MBNL, PTB, RBFOX, STAR and TIA family splicing factors, implicating them as ancestral mammalian splicing regulators.  Our data also indicates that alternative splicing is often used to alter protein phosphorylatability, delimiting the scope of kinase signaling. Overall design: Tissue transcriptomes from 9 tissues from 5 species, 3 individuals per species, were sequenced and compared (two samples for mouse_heart)		GSM1020654: mouse_b_skm; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired				Illumina HiSeq 2000	source_name;;mouse_skm|strain;;C57BL/6|tissue;;skeletal muscle	GEO Accession;;GSM1020654		GSM1020654	mouse_b_skm	18747477920	117171737	2015-07-22 17:02:37	12488535807	18747477920	117171737	2	117171737	index:0,count:117171737,average:80,stdev:0|index:1,count:117171737,average:80,stdev:0	GSM1020654_r1	GEO			in_mesa	23258891	9.61	1.43	0.03	16261428650	16544356311	15013378953	15356032779	101.74	102.28	110920359	104159518	188.215	461.904	180	2243944	85.62	92.82	123523173	94969529	123523173	94969529	87.92	87.75	123523173	97520667	123523173	89779159	976213228	6.00	0.25	0	7.35	0	0.84	0	0.05	0	0.00	0	4.45	0	110920359	0	160	0	157.36	0	2.00	0	0.00	0	1.71	0	0.00	0	274.26	0	0.87	0	295584	0	117171737	0	8609546	0	983158	0	53548	0	0	0	5214672	0	16185	0	0	0	201050	0	45715572	0	46380	0	45979187	0	87.32	0	102310813	0	220554	45496315	206.281976296054	117171737.0	110920359.0	295584.0	8609546.0	983158.0	53548.0	0.0	5214672.0	102310813.0	94.7	0.3	7.3	0.8	0.0	0.0	4.5	87.3	80	80	80.00	38	9373738960	22.2	26.1	24.9	26.6	0.2	31.1	12.9	bulk
2785563	SRR594408	SRP016501	SRS369716	SRX196279	SRA059960	GEO		Evolutionary dynamics of gene and isoform regulation in mammalian tissues	Most mammalian genes produce multiple distinct mRNAs through alternative splicing, but the extent of splicing conservation is not clear.  To assess tissue-specific transcriptome variation across mammals, we sequenced cDNA from 9 tissues from 4 mammals and one bird in biological triplicate, at unprecedented depth.  We find that while tissue-specific gene expression programs are largely conserved, alternative splicing is well conserved in only a subset of tissues and is frequently lineage-specific.  Thousands of novel, lineage-specific and conserved alternative exons were identified; widely conserved alternative exons had signatures of binding by MBNL, PTB, RBFOX, STAR and TIA family splicing factors, implicating them as ancestral mammalian splicing regulators.  Our data also indicates that alternative splicing is often used to alter protein phosphorylatability, delimiting the scope of kinase signaling. Overall design: Tissue transcriptomes from 9 tissues from 5 species, 3 individuals per species, were sequenced and compared (two samples for mouse_heart)		GSM1020655: mouse_b_spleen; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired				Illumina HiSeq 2000	source_name;;mouse_spleen|strain;;C57BL/6|tissue;;spleen	GEO Accession;;GSM1020655		GSM1020655	mouse_b_spleen	18370262720	114814142	2015-07-22 17:02:33	12172047883	18370262720	114814142	2	114814142	index:0,count:114814142,average:80,stdev:0|index:1,count:114814142,average:80,stdev:0	GSM1020655_r1	GEO			in_mesa	23258891	1.75	2.69	0.2	17045916105	16792751331	15760656258	15599746919	98.51	98.98	110578973	105031309	187.079	536.860	176	4066721	73.98	80.05	126909229	81809298	126909229	81809298	77.07	76.88	126909229	85226206	126909229	78577416	3158008513	18.53	0.22	0	7.30	0	0.38	0	0.15	0	0.00	0	3.16	0	110578973	0	160	0	158.26	0	1.75	0	0.00	0	1.37	0	0.00	0	299.52	0	0.72	0	254948	0	114814142	0	8375741	0	434524	0	173991	0	0	0	3626654	0	22379	0	0	0	188107	0	29911184	0	55677	0	30177347	0	89.02	0	102203232	0	268640	33499874	124.701734663490	114814142.0	110578973.0	254948.0	8375741.0	434524.0	173991.0	0.0	3626654.0	102203232.0	96.3	0.2	7.3	0.4	0.2	0.0	3.2	89.0	80	80	80.00	38	9185131360	23.6	26.0	24.8	25.4	0.1	31.7	13.4	bulk
2785595	SRR594409	SRP016501	SRS369717	SRX196280	SRA059960	GEO		Evolutionary dynamics of gene and isoform regulation in mammalian tissues	Most mammalian genes produce multiple distinct mRNAs through alternative splicing, but the extent of splicing conservation is not clear.  To assess tissue-specific transcriptome variation across mammals, we sequenced cDNA from 9 tissues from 4 mammals and one bird in biological triplicate, at unprecedented depth.  We find that while tissue-specific gene expression programs are largely conserved, alternative splicing is well conserved in only a subset of tissues and is frequently lineage-specific.  Thousands of novel, lineage-specific and conserved alternative exons were identified; widely conserved alternative exons had signatures of binding by MBNL, PTB, RBFOX, STAR and TIA family splicing factors, implicating them as ancestral mammalian splicing regulators.  Our data also indicates that alternative splicing is often used to alter protein phosphorylatability, delimiting the scope of kinase signaling. Overall design: Tissue transcriptomes from 9 tissues from 5 species, 3 individuals per species, were sequenced and compared (two samples for mouse_heart)		GSM1020656: mouse_b_testes; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired				Illumina HiSeq 2000	source_name;;mouse_testes|strain;;C57BL/6|tissue;;testes	GEO Accession;;GSM1020656		GSM1020656	mouse_b_testes	18644023520	116525147	2015-07-22 17:02:33	12339976490	18644023520	116525147	2	116525147	index:0,count:116525147,average:80,stdev:0|index:1,count:116525147,average:80,stdev:0	GSM1020656_r1	GEO			in_mesa	23258891	0.88	1.25	0.2	17239750808	16627709678	16574736810	16048096479	96.45	96.82	110998275	101165863	198.887	692.456	180	3351126	81.61	84.9	118835160	90588129	118835160	90588129	80.79	81.18	118835160	89678093	118835160	86619840	1928486641	11.19	0.18	0	3.69	0	0.29	0	0.18	0	0.00	0	4.27	0	110998275	0	160	0	157.86	0	2.19	0	0.00	0	1.89	0	0.00	0	270.46	0	0.79	0	213053	0	116525147	0	4295303	0	337795	0	212827	0	0	0	4976250	0	35986	0	0	0	342329	0	40381355	0	81688	0	40841358	0	91.57	0	106702972	0	354790	41788245	117.783040671947	116525147.0	110998275.0	213053.0	4295303.0	337795.0	212827.0	0.0	4976250.0	106702972.0	95.3	0.2	3.7	0.3	0.2	0.0	4.3	91.6	80	80	80.00	38	9322011760	22.2	26.4	25.4	25.9	0.1	31.4	13.0	bulk
6415395	SRR964790	SRP029464	SRS476313	SRX344333	SRA099825	GEO		Transcriptome modulation of ventricles, cardiomyocytes and cardiac fibroblasts during postnatal mouse development	During development the fetal heart undergoes a rapid and dramatic transition to adult function through transcriptional and post-transcriptional mechanisms, including alternative splicing (AS). We performed deep RNA-sequencing for high-resolution analysis of transcriptome changes during postnatal mouse heart development using RNA from ventricles and freshly isolated cardiomyocytes (CM) and cardiac fibroblasts (CF). Extensive changes in gene expression and AS occur primarily between postnatal days 1 and 28. CM and CF showed reciprocal regulation of gene expression during postnatal development reflecting differences in proliferative capacity, cell adhesion functions, and mitochondrial metabolism. We found that AS plays a novel role in vesicular trafficking and membrane organization during postnatal CM development. Interestingly, these AS transitions are enriched among targets of two RNA-binding proteins, Celf1 and Mbnl1, which undergo developmentally regulated change in expression. Vesicular traffic genes affected by AS during normal development where Celf1 is down-regulated, showed a reversion to neonatal AS patterns when Celf1 was over-expressed in adults. Overall design: RNA-seq was performed in RNA samples of ventricles, cardiomyocytes or cardiac fibroblast at different developmental stages; embryonic day 17, postnatal day (PN) 1, 10, 28 and 90 for ventricles, PN1-3, PN28 and PN60 for cardiac fibroblasts, and PN1-2, PN30, and PN67 for cardiomyocytes		GSM1223635: RNA-seq ventricle PN90 (adult); Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			RNeasy fibrous tissue mini kit was used for ventricles and cardiomyocytes, and micro RNeasy kit for cardiac fibroblasts (all from Qiagen) Illumina TruSeq RNA protocols were used for cardiomyocytes and cardiac fibroblast. For developmental ventricle analysis, RNA was rRNA depleted with the Ribo-Zero Magnetic Gold Kit and libraries were prepared using ScriptSeq v2 RNA-seq library preparation kits (Epicentre).	Illumina HiSeq 2000	age;;PN90 (adult)|genotype/variation;;wild type|source_name;;ventricle|strain;;FVB|tissue;;ventricle	GEO Accession;;GSM1223635		GSM1223635	RNA-seq ventricle PN90 (adult)	30920044400	154600222	2014-04-16 15:55:08	21619271078	30920044400	154600222	2	154600222	index:0,count:154600222,average:100,stdev:0|index:1,count:154600222,average:100,stdev:0	GSM1223635_r1	GEO			in_mesa	24752171	19.59	1.76	0.06	23052849849	23148042897	20140001575	20351093162	100.41	101.05	136506516	119683648	232.882	1101.189	152	899885	81.62	93.9	158535669	111414308	158535669	111414308	90.43	90.31	158535669	123439053	158535669	107147837	1147322805	4.98	1.80	0	11.55	0	0.12	0	0.05	0	0.00	0	11.53	0	136506516	0	200	0	196.09	0	2.02	0	0.01	0	2.06	0	0.01	0	270.57	0	0.63	0	2787762	0	154600222	0	17860280	0	192859	0	74225	0	0	0	17826622	0	24087	0	0	0	364062	0	57067895	0	119150	0	57575194	0	76.74	0	118646236	0	242126	53298753	220.128168804672	154600222.0	136506516.0	2787762.0	17860280.0	192859.0	74225.0	0.0	17826622.0	118646236.0	88.3	1.8	11.6	0.1	0.0	0.0	11.5	76.7	100	100	100.00	38	15460022200	28.4	23.4	23.5	24.6	0.1	34.6	17.7	bulk
6415460	SRR964791	SRP029464	SRS476314	SRX344334	SRA099825	GEO		Transcriptome modulation of ventricles, cardiomyocytes and cardiac fibroblasts during postnatal mouse development	During development the fetal heart undergoes a rapid and dramatic transition to adult function through transcriptional and post-transcriptional mechanisms, including alternative splicing (AS). We performed deep RNA-sequencing for high-resolution analysis of transcriptome changes during postnatal mouse heart development using RNA from ventricles and freshly isolated cardiomyocytes (CM) and cardiac fibroblasts (CF). Extensive changes in gene expression and AS occur primarily between postnatal days 1 and 28. CM and CF showed reciprocal regulation of gene expression during postnatal development reflecting differences in proliferative capacity, cell adhesion functions, and mitochondrial metabolism. We found that AS plays a novel role in vesicular trafficking and membrane organization during postnatal CM development. Interestingly, these AS transitions are enriched among targets of two RNA-binding proteins, Celf1 and Mbnl1, which undergo developmentally regulated change in expression. Vesicular traffic genes affected by AS during normal development where Celf1 is down-regulated, showed a reversion to neonatal AS patterns when Celf1 was over-expressed in adults. Overall design: RNA-seq was performed in RNA samples of ventricles, cardiomyocytes or cardiac fibroblast at different developmental stages; embryonic day 17, postnatal day (PN) 1, 10, 28 and 90 for ventricles, PN1-3, PN28 and PN60 for cardiac fibroblasts, and PN1-2, PN30, and PN67 for cardiomyocytes		GSM1223636: RNA-seq ventricle PN28; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			RNeasy fibrous tissue mini kit was used for ventricles and cardiomyocytes, and micro RNeasy kit for cardiac fibroblasts (all from Qiagen) Illumina TruSeq RNA protocols were used for cardiomyocytes and cardiac fibroblast. For developmental ventricle analysis, RNA was rRNA depleted with the Ribo-Zero Magnetic Gold Kit and libraries were prepared using ScriptSeq v2 RNA-seq library preparation kits (Epicentre).	Illumina HiSeq 2000	age;;PN28|genotype/variation;;wild type|source_name;;ventricle|strain;;FVB|tissue;;ventricle	GEO Accession;;GSM1223636		GSM1223636	RNA-seq ventricle PN28	31973304400	159866522	2014-04-16 15:55:08	22423109552	31973304400	159866522	2	159866522	index:0,count:159866522,average:100,stdev:0|index:1,count:159866522,average:100,stdev:0	GSM1223636_r1	GEO			in_mesa	24752171	18.58	1.74	0.06	24775032773	24795937571	21897811827	22045346833	100.08	100.67	144459179	127037485	235.946	1050.106	152	1006486	82.21	93.51	166566030	118763961	166566030	118763961	90.11	90.11	166566030	130171686	166566030	114441842	1242245726	5.01	1.56	0	10.92	0	0.14	0	0.06	0	0.00	0	9.44	0	144459179	0	200	0	196.39	0	1.99	0	0.01	0	2.41	0	0.01	0	292.14	0	0.63	0	2489745	0	159866522	0	17451326	0	217849	0	98281	0	0	0	15091213	0	25400	0	0	0	381200	0	60414287	0	117461	0	60938348	0	79.45	0	127007853	0	255176	57389086	224.900014107910	159866522.0	144459179.0	2489745.0	17451326.0	217849.0	98281.0	0.0	15091213.0	127007853.0	90.4	1.6	10.9	0.1	0.1	0.0	9.4	79.4	100	100	100.00	38	15986652200	28.2	23.6	23.7	24.4	0.1	34.6	17.8	bulk
6415525	SRR964792	SRP029464	SRS476315	SRX344335	SRA099825	GEO		Transcriptome modulation of ventricles, cardiomyocytes and cardiac fibroblasts during postnatal mouse development	During development the fetal heart undergoes a rapid and dramatic transition to adult function through transcriptional and post-transcriptional mechanisms, including alternative splicing (AS). We performed deep RNA-sequencing for high-resolution analysis of transcriptome changes during postnatal mouse heart development using RNA from ventricles and freshly isolated cardiomyocytes (CM) and cardiac fibroblasts (CF). Extensive changes in gene expression and AS occur primarily between postnatal days 1 and 28. CM and CF showed reciprocal regulation of gene expression during postnatal development reflecting differences in proliferative capacity, cell adhesion functions, and mitochondrial metabolism. We found that AS plays a novel role in vesicular trafficking and membrane organization during postnatal CM development. Interestingly, these AS transitions are enriched among targets of two RNA-binding proteins, Celf1 and Mbnl1, which undergo developmentally regulated change in expression. Vesicular traffic genes affected by AS during normal development where Celf1 is down-regulated, showed a reversion to neonatal AS patterns when Celf1 was over-expressed in adults. Overall design: RNA-seq was performed in RNA samples of ventricles, cardiomyocytes or cardiac fibroblast at different developmental stages; embryonic day 17, postnatal day (PN) 1, 10, 28 and 90 for ventricles, PN1-3, PN28 and PN60 for cardiac fibroblasts, and PN1-2, PN30, and PN67 for cardiomyocytes		GSM1223637: RNA-seq ventricle PN10; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			RNeasy fibrous tissue mini kit was used for ventricles and cardiomyocytes, and micro RNeasy kit for cardiac fibroblasts (all from Qiagen) Illumina TruSeq RNA protocols were used for cardiomyocytes and cardiac fibroblast. For developmental ventricle analysis, RNA was rRNA depleted with the Ribo-Zero Magnetic Gold Kit and libraries were prepared using ScriptSeq v2 RNA-seq library preparation kits (Epicentre).	Illumina HiSeq 2000	age;;PN10|genotype/variation;;wild type|source_name;;ventricle|strain;;FVB|tissue;;ventricle	GEO Accession;;GSM1223637		GSM1223637	RNA-seq ventricle PN10	31769192000	158845960	2014-04-16 15:55:08	22208434581	31769192000	158845960	2	158845960	index:0,count:158845960,average:100,stdev:0|index:1,count:158845960,average:100,stdev:0	GSM1223637_r1	GEO			in_mesa	24752171	16.46	2.1	0.05	24457446147	24358269000	21779221270	21832673659	99.59	100.25	143858432	128361885	230.241	993.458	152	1070450	78.83	88.92	164555357	113400897	164555357	113400897	86.23	85.9	164555357	124049349	164555357	109545915	2318031177	9.48	1.62	0	10.28	0	0.13	0	0.08	0	0.00	0	9.23	0	143858432	0	200	0	196.60	0	1.99	0	0.01	0	2.27	0	0.01	0	370.13	0	0.62	0	2565386	0	158845960	0	16328852	0	207176	0	120583	0	0	0	14659769	0	25256	0	0	0	380063	0	55827118	0	121116	0	56353553	0	80.29	0	127529580	0	261604	52643496	201.233528539319	158845960.0	143858432.0	2565386.0	16328852.0	207176.0	120583.0	0.0	14659769.0	127529580.0	90.6	1.6	10.3	0.1	0.1	0.0	9.2	80.3	100	100	100.00	38	15884596000	28.6	23.1	23.2	24.9	0.1	34.7	17.8	bulk
6415591	SRR964793	SRP029464	SRS476316	SRX344336	SRA099825	GEO		Transcriptome modulation of ventricles, cardiomyocytes and cardiac fibroblasts during postnatal mouse development	During development the fetal heart undergoes a rapid and dramatic transition to adult function through transcriptional and post-transcriptional mechanisms, including alternative splicing (AS). We performed deep RNA-sequencing for high-resolution analysis of transcriptome changes during postnatal mouse heart development using RNA from ventricles and freshly isolated cardiomyocytes (CM) and cardiac fibroblasts (CF). Extensive changes in gene expression and AS occur primarily between postnatal days 1 and 28. CM and CF showed reciprocal regulation of gene expression during postnatal development reflecting differences in proliferative capacity, cell adhesion functions, and mitochondrial metabolism. We found that AS plays a novel role in vesicular trafficking and membrane organization during postnatal CM development. Interestingly, these AS transitions are enriched among targets of two RNA-binding proteins, Celf1 and Mbnl1, which undergo developmentally regulated change in expression. Vesicular traffic genes affected by AS during normal development where Celf1 is down-regulated, showed a reversion to neonatal AS patterns when Celf1 was over-expressed in adults. Overall design: RNA-seq was performed in RNA samples of ventricles, cardiomyocytes or cardiac fibroblast at different developmental stages; embryonic day 17, postnatal day (PN) 1, 10, 28 and 90 for ventricles, PN1-3, PN28 and PN60 for cardiac fibroblasts, and PN1-2, PN30, and PN67 for cardiomyocytes		GSM1223638: RNA-seq ventricle PN1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			RNeasy fibrous tissue mini kit was used for ventricles and cardiomyocytes, and micro RNeasy kit for cardiac fibroblasts (all from Qiagen) Illumina TruSeq RNA protocols were used for cardiomyocytes and cardiac fibroblast. For developmental ventricle analysis, RNA was rRNA depleted with the Ribo-Zero Magnetic Gold Kit and libraries were prepared using ScriptSeq v2 RNA-seq library preparation kits (Epicentre).	Illumina HiSeq 2000	age;;PN1|genotype/variation;;wild type|source_name;;ventricle|strain;;FVB|tissue;;ventricle	GEO Accession;;GSM1223638		GSM1223638	RNA-seq ventricle PN1	33336885600	166684428	2014-04-16 15:55:08	23563265064	33336885600	166684428	2	166684428	index:0,count:166684428,average:100,stdev:0|index:1,count:166684428,average:100,stdev:0	GSM1223638_r1	GEO			in_mesa	24752171	9.38	2.67	0.06	25294990575	25431157305	22774598882	22982189335	100.54	100.91	149788436	130608040	230.800	1128.183	152	1193624	81.43	90.94	172352510	121973537	172352510	121973537	87.38	87.25	172352510	130879670	172352510	117025776	2050250865	8.11	1.68	0	9.40	0	0.15	0	0.06	0	0.00	0	9.94	0	149788436	0	200	0	196.21	0	1.96	0	0.01	0	2.04	0	0.01	0	336.17	0	0.65	0	2797976	0	166684428	0	15660875	0	242630	0	92716	0	0	0	16560646	0	35419	0	0	0	437154	0	67040839	0	139305	0	67652717	0	80.47	0	134127561	0	273997	63397638	231.380774242054	166684428.0	149788436.0	2797976.0	15660875.0	242630.0	92716.0	0.0	16560646.0	134127561.0	89.9	1.7	9.4	0.1	0.1	0.0	9.9	80.5	100	100	100.00	38	16668442800	27.7	23.3	24.8	24.1	0.1	34.3	17.3	bulk
6415657	SRR964794	SRP029464	SRS476317	SRX344337	SRA099825	GEO		Transcriptome modulation of ventricles, cardiomyocytes and cardiac fibroblasts during postnatal mouse development	During development the fetal heart undergoes a rapid and dramatic transition to adult function through transcriptional and post-transcriptional mechanisms, including alternative splicing (AS). We performed deep RNA-sequencing for high-resolution analysis of transcriptome changes during postnatal mouse heart development using RNA from ventricles and freshly isolated cardiomyocytes (CM) and cardiac fibroblasts (CF). Extensive changes in gene expression and AS occur primarily between postnatal days 1 and 28. CM and CF showed reciprocal regulation of gene expression during postnatal development reflecting differences in proliferative capacity, cell adhesion functions, and mitochondrial metabolism. We found that AS plays a novel role in vesicular trafficking and membrane organization during postnatal CM development. Interestingly, these AS transitions are enriched among targets of two RNA-binding proteins, Celf1 and Mbnl1, which undergo developmentally regulated change in expression. Vesicular traffic genes affected by AS during normal development where Celf1 is down-regulated, showed a reversion to neonatal AS patterns when Celf1 was over-expressed in adults. Overall design: RNA-seq was performed in RNA samples of ventricles, cardiomyocytes or cardiac fibroblast at different developmental stages; embryonic day 17, postnatal day (PN) 1, 10, 28 and 90 for ventricles, PN1-3, PN28 and PN60 for cardiac fibroblasts, and PN1-2, PN30, and PN67 for cardiomyocytes		GSM1223639: RNA-seq ventricle E17; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			RNeasy fibrous tissue mini kit was used for ventricles and cardiomyocytes, and micro RNeasy kit for cardiac fibroblasts (all from Qiagen) Illumina TruSeq RNA protocols were used for cardiomyocytes and cardiac fibroblast. For developmental ventricle analysis, RNA was rRNA depleted with the Ribo-Zero Magnetic Gold Kit and libraries were prepared using ScriptSeq v2 RNA-seq library preparation kits (Epicentre).	Illumina HiSeq 2000	age;;E17|genotype/variation;;wild type|source_name;;ventricle|strain;;FVB|tissue;;ventricle	GEO Accession;;GSM1223639		GSM1223639	RNA-seq ventricle E17	33205582800	166027914	2014-04-16 15:55:08	23551488900	33205582800	166027914	2	166027914	index:0,count:166027914,average:100,stdev:0|index:1,count:166027914,average:100,stdev:0	GSM1223639_r1	GEO			in_mesa	24752171	4.97	2.91	0.06	25147476332	25206031993	22152773664	22285033948	100.23	100.6	149640277	131562065	227.118	1110.281	158	1151674	77.02	87.84	179533476	115252031	179533476	115252031	84.34	83.69	179533476	126202628	179533476	109803630	2641191967	10.50	1.53	0	11.10	0	0.19	0	0.07	0	0.00	0	9.60	0	149640277	0	200	0	196.20	0	1.98	0	0.01	0	2.15	0	0.01	0	266.00	0	0.67	0	2541990	0	166027914	0	18434838	0	318021	0	123590	0	0	0	15946026	0	36962	0	0	0	409918	0	63602893	0	143805	0	64193578	0	79.03	0	131205439	0	289605	65687196	226.816512145854	166027914.0	149640277.0	2541990.0	18434838.0	318021.0	123590.0	0.0	15946026.0	131205439.0	90.1	1.5	11.1	0.2	0.1	0.0	9.6	79.0	100	100	100.00	38	16602791400	27.4	23.3	25.2	24.0	0.1	34.2	17.3	bulk
6415719	SRR964795	SRP029464	SRS476318	SRX344338	SRA099825	GEO		Transcriptome modulation of ventricles, cardiomyocytes and cardiac fibroblasts during postnatal mouse development	During development the fetal heart undergoes a rapid and dramatic transition to adult function through transcriptional and post-transcriptional mechanisms, including alternative splicing (AS). We performed deep RNA-sequencing for high-resolution analysis of transcriptome changes during postnatal mouse heart development using RNA from ventricles and freshly isolated cardiomyocytes (CM) and cardiac fibroblasts (CF). Extensive changes in gene expression and AS occur primarily between postnatal days 1 and 28. CM and CF showed reciprocal regulation of gene expression during postnatal development reflecting differences in proliferative capacity, cell adhesion functions, and mitochondrial metabolism. We found that AS plays a novel role in vesicular trafficking and membrane organization during postnatal CM development. Interestingly, these AS transitions are enriched among targets of two RNA-binding proteins, Celf1 and Mbnl1, which undergo developmentally regulated change in expression. Vesicular traffic genes affected by AS during normal development where Celf1 is down-regulated, showed a reversion to neonatal AS patterns when Celf1 was over-expressed in adults. Overall design: RNA-seq was performed in RNA samples of ventricles, cardiomyocytes or cardiac fibroblast at different developmental stages; embryonic day 17, postnatal day (PN) 1, 10, 28 and 90 for ventricles, PN1-3, PN28 and PN60 for cardiac fibroblasts, and PN1-2, PN30, and PN67 for cardiomyocytes		GSM1223640: RNA-seq cardiac fibroblasts PN60 (adult); Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			RNeasy fibrous tissue mini kit was used for ventricles and cardiomyocytes, and micro RNeasy kit for cardiac fibroblasts (all from Qiagen) Illumina TruSeq RNA protocols were used for cardiomyocytes and cardiac fibroblast. For developmental ventricle analysis, RNA was rRNA depleted with the Ribo-Zero Magnetic Gold Kit and libraries were prepared using ScriptSeq v2 RNA-seq library preparation kits (Epicentre).	Illumina HiSeq 2000	age;;PN60 (adult)|genotype/variation;;wild type|source_name;;Cardiac fibroblasts|strain;;FVB|tissue;;Cardiac fibroblasts	GEO Accession;;GSM1223640		GSM1223640	RNA-seq cardiac fibroblasts PN60 (adult)	37343559614	184869107	2014-04-16 15:55:08	25391402007	37343559614	184869107	2	184869107	index:0,count:184869107,average:101,stdev:0|index:1,count:184869107,average:101,stdev:0	GSM1223640_r1	GEO			in_mesa	24752171	3.43	2.77	0.29	27825676809	26782612289	25321280200	24942788757	96.25	98.51	173147606	160827439	189.818	621.911	145	1651012	84.39	92.83	205339748	146124355	205339748	146124355	87.12	89.73	205339748	150846534	205339748	141248592	1454495080	5.23	1.18	0	8.51	0	1.24	0	0.05	0	0.00	0	5.05	0	173147606	0	202	0	199.17	0	2.12	0	0.01	0	1.89	0	0.02	0	310.70	0	0.39	0	2180474	0	184869107	0	15734302	0	2288865	0	100397	0	0	0	9332239	0	33600	0	0	0	548045	0	80367728	0	175615	0	81124988	0	85.15	0	157413304	0	405074	71534450	176.596004680626	184869107.0	173147606.0	2180474.0	15734302.0	2288865.0	100397.0	0.0	9332239.0	157413304.0	93.7	1.2	8.5	1.2	0.1	0.0	5.0	85.1	101	101	101.00	38	18671779807	24.9	25.1	25.0	24.9	0.0	35.2	18.8	bulk
6415782	SRR964796	SRP029464	SRS476319	SRX344339	SRA099825	GEO		Transcriptome modulation of ventricles, cardiomyocytes and cardiac fibroblasts during postnatal mouse development	During development the fetal heart undergoes a rapid and dramatic transition to adult function through transcriptional and post-transcriptional mechanisms, including alternative splicing (AS). We performed deep RNA-sequencing for high-resolution analysis of transcriptome changes during postnatal mouse heart development using RNA from ventricles and freshly isolated cardiomyocytes (CM) and cardiac fibroblasts (CF). Extensive changes in gene expression and AS occur primarily between postnatal days 1 and 28. CM and CF showed reciprocal regulation of gene expression during postnatal development reflecting differences in proliferative capacity, cell adhesion functions, and mitochondrial metabolism. We found that AS plays a novel role in vesicular trafficking and membrane organization during postnatal CM development. Interestingly, these AS transitions are enriched among targets of two RNA-binding proteins, Celf1 and Mbnl1, which undergo developmentally regulated change in expression. Vesicular traffic genes affected by AS during normal development where Celf1 is down-regulated, showed a reversion to neonatal AS patterns when Celf1 was over-expressed in adults. Overall design: RNA-seq was performed in RNA samples of ventricles, cardiomyocytes or cardiac fibroblast at different developmental stages; embryonic day 17, postnatal day (PN) 1, 10, 28 and 90 for ventricles, PN1-3, PN28 and PN60 for cardiac fibroblasts, and PN1-2, PN30, and PN67 for cardiomyocytes		GSM1223641: RNA-seq cardiac fibroblasts PN28; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			RNeasy fibrous tissue mini kit was used for ventricles and cardiomyocytes, and micro RNeasy kit for cardiac fibroblasts (all from Qiagen) Illumina TruSeq RNA protocols were used for cardiomyocytes and cardiac fibroblast. For developmental ventricle analysis, RNA was rRNA depleted with the Ribo-Zero Magnetic Gold Kit and libraries were prepared using ScriptSeq v2 RNA-seq library preparation kits (Epicentre).	Illumina HiSeq 2000	age;;PN28|genotype/variation;;wild type|source_name;;Cardiac fibroblasts|strain;;FVB|tissue;;Cardiac fibroblasts	GEO Accession;;GSM1223641		GSM1223641	RNA-seq cardiac fibroblasts PN28	39480464892	195447846	2014-04-16 15:55:08	27647865615	39480464892	195447846	2	195447846	index:0,count:195447846,average:101,stdev:0|index:1,count:195447846,average:101,stdev:0	GSM1223641_r1	GEO			in_mesa	24752171	2.18	2.61	0.31	29314587886	28034535425	26842078799	26275783058	95.63	97.89	182120803	169005187	190.235	629.856	145	1727860	83.17	90.93	214770344	151464546	214770344	151464546	85.13	87.84	214770344	155033270	214770344	146323273	1971879101	6.73	1.18	0	7.95	0	1.15	0	0.06	0	0.00	0	5.61	0	182120803	0	202	0	199.12	0	2.17	0	0.01	0	1.93	0	0.02	0	261.57	0	0.50	0	2306476	0	195447846	0	15544648	0	2256751	0	108730	0	0	0	10961562	0	38042	0	0	0	628077	0	83582147	0	199625	0	84447891	0	85.23	0	166576155	0	403126	74663891	185.212293426869	195447846.0	182120803.0	2306476.0	15544648.0	2256751.0	108730.0	0.0	10961562.0	166576155.0	93.2	1.2	8.0	1.2	0.1	0.0	5.6	85.2	101	101	101.00	38	19740232446	24.9	25.1	25.0	24.9	0.0	34.6	17.9	bulk
6415845	SRR964797	SRP029464	SRS476320	SRX344340	SRA099825	GEO		Transcriptome modulation of ventricles, cardiomyocytes and cardiac fibroblasts during postnatal mouse development	During development the fetal heart undergoes a rapid and dramatic transition to adult function through transcriptional and post-transcriptional mechanisms, including alternative splicing (AS). We performed deep RNA-sequencing for high-resolution analysis of transcriptome changes during postnatal mouse heart development using RNA from ventricles and freshly isolated cardiomyocytes (CM) and cardiac fibroblasts (CF). Extensive changes in gene expression and AS occur primarily between postnatal days 1 and 28. CM and CF showed reciprocal regulation of gene expression during postnatal development reflecting differences in proliferative capacity, cell adhesion functions, and mitochondrial metabolism. We found that AS plays a novel role in vesicular trafficking and membrane organization during postnatal CM development. Interestingly, these AS transitions are enriched among targets of two RNA-binding proteins, Celf1 and Mbnl1, which undergo developmentally regulated change in expression. Vesicular traffic genes affected by AS during normal development where Celf1 is down-regulated, showed a reversion to neonatal AS patterns when Celf1 was over-expressed in adults. Overall design: RNA-seq was performed in RNA samples of ventricles, cardiomyocytes or cardiac fibroblast at different developmental stages; embryonic day 17, postnatal day (PN) 1, 10, 28 and 90 for ventricles, PN1-3, PN28 and PN60 for cardiac fibroblasts, and PN1-2, PN30, and PN67 for cardiomyocytes		GSM1223642: RNA-seq cardiac fibroblasts PN1-3; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			RNeasy fibrous tissue mini kit was used for ventricles and cardiomyocytes, and micro RNeasy kit for cardiac fibroblasts (all from Qiagen) Illumina TruSeq RNA protocols were used for cardiomyocytes and cardiac fibroblast. For developmental ventricle analysis, RNA was rRNA depleted with the Ribo-Zero Magnetic Gold Kit and libraries were prepared using ScriptSeq v2 RNA-seq library preparation kits (Epicentre).	Illumina HiSeq 2000	age;;PN1|genotype/variation;;wild type|source_name;;Cardiac fibroblasts neonatal|strain;;FVB|tissue;;Cardiac fibroblasts	GEO Accession;;GSM1223642		GSM1223642	RNA-seq cardiac fibroblasts PN1-3	36486689350	180627175	2014-04-16 15:55:08	24765002861	36486689350	180627175	2	180627175	index:0,count:180627175,average:101,stdev:0|index:1,count:180627175,average:101,stdev:0	GSM1223642_r1	GEO			in_mesa	24752171	1.83	2.96	0.09	27466776816	27157442777	25628066687	25507586499	98.87	99.53	170554302	157061963	192.968	640.626	146	1582649	87.04	93.41	191262093	148442115	191262093	148442115	88.85	89.78	191262093	151529214	191262093	142672400	1462128746	5.32	1.14	0	6.44	0	0.39	0	0.06	0	0.00	0	5.12	0	170554302	0	202	0	199.21	0	2.16	0	0.01	0	1.96	0	0.02	0	293.70	0	0.39	0	2055081	0	180627175	0	11638014	0	713430	0	110180	0	0	0	9249263	0	47677	0	0	0	528847	0	86772222	0	157474	0	87506220	0	87.98	0	158916288	0	398607	77206788	193.691500651017	180627175.0	170554302.0	2055081.0	11638014.0	713430.0	110180.0	0.0	9249263.0	158916288.0	94.4	1.1	6.4	0.4	0.1	0.0	5.1	88.0	101	101	101.00	38	18243344675	24.6	25.4	25.3	24.6	0.0	35.2	18.8	bulk
6415972	SRR964799	SRP029464	SRS476322	SRX344342	SRA099825	GEO		Transcriptome modulation of ventricles, cardiomyocytes and cardiac fibroblasts during postnatal mouse development	During development the fetal heart undergoes a rapid and dramatic transition to adult function through transcriptional and post-transcriptional mechanisms, including alternative splicing (AS). We performed deep RNA-sequencing for high-resolution analysis of transcriptome changes during postnatal mouse heart development using RNA from ventricles and freshly isolated cardiomyocytes (CM) and cardiac fibroblasts (CF). Extensive changes in gene expression and AS occur primarily between postnatal days 1 and 28. CM and CF showed reciprocal regulation of gene expression during postnatal development reflecting differences in proliferative capacity, cell adhesion functions, and mitochondrial metabolism. We found that AS plays a novel role in vesicular trafficking and membrane organization during postnatal CM development. Interestingly, these AS transitions are enriched among targets of two RNA-binding proteins, Celf1 and Mbnl1, which undergo developmentally regulated change in expression. Vesicular traffic genes affected by AS during normal development where Celf1 is down-regulated, showed a reversion to neonatal AS patterns when Celf1 was over-expressed in adults. Overall design: RNA-seq was performed in RNA samples of ventricles, cardiomyocytes or cardiac fibroblast at different developmental stages; embryonic day 17, postnatal day (PN) 1, 10, 28 and 90 for ventricles, PN1-3, PN28 and PN60 for cardiac fibroblasts, and PN1-2, PN30, and PN67 for cardiomyocytes		GSM1223644: RNA-seq cardiomyocytes PN67 (adult); Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			RNeasy fibrous tissue mini kit was used for ventricles and cardiomyocytes, and micro RNeasy kit for cardiac fibroblasts (all from Qiagen) Illumina TruSeq RNA protocols were used for cardiomyocytes and cardiac fibroblast. For developmental ventricle analysis, RNA was rRNA depleted with the Ribo-Zero Magnetic Gold Kit and libraries were prepared using ScriptSeq v2 RNA-seq library preparation kits (Epicentre).	Illumina HiSeq 2000	age;;PN67 (adult)|genotype/variation;;wild type|source_name;;Cardiomyocytes|strain;;FVB|tissue;;Cardiomyocytes	GEO Accession;;GSM1223644		GSM1223644	RNA-seq cardiomyocytes PN67 (adult)	33117300666	163947033	2014-04-16 15:55:08	22016877940	33117300666	163947033	2	163947033	index:0,count:163947033,average:101,stdev:0|index:1,count:163947033,average:101,stdev:0	GSM1223644_r1	GEO			in_mesa	24752171	26.38	1.4	0.02	24834169274	24960471067	20612969107	20910285995	100.51	101.44	156208298	145842099	187.159	541.458	136	1516017	80.61	97.24	186664741	125917783	186664741	125917783	93.54	93.29	186664741	146110944	186664741	120803778	516997137	2.08	1.18	0	16.29	0	0.23	0	0.07	0	0.00	0	4.42	0	156208298	0	202	0	199.40	0	2.01	0	0.01	0	1.57	0	0.01	0	320.59	0	0.30	0	1940620	0	163947033	0	26711607	0	382012	0	117142	0	0	0	7239581	0	38649	0	0	0	456385	0	66994744	0	110169	0	67599947	0	78.99	0	129496691	0	278680	59160597	212.288635711210	163947033.0	156208298.0	1940620.0	26711607.0	382012.0	117142.0	0.0	7239581.0	129496691.0	95.3	1.2	16.3	0.2	0.1	0.0	4.4	79.0	101	101	101.00	38	16558650333	26.3	23.7	23.6	26.3	0.0	35.8	19.7	bulk
6422564	SRR964800	SRP029464	SRS476323	SRX344343	SRA099825	GEO		Transcriptome modulation of ventricles, cardiomyocytes and cardiac fibroblasts during postnatal mouse development	During development the fetal heart undergoes a rapid and dramatic transition to adult function through transcriptional and post-transcriptional mechanisms, including alternative splicing (AS). We performed deep RNA-sequencing for high-resolution analysis of transcriptome changes during postnatal mouse heart development using RNA from ventricles and freshly isolated cardiomyocytes (CM) and cardiac fibroblasts (CF). Extensive changes in gene expression and AS occur primarily between postnatal days 1 and 28. CM and CF showed reciprocal regulation of gene expression during postnatal development reflecting differences in proliferative capacity, cell adhesion functions, and mitochondrial metabolism. We found that AS plays a novel role in vesicular trafficking and membrane organization during postnatal CM development. Interestingly, these AS transitions are enriched among targets of two RNA-binding proteins, Celf1 and Mbnl1, which undergo developmentally regulated change in expression. Vesicular traffic genes affected by AS during normal development where Celf1 is down-regulated, showed a reversion to neonatal AS patterns when Celf1 was over-expressed in adults. Overall design: RNA-seq was performed in RNA samples of ventricles, cardiomyocytes or cardiac fibroblast at different developmental stages; embryonic day 17, postnatal day (PN) 1, 10, 28 and 90 for ventricles, PN1-3, PN28 and PN60 for cardiac fibroblasts, and PN1-2, PN30, and PN67 for cardiomyocytes		GSM1223645: RNA-seq cardiomyocytes PN30; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			RNeasy fibrous tissue mini kit was used for ventricles and cardiomyocytes, and micro RNeasy kit for cardiac fibroblasts (all from Qiagen) Illumina TruSeq RNA protocols were used for cardiomyocytes and cardiac fibroblast. For developmental ventricle analysis, RNA was rRNA depleted with the Ribo-Zero Magnetic Gold Kit and libraries were prepared using ScriptSeq v2 RNA-seq library preparation kits (Epicentre).	Illumina HiSeq 2000	age;;PN30|genotype/variation;;wild type|source_name;;Cardiomyocytes|strain;;FVB|tissue;;Cardiomyocytes	GEO Accession;;GSM1223645		GSM1223645	RNA-seq cardiomyocytes PN30	34716171874	171862237	2014-04-16 15:55:08	23389877007	34716171874	171862237	2	171862237	index:0,count:171862237,average:101,stdev:0|index:1,count:171862237,average:101,stdev:0	GSM1223645_r1	GEO			in_mesa	24752171	24.26	1.5	0.02	26694896988	26873146123	22524381342	22858283350	100.67	101.48	164093684	152062663	195.461	580.531	145	1490499	81.91	97.19	193638547	134408140	193638547	134408140	93.55	93.32	193638547	153506727	193638547	129055625	585110931	2.19	1.14	0	15.01	0	0.21	0	0.06	0	0.00	0	4.25	0	164093684	0	202	0	199.46	0	2.01	0	0.01	0	1.51	0	0.01	0	314.06	0	0.33	0	1957113	0	171862237	0	25803999	0	365955	0	104003	0	0	0	7298595	0	40590	0	0	0	496501	0	73564311	0	116349	0	74217751	0	80.47	0	138289685	0	281308	66313604	235.733089709500	171862237.0	164093684.0	1957113.0	25803999.0	365955.0	104003.0	0.0	7298595.0	138289685.0	95.5	1.1	15.0	0.2	0.1	0.0	4.2	80.5	101	101	101.00	38	17358085937	26.1	23.9	23.8	26.2	0.0	35.6	19.4	bulk
6422628	SRR964801	SRP029464	SRS476324	SRX344344	SRA099825	GEO		Transcriptome modulation of ventricles, cardiomyocytes and cardiac fibroblasts during postnatal mouse development	During development the fetal heart undergoes a rapid and dramatic transition to adult function through transcriptional and post-transcriptional mechanisms, including alternative splicing (AS). We performed deep RNA-sequencing for high-resolution analysis of transcriptome changes during postnatal mouse heart development using RNA from ventricles and freshly isolated cardiomyocytes (CM) and cardiac fibroblasts (CF). Extensive changes in gene expression and AS occur primarily between postnatal days 1 and 28. CM and CF showed reciprocal regulation of gene expression during postnatal development reflecting differences in proliferative capacity, cell adhesion functions, and mitochondrial metabolism. We found that AS plays a novel role in vesicular trafficking and membrane organization during postnatal CM development. Interestingly, these AS transitions are enriched among targets of two RNA-binding proteins, Celf1 and Mbnl1, which undergo developmentally regulated change in expression. Vesicular traffic genes affected by AS during normal development where Celf1 is down-regulated, showed a reversion to neonatal AS patterns when Celf1 was over-expressed in adults. Overall design: RNA-seq was performed in RNA samples of ventricles, cardiomyocytes or cardiac fibroblast at different developmental stages; embryonic day 17, postnatal day (PN) 1, 10, 28 and 90 for ventricles, PN1-3, PN28 and PN60 for cardiac fibroblasts, and PN1-2, PN30, and PN67 for cardiomyocytes		GSM1223646: RNA-seq cardiomyocytes PN1-2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			RNeasy fibrous tissue mini kit was used for ventricles and cardiomyocytes, and micro RNeasy kit for cardiac fibroblasts (all from Qiagen) Illumina TruSeq RNA protocols were used for cardiomyocytes and cardiac fibroblast. For developmental ventricle analysis, RNA was rRNA depleted with the Ribo-Zero Magnetic Gold Kit and libraries were prepared using ScriptSeq v2 RNA-seq library preparation kits (Epicentre).	Illumina HiSeq 2000	age;;PN1-2|genotype/variation;;wild type|source_name;;Cardiomyocytes neonatal|strain;;FVB|tissue;;Cardiomyocytes	GEO Accession;;GSM1223646		GSM1223646	RNA-seq cardiomyocytes PN1-2	38456078654	190376627	2014-04-16 15:55:08	26588370513	38456078654	190376627	2	190376627	index:0,count:190376627,average:101,stdev:0|index:1,count:190376627,average:101,stdev:0	GSM1223646_r1	GEO			in_mesa	24752171	26.11	1.7	0.04	29052755018	28980512230	22653801058	22805832417	99.75	100.67	181898191	172174751	185.239	491.130	134	1812432	74.89	96.18	234160897	136215156	234160897	136215156	93.46	92.79	234160897	170005086	234160897	131418881	828996249	2.85	1.05	0	21.15	0	0.28	0	0.05	0	0.00	0	4.13	0	181898191	0	202	0	199.53	0	2.02	0	0.01	0	1.51	0	0.01	0	307.47	0	0.40	0	1996762	0	190376627	0	40269319	0	524128	0	95563	0	0	0	7858745	0	38352	0	0	0	421733	0	62491268	0	125578	0	63076931	0	74.39	0	141628872	0	381541	63011260	165.149381062586	190376627.0	181898191.0	1996762.0	40269319.0	524128.0	95563.0	0.0	7858745.0	141628872.0	95.5	1.0	21.2	0.3	0.1	0.0	4.1	74.4	101	101	101.00	38	19228039327	26.5	23.5	23.5	26.5	0.0	35.2	18.9	bulk
6422691	SRR964802	SRP029464	SRS476325	SRX344345	SRA099825	GEO		Transcriptome modulation of ventricles, cardiomyocytes and cardiac fibroblasts during postnatal mouse development	During development the fetal heart undergoes a rapid and dramatic transition to adult function through transcriptional and post-transcriptional mechanisms, including alternative splicing (AS). We performed deep RNA-sequencing for high-resolution analysis of transcriptome changes during postnatal mouse heart development using RNA from ventricles and freshly isolated cardiomyocytes (CM) and cardiac fibroblasts (CF). Extensive changes in gene expression and AS occur primarily between postnatal days 1 and 28. CM and CF showed reciprocal regulation of gene expression during postnatal development reflecting differences in proliferative capacity, cell adhesion functions, and mitochondrial metabolism. We found that AS plays a novel role in vesicular trafficking and membrane organization during postnatal CM development. Interestingly, these AS transitions are enriched among targets of two RNA-binding proteins, Celf1 and Mbnl1, which undergo developmentally regulated change in expression. Vesicular traffic genes affected by AS during normal development where Celf1 is down-regulated, showed a reversion to neonatal AS patterns when Celf1 was over-expressed in adults. Overall design: RNA-seq was performed in RNA samples of ventricles, cardiomyocytes or cardiac fibroblast at different developmental stages; embryonic day 17, postnatal day (PN) 1, 10, 28 and 90 for ventricles, PN1-3, PN28 and PN60 for cardiac fibroblasts, and PN1-2, PN30, and PN67 for cardiomyocytes		GSM1223647: RNA-seq cardiomyocytes PN1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			RNeasy fibrous tissue mini kit was used for ventricles and cardiomyocytes, and micro RNeasy kit for cardiac fibroblasts (all from Qiagen) Illumina TruSeq RNA protocols were used for cardiomyocytes and cardiac fibroblast. For developmental ventricle analysis, RNA was rRNA depleted with the Ribo-Zero Magnetic Gold Kit and libraries were prepared using ScriptSeq v2 RNA-seq library preparation kits (Epicentre).	Illumina HiSeq 2000	age;;PN1|genotype/variation;;wild type|source_name;;Cardiomyocytes neonatal|strain;;FVB|tissue;;Cardiomyocytes	GEO Accession;;GSM1223647		GSM1223647	RNA-seq cardiomyocytes PN1	35946118362	177951081	2014-04-16 15:55:08	24443809144	35946118362	177951081	2	177951081	index:0,count:177951081,average:101,stdev:0|index:1,count:177951081,average:101,stdev:0	GSM1223647_r1	GEO			in_mesa	24752171	20.96	1.82	0.04	27489555280	27460927727	21989159418	22141051425	99.9	100.69	170190764	160284448	189.632	515.587	145	1641045	76.74	96.14	218401918	130612254	218401918	130612254	93.14	92.6	218401918	158512865	218401918	125802175	800826322	2.91	0.99	0	19.29	0	0.30	0	0.06	0	0.00	0	4.01	0	170190764	0	202	0	199.58	0	2.06	0	0.01	0	1.55	0	0.01	0	299.08	0	0.37	0	1768727	0	177951081	0	34329619	0	525635	0	98265	0	0	0	7136417	0	39923	0	0	0	431138	0	62582880	0	125750	0	63179691	0	76.35	0	135861145	0	375786	66248326	176.292693181758	177951081.0	170190764.0	1768727.0	34329619.0	525635.0	98265.0	0.0	7136417.0	135861145.0	95.6	1.0	19.3	0.3	0.1	0.0	4.0	76.3	101	101	101.00	38	17973059181	26.0	24.0	24.0	26.0	0.0	35.3	19.0	bulk
1405290	SRR1035716	SRP030031	SRS483726	SRX355536	SRA098368	UCSD	Yeo	Mus musculus Transcriptome or Gene expression	Whole mouse brain RNA-seq		Rbfox1 KO	Rbfox1 KO (sibling pair of Rbfox1 WT) dUTP RNAseq, whole brain	dUTP RNAseq	Rbfox1 KO	RNA-Seq	TRANSCRIPTOMIC	unspecified	single				Illumina HiSeq 2000	isolate;;Whole Brain|label;;Rbfox1 KO RNAseq|sample type;;hiseq 2000		101	Rbfox1 KO RNAseq	Rbfox1 KO RNAseq	22338480878	221173078	2014-01-02 20:52:07	14270058115	22338480878	221173078	1	221173078	index:0,count:221173078,average:101,stdev:0	Rbfox1KO	UCSD					5.72	3.24	0.06	16998139981	16702344355	15466636080	15392220588	98.26	99.52	0	0	0	0	0	0	81.59	89.67	194467730	138712347	194467730	138712347	83.22	84.46	194467730	141480951	194467730	130651389	1196711902	7.04	0.74	0	6.93	0	0.22	0	0.23	0	0.00	0	22.69	0	170002441	0	101	0	99.99	0	2.36	0	0.02	0	1.35	0	0.04	0	295.44	0	0.98	0	1636683	0	221173078	0	15318289	0	492467	0	502711	0	0	0	50175459	0	16978	0	0	0	194321	0	27939143	0	273012	0	28423454	0	69.94	0	154684152	0	307179	29945309	97.484883406743	221173078.0	170002441.0	1636683.0	15318289.0	492467.0	502711.0	0.0	50175459.0	154684152.0	76.9	0.7	6.9	0.2	0.2	0.0	22.7	69.9	101	101	101.00	38	22338480878	22.3	23.4	24.5	29.5	0.3	30.5	11.1	bulk
1405306	SRR1035717	SRP030031	SRS483727	SRX355537	SRA098368	UCSD	Yeo	Mus musculus Transcriptome or Gene expression	Whole mouse brain RNA-seq		Rbfox2 WT	Rbfox2 WT (sibling pair of Rbfox2 KO) dUTP RNAseq, whole brain	dUTP RNAseq	Rbfox2 WT	RNA-Seq	TRANSCRIPTOMIC	unspecified	single				Illumina HiSeq 2000	isolate;;Whole Brain|label;;Rbfox2 WT RNAseq|sample type;;hiseq 2000		101	Rbfox2 WT RNAseq	Rbfox2 WT RNAseq	21767874409	215523509	2014-01-02 22:00:06	13647939953	21767874409	215523509	1	215523509	index:0,count:215523509,average:101,stdev:0	Rbfox2 WT	UCSD					5.02	3.44	0.06	16340058874	16095622726	14989103707	14877575031	98.5	99.26	0	0	0	0	0	0	81.94	89.33	185834066	134982712	185834066	134982712	84.79	85.33	185834066	139676432	185834066	128935934	1325580364	8.11	0.87	0	6.32	0	0.23	0	0.36	0	0.00	0	22.97	0	164739517	0	101	0	99.19	0	2.16	0	0.02	0	1.10	0	0.08	0	297.73	0	1.01	0	1865450	0	215523509	0	13631561	0	499773	0	782227	0	0	0	49501992	0	17671	0	0	0	203628	0	28315218	0	377940	0	28914457	0	70.11	0	151107956	0	296448	30362613	102.421379128886	215523509.0	164739517.0	1865450.0	13631561.0	499773.0	782227.0	0.0	49501992.0	151107956.0	76.4	0.9	6.3	0.2	0.4	0.0	23.0	70.1	101	101	101.00	38	21767874409	22.6	23.0	24.5	29.6	0.4	29.9	10.6	bulk
1405322	SRR1035718	SRP030031	SRS483728	SRX355538	SRA098368	UCSD	Yeo	Mus musculus Transcriptome or Gene expression	Whole mouse brain RNA-seq		Rbfox2KO	Rbfox2 KO (sibling pair of Rbfox2 WT) dUTP RNAseq, whole brain	dUTP RNAseq	Rbfox2KO	RNA-Seq	TRANSCRIPTOMIC	unspecified	single				Illumina HiSeq 2000	isolate;;Whole Brain|label;;Rbfox2 KO RNAseq|sample type;;hiseq 2000		101	Rbfox2 KO RNAseq	Rbfox2 KO RNAseq	11623376839	115082939	2014-01-02 21:28:07	6880920924	11623376839	115082939	1	115082939	index:0,count:115082939,average:101,stdev:0	Rbfox2 KO	UCSD					4.5	3.36	0.06	8775547397	8668378398	8140470563	8093083494	98.78	99.42	0	0	0	0	0	0	83.78	90.32	98221273	73684643	98221273	73684643	85.68	86.15	98221273	75358540	98221273	70283899	639754756	7.29	0.85	0	5.53	0	0.25	0	0.33	0	0.00	0	23.00	0	87948399	0	101	0	99.79	0	2.19	0	0.02	0	1.28	0	0.05	0	290.94	0	0.75	0	979868	0	115082939	0	6369511	0	287731	0	375141	0	0	0	26471668	0	9990	0	0	0	117631	0	16631649	0	177121	0	16936391	0	70.89	0	81578888	0	228822	17755461	77.595078270446	115082939.0	87948399.0	979868.0	6369511.0	287731.0	375141.0	0.0	26471668.0	81578888.0	76.4	0.9	5.5	0.3	0.3	0.0	23.0	70.9	101	101	101.00	38	11623376839	21.6	23.5	25.0	29.7	0.3	32.8	12.5	bulk
5554353	SRR997302	SRP030031	SRS483725	SRX355535	SRA098368	UCSD	Yeo	Mus musculus Transcriptome or Gene expression	Whole mouse brain RNA-seq		Rbfox1 WT	Rbfox1 WT (sibling pair of Rbfox1 KO) dUTP RNAseq, whole brain	dUTP RNAseq	Rbfox1 WT	RNA-Seq	TRANSCRIPTOMIC	unspecified	single				Illumina HiSeq 2000	isolate;;Whole Brain|label;;Rbfox1 WT RNAseq|sample_type;;hiseq 2000		101	Rbfox1 WT RNAseq	Rbfox1 WT RNAseq	26637785147	263740447	2014-01-02 21:24:11	17280151046	26637785147	263740447	1	263740447	index:0,count:263740447,average:101,stdev:0	Rbfox1WT	UCSD					5.84	3.49	0.05	19226932122	18956929715	17595999133	17485705812	98.6	99.37	0	0	0	0	0	0	83.46	91.18	217885909	160839128	217885909	160839128	86.56	87.14	217885909	166827099	217885909	153705058	1240716829	6.45	0.52	0	6.19	0	0.21	0	0.23	0	0.00	0	26.49	0	192721880	0	101	0	99.76	0	2.15	0	0.01	0	1.26	0	0.04	0	430.21	0	1.34	0	1375173	0	263740447	0	16330825	0	543090	0	604796	0	0	0	69870681	0	19909	0	0	0	214240	0	33616418	0	450884	0	34301451	0	66.88	0	176391055	0	335771	36077060	107.445431559009	263740447.0	192721880.0	1375173.0	16330825.0	543090.0	604796.0	0.0	69870681.0	176391055.0	73.1	0.5	6.2	0.2	0.2	0.0	26.5	66.9	101	101	101.00	38	26637785147	21.4	22.7	24.3	30.7	0.9	27.2	9.5	bulk
1839256	SRR1945109	SRP033468	SRS886940	SRX971927	SRA249131	Beijing Proteome Research Center	Functional proteome	Mus musculus Transcriptome or Gene expression	Normal mouse liver transcriptome landscape		HC1		hepatocyte		RNA-Seq	TRANSCRIPTOMIC	PolyA	paired		0.0E0		Illumina HiSeq 2000	age;;8 weeks|BioSampleModel;;Model organism or animal|sample_type;;HC|sex;;male|strain;;C57-BL|tissue;;liver		180	HC1	hepatocyte	3546478980	19702662	2016-03-03 19:57:56	2469142362	3546478980	19702662	2	19702662	index:0,count:19702662,average:90,stdev:0|index:1,count:19702660,average:90,stdev:0	HC1	Beijing Proteome Research Center			in_mesa	27562671	11.83	0.93	0.05	3400618626	3402664336	3003502690	3026132024	100.06	100.75	19142936	17436535	219.182	508.537	187	409951	85.69	96.99	22575357	16403823	22575357	16403823	94.53	94.47	22575357	18096124	22575357	15976658	81311789	2.39	0.43	0.00	11.32	50.00	0.62	0.00	1.58	0.00	0.00	0.00	0.65	0.00	19142936	2	180	90	178.67	90.00	1.60	0.00	0.00	0.00	1.25	0.00	0.00	0.00	155.55	0.01	0.28	0.00	85130	0	19702660	2	2230877	1	121371	0	310353	0	0	0	128000	0	2553	0	0	0	51107	0	8756078	0	7384	0	8817122	0	85.84	50.00	16912059	1	127903	9955897	77.839433007826	19702662.0	19142938.0	85130.0	2230878.0	121371.0	310353.0	0.0	128000.0	16912060.0	97.2	0.4	11.3	0.6	1.6	0.0	0.6	85.8	90	90	90.00	10	180	31.7	17.2	24.4	26.7	0.0	38.4	36.2	bulk
461159	SRR1945259	SRP033468	SRS886942	SRX971928	SRA249131	Beijing Proteome Research Center	Functional proteome	Mus musculus Transcriptome or Gene expression	Normal mouse liver transcriptome landscape		LSEC1		liver sinusoidal endothelial cell		RNA-Seq	TRANSCRIPTOMIC	PolyA	paired		0.0E0		Illumina HiSeq 2000	age;;9 weeks|BioSampleModel;;Model organism or animal|sample_type;;LSEC|sex;;male|strain;;C57-BL|tissue;;liver		180	LSEC1	liver sinusoidal endothelial cell	3743672220	20798179	2017-01-22 00:00:00	2691849298	3743672220	20798179	2	20798179	index:0,count:20798179,average:90,stdev:0|index:1,count:20798179,average:90,stdev:0	LSEC1	Beijing Proteome Research Center			in_mesa	27562671	6.55	2.61	0.09	3545133370	3513748206	3311315415	3309580138	99.11	99.95	20458360	19154602	204.561	561.527	191	403140	85.8	91.88	22453824	17554087	22453824	17554087	88.25	88.62	22453824	18054222	22453824	16930637	241265062	6.81	1.62	0	6.50	0	0.30	0	0.10	0	0.00	0	1.23	0	20458360	0	180	0	178.43	0	1.54	0	0.00	0	1.24	0	0.00	0	367.03	0	0.27	0	336265	0	20798179	0	1352742	0	62556	0	20733	0	0	0	256530	0	4937	0	0	0	39409	0	7191060	0	12677	0	7248083	0	91.86	0	19105618	0	171961	7240804	42.107245247469	20798179.0	20458360.0	336265.0	1352742.0	62556.0	20733.0	0.0	256530.0	19105618.0	98.4	1.6	6.5	0.3	0.1	0.0	1.2	91.9	90	90	90.00	38	1871836110	25.4	23.8	24.8	26.0	0.0	35.4	21.5	bulk
921750	SRR1042212	SRP033468	SRS510481	SRX386467	SRA115139	Beijing Proteome Research Center	Functional proteome	Mus musculus Transcriptome or Gene expression	Normal mouse liver transcriptome landscape		Normal mouse liver tissue transcriptome				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired		0.0E0		Illumina HiSeq 2000	strain;;C57BL/6J		180	BPRC_mouse_liver_tissue	Normal mouse liver tissue	3371145480	18728586	2015-07-22 17:10:15	1985204879	3371145480	18728586	2	18728586	index:0,count:18728586,average:90,stdev:0|index:1,count:18728586,average:90,stdev:0	mouse liver tissue	Beijing Proteome Research Center			in_mesa	27562671	24.11	0.94	0.02	3150439464	3126306694	2718375884	2720781670	99.23	100.09	17846429	16541474	220.500	540.179	199	664942	82.55	95.66	21088445	14732158	21088445	14732158	93.88	93.45	21088445	16753783	21088445	14392392	106585013	3.38	4.54	0	13.06	0	0.37	0	0.36	0	0.00	0	3.98	0	17846429	0	180	0	176.97	0	1.43	0	0.00	0	1.28	0	0.00	0	140.76	0	0.42	0	849749	0	18728586	0	2445493	0	68391	0	67630	0	0	0	746136	0	1845	0	0	0	29351	0	6286705	0	11392	0	6329293	0	82.23	0	15400936	0	114392	6826417	59.675650395133	18728586.0	17846429.0	849749.0	2445493.0	68391.0	67630.0	0.0	746136.0	15400936.0	95.3	4.5	13.1	0.4	0.4	0.0	4.0	82.2	90	90	90.00	38	1685572740	26.6	22.7	24.1	26.7	0.0	35.0	16.9	bulk
922374	SRR1945260	SRP033468	SRS886943	SRX971929	SRA249131	Beijing Proteome Research Center	Functional proteome	Mus musculus Transcriptome or Gene expression	Normal mouse liver transcriptome landscape		KC1		kupffer		RNA-Seq	TRANSCRIPTOMIC	PolyA	paired		0.0E0		Illumina HiSeq 2000	age;;10 weeks|BioSampleModel;;Model organism or animal|sample_type;;KC|sex;;male|strain;;C57-BL|tissue;;liver		180	KC1	kupffer	3431500920	19063894	2017-01-22 00:00:00	2403057398	3431500920	19063894	2	19063894	index:0,count:19063894,average:90,stdev:0|index:1,count:19063894,average:90,stdev:0	KC1	Beijing Proteome Research Center			in_mesa	27562671	5.94	2.67	0.13	3327696625	3297811973	3083127740	3077971454	99.1	99.83	18819946	17921119	206.415	453.282	187	422519	85.04	91.78	20942515	16004509	20942515	16004509	88.08	88.32	20942515	16576311	20942515	15401118	219854534	6.61	0.50	0	7.25	0	0.38	0	0.08	0	0.00	0	0.82	0	18819946	0	180	0	178.73	0	1.56	0	0.00	0	1.19	0	0.00	0	313.38	0	0.33	0	94540	0	19063894	0	1382407	0	72329	0	15499	0	0	0	156120	0	6908	0	0	0	32274	0	6377755	0	9749	0	6426686	0	91.47	0	17437539	0	152603	6560202	42.988683053413	19063894.0	18819946.0	94540.0	1382407.0	72329.0	15499.0	0.0	156120.0	17437539.0	98.7	0.5	7.3	0.4	0.1	0.0	0.8	91.5	90	90	90.00	38	1715750460	24.5	24.4	26.6	24.4	0.0	35.2	19.4	bulk
922389	SRR1945262	SRP033468	SRS886980	SRX971930	SRA249131	Beijing Proteome Research Center	Functional proteome	Mus musculus Transcriptome or Gene expression	Normal mouse liver transcriptome landscape		HSC1		Hepatic stellate cell		RNA-Seq	TRANSCRIPTOMIC	PolyA	paired		0.0E0		Illumina HiSeq 2000	age;;11 weeks|BioSampleModel;;Model organism or animal|sample_type;;HSC|sex;;male|strain;;C57-BL|tissue;;liver		180	HSC1	Hepatic stellate cell	4671310320	25951724	2017-01-22 00:00:00	3221035082	4671310320	25951724	2	25951724	index:0,count:25951724,average:90,stdev:0|index:1,count:25951724,average:90,stdev:0	HSC1	Beijing Proteome Research Center			in_mesa	27562671	4.2	2.81	0.12	4317434643	4273626106	4060702830	4048141754	98.99	99.69	24444918	22082033	241.785	752.472	203	319359	84.85	90.22	26808532	20741437	26808532	20741437	86.79	87.2	26808532	21214582	26808532	20046502	369312339	8.55	4.04	0	5.61	0	0.27	0	0.12	0	0.00	0	5.41	0	24444918	0	180	0	177.65	0	1.50	0	0.00	0	1.19	0	0.00	0	167.73	0	0.23	0	1049541	0	25951724	0	1455848	0	70192	0	32300	0	0	0	1404314	0	7205	0	0	0	51135	0	8402953	0	18012	0	8479305	0	88.58	0	22989070	0	185193	8687364	46.909786007031	25951724.0	24444918.0	1049541.0	1455848.0	70192.0	32300.0	0.0	1404314.0	22989070.0	94.2	4.0	5.6	0.3	0.1	0.0	5.4	88.6	90	90	90.00	38	2335655160	25.8	23.5	25.3	25.4	0.0	35.7	21.3	bulk
655500	SRR1056011	SRP034660	SRS517822	SRX396841	SRA122184	GEO		The GYF domain protein CD2BP2 plays a crucial role in alternative splicing, embryonic development and podocyte integrity	The spliceosome is a multimolecular ribonucleoprotein complex, which catalyzes the removal of introns from pre-mRNA and extends the complexity of genetic information by defining alternative transcripts. Here we analyzed the in vivo function of CD2BP2, which is a marker of early spliceosomal complexes.   Using gene targeting in mice, we show that constitutive or mesoderm- specific ablation of the CD2BP2 gene causes embryonic lethality by E10.5 associated with delayed development, growth retardation and pericard effusion.   Transcriptome analysis in CD2BP2 deficient bone-marrow-derived macrophages (BMM) and podocytes revealed dramatic alterations in the alternative splicing pattern of several mRNAs including VEGFA. Consistent with a previously described critical role of specific VEGFA isoforms for podocyte integrity, mice, which specifically lack CD2BP2flox/flox in this cell type, develop progressive albuminuria followed by lethal kidney failure. We further identified the phosphatase PP1 as a GYF domain independent CD2BP2 interaction partner, suggesting that CD2BP2 acts as an important modulator for spliceosome dephosphorylation, thereby affecting alternative splicing of  physiologically highly relevant transcripts. Overall design: 3x KO vs 3x WT mus m.		GSM1295648: WT Control 1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Tissue was mixed with 700 μL Qiazol®. Samples were homogenized with 5 2.8 diameter ceramic beads for 20 sec, 5000 rpm in a homogenizer (SeqLab). After 5 min incubation at RT, samples were mixed with 140 μL chloroform, incubated for 3 min at RT and centrifuged at 12 000 x g, 15min at 4°C. Samples were transferred into fresh tubes, mixed with same volume of 70% Ethanol and transferred on RNeasy Mini columns (Qiagen). Columns were centrifuged for 15 sec at 8 000 x g at RT. Flow through was mixed with 350 μL RWI buffer and centrifuged.   For DNA depletion, samples were treated with 70 μL RDD-Buffer with 10 μL DNase and incubated for 15 min at RT. Columns were one time washed with 350 μL RWI-buffer and centrifuged for 20 sec at 8 600 x g at RT and again washed with 700 μL RPE buffer, centrifugation lasted 2 min at 8 600 x g. RNA was eluted by applying 30 μL RNase free water onto the column, one min incubation and centrifugation for one min with full speed at RT. RNA concentration was determined at the Nano Drop (peqlab).  Tissue was mixed with 700 μL Qiazol®. Samples were homogenized with 5 2.8 diameter ceramic beads for 20 sec, 5000 rpm in a homogenizer (SeqLab). After 5 min incubation at RT, samples were mixed with 140 μL chloroform, incubated for 3 min at RT and centrifuged at 12 000 x g, 15min at 4°C. Samples were transferred into fresh tubes, mixed with same volume of 70% Ethanol and transferred on RNeasy Mini columns (Qiagen). Columns were centrifuged for 15 sec at 8 000 x g at RT. Flow through was mixed with 350 μL RWI buffer and centrifuged.   For DNA depletion, samples were treated with 70 μL RDD-Buffer with 10 μL DNase and incubated for 15 min at RT. Columns were one time washed with 350 μL RWI-buffer and centrifuged for 20 sec at 8 600 x g at RT and again washed with 700 μL RPE buffer, centrifugation lasted 2 min at 8 600 x g. RNA was eluted by applying 30 μL RNase free water onto the column, one min incubation and centrifugation for one min with full speed at RT. RNA concentration was determined at the Nano Drop (peqlab). RNA quality was estimated (2100 Bioanalyzer, Agilent) and samples with a RIN > 8 were used as input material for the TruSeq RNA Sample Preparation Kit (Illumina). All cDNA fragments were derived from poly(A)+ RNA, subsequently barcoded and sequenced on a HiSeq 2000 instrument (Illumina) with 2 x 100 bp PE chemistry.	Illumina HiSeq 2000	cell type;;Podocytes|genetic background;;C57BL/6|genotype;;Wildtype|source_name;;Podocytes	GEO Accession;;GSM1295648		GSM1295648	WT Control 1	4468624608	22121904	2017-01-03 09:54:06	3342351692	4468624608	22121904	2	22121904	index:0,count:22121904,average:101,stdev:0|index:1,count:22121904,average:101,stdev:0	GSM1295648_r1	GEO			in_mesa	26082520	2.28	2.95	0.03	3721572644	3696865080	3569541921	3559039820	99.34	99.71	21612543	20126603	200.265	642.917	157	195290	84.13	87.76	23023793	18182833	23023793	18182833	84.41	84.62	23023793	18244041	23023793	17532859	421173250	11.32	1.03	0	4.04	0	0.17	0	0.07	0	0.00	0	2.07	0	21612543	0	202	0	199.94	0	1.80	0	0.01	0	1.44	0	0.01	0	262.83	0	0.49	0	227794	0	22121904	0	893649	0	37128	0	15204	0	0	0	457029	0	5576	0	0	0	54710	0	8954050	0	16682	0	9031018	0	93.66	0	20718894	0	200670	8420969	41.964264713211	22121904.0	21612543.0	227794.0	893649.0	37128.0	15204.0	0.0	457029.0	20718894.0	97.7	1.0	4.0	0.2	0.1	0.0	2.1	93.7	101	101	101.00	38	2234312304	25.6	24.4	24.2	25.8	0.0	33.0	15.9	bulk
655508	SRR1056012	SRP034660	SRS517822	SRX396841	SRA122184	GEO		The GYF domain protein CD2BP2 plays a crucial role in alternative splicing, embryonic development and podocyte integrity	The spliceosome is a multimolecular ribonucleoprotein complex, which catalyzes the removal of introns from pre-mRNA and extends the complexity of genetic information by defining alternative transcripts. Here we analyzed the in vivo function of CD2BP2, which is a marker of early spliceosomal complexes.   Using gene targeting in mice, we show that constitutive or mesoderm- specific ablation of the CD2BP2 gene causes embryonic lethality by E10.5 associated with delayed development, growth retardation and pericard effusion.   Transcriptome analysis in CD2BP2 deficient bone-marrow-derived macrophages (BMM) and podocytes revealed dramatic alterations in the alternative splicing pattern of several mRNAs including VEGFA. Consistent with a previously described critical role of specific VEGFA isoforms for podocyte integrity, mice, which specifically lack CD2BP2flox/flox in this cell type, develop progressive albuminuria followed by lethal kidney failure. We further identified the phosphatase PP1 as a GYF domain independent CD2BP2 interaction partner, suggesting that CD2BP2 acts as an important modulator for spliceosome dephosphorylation, thereby affecting alternative splicing of  physiologically highly relevant transcripts. Overall design: 3x KO vs 3x WT mus m.		GSM1295648: WT Control 1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Tissue was mixed with 700 μL Qiazol®. Samples were homogenized with 5 2.8 diameter ceramic beads for 20 sec, 5000 rpm in a homogenizer (SeqLab). After 5 min incubation at RT, samples were mixed with 140 μL chloroform, incubated for 3 min at RT and centrifuged at 12 000 x g, 15min at 4°C. Samples were transferred into fresh tubes, mixed with same volume of 70% Ethanol and transferred on RNeasy Mini columns (Qiagen). Columns were centrifuged for 15 sec at 8 000 x g at RT. Flow through was mixed with 350 μL RWI buffer and centrifuged.   For DNA depletion, samples were treated with 70 μL RDD-Buffer with 10 μL DNase and incubated for 15 min at RT. Columns were one time washed with 350 μL RWI-buffer and centrifuged for 20 sec at 8 600 x g at RT and again washed with 700 μL RPE buffer, centrifugation lasted 2 min at 8 600 x g. RNA was eluted by applying 30 μL RNase free water onto the column, one min incubation and centrifugation for one min with full speed at RT. RNA concentration was determined at the Nano Drop (peqlab).  Tissue was mixed with 700 μL Qiazol®. Samples were homogenized with 5 2.8 diameter ceramic beads for 20 sec, 5000 rpm in a homogenizer (SeqLab). After 5 min incubation at RT, samples were mixed with 140 μL chloroform, incubated for 3 min at RT and centrifuged at 12 000 x g, 15min at 4°C. Samples were transferred into fresh tubes, mixed with same volume of 70% Ethanol and transferred on RNeasy Mini columns (Qiagen). Columns were centrifuged for 15 sec at 8 000 x g at RT. Flow through was mixed with 350 μL RWI buffer and centrifuged.   For DNA depletion, samples were treated with 70 μL RDD-Buffer with 10 μL DNase and incubated for 15 min at RT. Columns were one time washed with 350 μL RWI-buffer and centrifuged for 20 sec at 8 600 x g at RT and again washed with 700 μL RPE buffer, centrifugation lasted 2 min at 8 600 x g. RNA was eluted by applying 30 μL RNase free water onto the column, one min incubation and centrifugation for one min with full speed at RT. RNA concentration was determined at the Nano Drop (peqlab). RNA quality was estimated (2100 Bioanalyzer, Agilent) and samples with a RIN > 8 were used as input material for the TruSeq RNA Sample Preparation Kit (Illumina). All cDNA fragments were derived from poly(A)+ RNA, subsequently barcoded and sequenced on a HiSeq 2000 instrument (Illumina) with 2 x 100 bp PE chemistry.	Illumina HiSeq 2000	cell type;;Podocytes|genetic background;;C57BL/6|genotype;;Wildtype|source_name;;Podocytes	GEO Accession;;GSM1295648		GSM1295648	WT Control 1	4322265508	21397354	2017-01-03 09:54:06	3253555937	4322265508	21397354	2	21397354	index:0,count:21397354,average:101,stdev:0|index:1,count:21397354,average:101,stdev:0	GSM1295648_r2	GEO			in_mesa	26082520	2.31	2.98	0.03	3588991320	3563836629	3441593706	3430330596	99.3	99.67	20872717	19447288	199.750	639.554	158	188370	84.03	87.68	22242965	17540379	22242965	17540379	84.35	84.56	22242965	17606161	22242965	16916076	408684241	11.39	1.01	0	4.05	0	0.17	0	0.07	0	0.00	0	2.22	0	20872717	0	202	0	199.71	0	1.81	0	0.01	0	1.44	0	0.01	0	216.38	0	0.52	0	215074	0	21397354	0	867240	0	35469	0	14193	0	0	0	474975	0	5404	0	0	0	52499	0	8513276	0	16007	0	8587186	0	93.50	0	20005477	0	198499	8007183	40.338656617917	21397354.0	20872717.0	215074.0	867240.0	35469.0	14193.0	0.0	474975.0	20005477.0	97.5	1.0	4.1	0.2	0.1	0.0	2.2	93.5	101	101	101.00	38	2161132754	25.7	24.3	24.1	25.9	0.0	32.8	15.8	bulk
655516	SRR1056013	SRP034660	SRS517822	SRX396841	SRA122184	GEO		The GYF domain protein CD2BP2 plays a crucial role in alternative splicing, embryonic development and podocyte integrity	The spliceosome is a multimolecular ribonucleoprotein complex, which catalyzes the removal of introns from pre-mRNA and extends the complexity of genetic information by defining alternative transcripts. Here we analyzed the in vivo function of CD2BP2, which is a marker of early spliceosomal complexes.   Using gene targeting in mice, we show that constitutive or mesoderm- specific ablation of the CD2BP2 gene causes embryonic lethality by E10.5 associated with delayed development, growth retardation and pericard effusion.   Transcriptome analysis in CD2BP2 deficient bone-marrow-derived macrophages (BMM) and podocytes revealed dramatic alterations in the alternative splicing pattern of several mRNAs including VEGFA. Consistent with a previously described critical role of specific VEGFA isoforms for podocyte integrity, mice, which specifically lack CD2BP2flox/flox in this cell type, develop progressive albuminuria followed by lethal kidney failure. We further identified the phosphatase PP1 as a GYF domain independent CD2BP2 interaction partner, suggesting that CD2BP2 acts as an important modulator for spliceosome dephosphorylation, thereby affecting alternative splicing of  physiologically highly relevant transcripts. Overall design: 3x KO vs 3x WT mus m.		GSM1295648: WT Control 1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Tissue was mixed with 700 μL Qiazol®. Samples were homogenized with 5 2.8 diameter ceramic beads for 20 sec, 5000 rpm in a homogenizer (SeqLab). After 5 min incubation at RT, samples were mixed with 140 μL chloroform, incubated for 3 min at RT and centrifuged at 12 000 x g, 15min at 4°C. Samples were transferred into fresh tubes, mixed with same volume of 70% Ethanol and transferred on RNeasy Mini columns (Qiagen). Columns were centrifuged for 15 sec at 8 000 x g at RT. Flow through was mixed with 350 μL RWI buffer and centrifuged.   For DNA depletion, samples were treated with 70 μL RDD-Buffer with 10 μL DNase and incubated for 15 min at RT. Columns were one time washed with 350 μL RWI-buffer and centrifuged for 20 sec at 8 600 x g at RT and again washed with 700 μL RPE buffer, centrifugation lasted 2 min at 8 600 x g. RNA was eluted by applying 30 μL RNase free water onto the column, one min incubation and centrifugation for one min with full speed at RT. RNA concentration was determined at the Nano Drop (peqlab).  Tissue was mixed with 700 μL Qiazol®. Samples were homogenized with 5 2.8 diameter ceramic beads for 20 sec, 5000 rpm in a homogenizer (SeqLab). After 5 min incubation at RT, samples were mixed with 140 μL chloroform, incubated for 3 min at RT and centrifuged at 12 000 x g, 15min at 4°C. Samples were transferred into fresh tubes, mixed with same volume of 70% Ethanol and transferred on RNeasy Mini columns (Qiagen). Columns were centrifuged for 15 sec at 8 000 x g at RT. Flow through was mixed with 350 μL RWI buffer and centrifuged.   For DNA depletion, samples were treated with 70 μL RDD-Buffer with 10 μL DNase and incubated for 15 min at RT. Columns were one time washed with 350 μL RWI-buffer and centrifuged for 20 sec at 8 600 x g at RT and again washed with 700 μL RPE buffer, centrifugation lasted 2 min at 8 600 x g. RNA was eluted by applying 30 μL RNase free water onto the column, one min incubation and centrifugation for one min with full speed at RT. RNA concentration was determined at the Nano Drop (peqlab). RNA quality was estimated (2100 Bioanalyzer, Agilent) and samples with a RIN > 8 were used as input material for the TruSeq RNA Sample Preparation Kit (Illumina). All cDNA fragments were derived from poly(A)+ RNA, subsequently barcoded and sequenced on a HiSeq 2000 instrument (Illumina) with 2 x 100 bp PE chemistry.	Illumina HiSeq 2000	cell type;;Podocytes|genetic background;;C57BL/6|genotype;;Wildtype|source_name;;Podocytes	GEO Accession;;GSM1295648		GSM1295648	WT Control 1	4344784872	21508836	2017-01-03 09:54:06	3269810243	4344784872	21508836	2	21508836	index:0,count:21508836,average:101,stdev:0|index:1,count:21508836,average:101,stdev:0	GSM1295648_r3	GEO			in_mesa	26082520	2.33	2.97	0.03	3616218727	3591016782	3467344991	3456199301	99.3	99.68	21005464	19569056	200.039	639.258	157	190330	84.02	87.68	22384842	17649808	22384842	17649808	84.35	84.55	22384842	17718137	22384842	17021327	412069140	11.40	1.03	0	4.07	0	0.16	0	0.07	0	0.00	0	2.11	0	21005464	0	202	0	199.88	0	1.80	0	0.01	0	1.45	0	0.01	0	212.72	0	0.52	0	221304	0	21508836	0	874818	0	35342	0	14317	0	0	0	453713	0	5380	0	0	0	52864	0	8614416	0	16373	0	8689033	0	93.59	0	20130646	0	198746	8099185	40.751436506898	21508836.0	21005464.0	221304.0	874818.0	35342.0	14317.0	0.0	453713.0	20130646.0	97.7	1.0	4.1	0.2	0.1	0.0	2.1	93.6	101	101	101.00	38	2172392436	25.7	24.3	24.1	25.9	0.0	32.9	15.9	bulk
655524	SRR1056014	SRP034660	SRS517822	SRX396841	SRA122184	GEO		The GYF domain protein CD2BP2 plays a crucial role in alternative splicing, embryonic development and podocyte integrity	The spliceosome is a multimolecular ribonucleoprotein complex, which catalyzes the removal of introns from pre-mRNA and extends the complexity of genetic information by defining alternative transcripts. Here we analyzed the in vivo function of CD2BP2, which is a marker of early spliceosomal complexes.   Using gene targeting in mice, we show that constitutive or mesoderm- specific ablation of the CD2BP2 gene causes embryonic lethality by E10.5 associated with delayed development, growth retardation and pericard effusion.   Transcriptome analysis in CD2BP2 deficient bone-marrow-derived macrophages (BMM) and podocytes revealed dramatic alterations in the alternative splicing pattern of several mRNAs including VEGFA. Consistent with a previously described critical role of specific VEGFA isoforms for podocyte integrity, mice, which specifically lack CD2BP2flox/flox in this cell type, develop progressive albuminuria followed by lethal kidney failure. We further identified the phosphatase PP1 as a GYF domain independent CD2BP2 interaction partner, suggesting that CD2BP2 acts as an important modulator for spliceosome dephosphorylation, thereby affecting alternative splicing of  physiologically highly relevant transcripts. Overall design: 3x KO vs 3x WT mus m.		GSM1295648: WT Control 1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Tissue was mixed with 700 μL Qiazol®. Samples were homogenized with 5 2.8 diameter ceramic beads for 20 sec, 5000 rpm in a homogenizer (SeqLab). After 5 min incubation at RT, samples were mixed with 140 μL chloroform, incubated for 3 min at RT and centrifuged at 12 000 x g, 15min at 4°C. Samples were transferred into fresh tubes, mixed with same volume of 70% Ethanol and transferred on RNeasy Mini columns (Qiagen). Columns were centrifuged for 15 sec at 8 000 x g at RT. Flow through was mixed with 350 μL RWI buffer and centrifuged.   For DNA depletion, samples were treated with 70 μL RDD-Buffer with 10 μL DNase and incubated for 15 min at RT. Columns were one time washed with 350 μL RWI-buffer and centrifuged for 20 sec at 8 600 x g at RT and again washed with 700 μL RPE buffer, centrifugation lasted 2 min at 8 600 x g. RNA was eluted by applying 30 μL RNase free water onto the column, one min incubation and centrifugation for one min with full speed at RT. RNA concentration was determined at the Nano Drop (peqlab).  Tissue was mixed with 700 μL Qiazol®. Samples were homogenized with 5 2.8 diameter ceramic beads for 20 sec, 5000 rpm in a homogenizer (SeqLab). After 5 min incubation at RT, samples were mixed with 140 μL chloroform, incubated for 3 min at RT and centrifuged at 12 000 x g, 15min at 4°C. Samples were transferred into fresh tubes, mixed with same volume of 70% Ethanol and transferred on RNeasy Mini columns (Qiagen). Columns were centrifuged for 15 sec at 8 000 x g at RT. Flow through was mixed with 350 μL RWI buffer and centrifuged.   For DNA depletion, samples were treated with 70 μL RDD-Buffer with 10 μL DNase and incubated for 15 min at RT. Columns were one time washed with 350 μL RWI-buffer and centrifuged for 20 sec at 8 600 x g at RT and again washed with 700 μL RPE buffer, centrifugation lasted 2 min at 8 600 x g. RNA was eluted by applying 30 μL RNase free water onto the column, one min incubation and centrifugation for one min with full speed at RT. RNA concentration was determined at the Nano Drop (peqlab). RNA quality was estimated (2100 Bioanalyzer, Agilent) and samples with a RIN > 8 were used as input material for the TruSeq RNA Sample Preparation Kit (Illumina). All cDNA fragments were derived from poly(A)+ RNA, subsequently barcoded and sequenced on a HiSeq 2000 instrument (Illumina) with 2 x 100 bp PE chemistry.	Illumina HiSeq 2000	cell type;;Podocytes|genetic background;;C57BL/6|genotype;;Wildtype|source_name;;Podocytes	GEO Accession;;GSM1295648		GSM1295648	WT Control 1	4489870564	22227082	2017-01-03 09:54:06	3357532911	4489870564	22227082	2	22227082	index:0,count:22227082,average:101,stdev:0|index:1,count:22227082,average:101,stdev:0	GSM1295648_r4	GEO			in_mesa	26082520	2.29	2.96	0.03	3741955939	3716766649	3589009616	3578143762	99.33	99.7	21718475	20220866	200.485	643.390	157	195511	84.11	87.74	23137740	18266519	23137740	18266519	84.4	84.61	23137740	18330826	23137740	17615529	424329281	11.34	1.06	0	4.04	0	0.17	0	0.07	0	0.00	0	2.05	0	21718475	0	202	0	199.94	0	1.81	0	0.01	0	1.45	0	0.01	0	208.92	0	0.48	0	235869	0	22227082	0	898391	0	36892	0	15482	0	0	0	456233	0	5637	0	0	0	56158	0	9005968	0	16863	0	9084626	0	93.67	0	20820084	0	201169	8466820	42.088095084233	22227082.0	21718475.0	235869.0	898391.0	36892.0	15482.0	0.0	456233.0	20820084.0	97.7	1.1	4.0	0.2	0.1	0.0	2.1	93.7	101	101	101.00	38	2244935282	25.6	24.4	24.1	25.9	0.0	33.3	16.4	bulk
655533	SRR1056015	SRP034660	SRS517821	SRX396842	SRA122184	GEO		The GYF domain protein CD2BP2 plays a crucial role in alternative splicing, embryonic development and podocyte integrity	The spliceosome is a multimolecular ribonucleoprotein complex, which catalyzes the removal of introns from pre-mRNA and extends the complexity of genetic information by defining alternative transcripts. Here we analyzed the in vivo function of CD2BP2, which is a marker of early spliceosomal complexes.   Using gene targeting in mice, we show that constitutive or mesoderm- specific ablation of the CD2BP2 gene causes embryonic lethality by E10.5 associated with delayed development, growth retardation and pericard effusion.   Transcriptome analysis in CD2BP2 deficient bone-marrow-derived macrophages (BMM) and podocytes revealed dramatic alterations in the alternative splicing pattern of several mRNAs including VEGFA. Consistent with a previously described critical role of specific VEGFA isoforms for podocyte integrity, mice, which specifically lack CD2BP2flox/flox in this cell type, develop progressive albuminuria followed by lethal kidney failure. We further identified the phosphatase PP1 as a GYF domain independent CD2BP2 interaction partner, suggesting that CD2BP2 acts as an important modulator for spliceosome dephosphorylation, thereby affecting alternative splicing of  physiologically highly relevant transcripts. Overall design: 3x KO vs 3x WT mus m.		GSM1295649: WT Control 2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Tissue was mixed with 700 μL Qiazol®. Samples were homogenized with 5 2.8 diameter ceramic beads for 20 sec, 5000 rpm in a homogenizer (SeqLab). After 5 min incubation at RT, samples were mixed with 140 μL chloroform, incubated for 3 min at RT and centrifuged at 12 000 x g, 15min at 4°C. Samples were transferred into fresh tubes, mixed with same volume of 70% Ethanol and transferred on RNeasy Mini columns (Qiagen). Columns were centrifuged for 15 sec at 8 000 x g at RT. Flow through was mixed with 350 μL RWI buffer and centrifuged.   For DNA depletion, samples were treated with 70 μL RDD-Buffer with 10 μL DNase and incubated for 15 min at RT. Columns were one time washed with 350 μL RWI-buffer and centrifuged for 20 sec at 8 600 x g at RT and again washed with 700 μL RPE buffer, centrifugation lasted 2 min at 8 600 x g. RNA was eluted by applying 30 μL RNase free water onto the column, one min incubation and centrifugation for one min with full speed at RT. RNA concentration was determined at the Nano Drop (peqlab).  Tissue was mixed with 700 μL Qiazol®. Samples were homogenized with 5 2.8 diameter ceramic beads for 20 sec, 5000 rpm in a homogenizer (SeqLab). After 5 min incubation at RT, samples were mixed with 140 μL chloroform, incubated for 3 min at RT and centrifuged at 12 000 x g, 15min at 4°C. Samples were transferred into fresh tubes, mixed with same volume of 70% Ethanol and transferred on RNeasy Mini columns (Qiagen). Columns were centrifuged for 15 sec at 8 000 x g at RT. Flow through was mixed with 350 μL RWI buffer and centrifuged.   For DNA depletion, samples were treated with 70 μL RDD-Buffer with 10 μL DNase and incubated for 15 min at RT. Columns were one time washed with 350 μL RWI-buffer and centrifuged for 20 sec at 8 600 x g at RT and again washed with 700 μL RPE buffer, centrifugation lasted 2 min at 8 600 x g. RNA was eluted by applying 30 μL RNase free water onto the column, one min incubation and centrifugation for one min with full speed at RT. RNA concentration was determined at the Nano Drop (peqlab). RNA quality was estimated (2100 Bioanalyzer, Agilent) and samples with a RIN > 8 were used as input material for the TruSeq RNA Sample Preparation Kit (Illumina). All cDNA fragments were derived from poly(A)+ RNA, subsequently barcoded and sequenced on a HiSeq 2000 instrument (Illumina) with 2 x 100 bp PE chemistry.	Illumina HiSeq 2000	cell type;;Podocytes|genetic background;;C57BL/6|genotype;;Wildtype|source_name;;Podocytes	GEO Accession;;GSM1295649		GSM1295649	WT Control 2	4320818582	21390191	2017-01-03 09:54:06	3249085576	4320818582	21390191	2	21390191	index:0,count:21390191,average:101,stdev:0|index:1,count:21390191,average:101,stdev:0	GSM1295649_r1	GEO			in_mesa	26082520	2.13	2.9	0.03	3615251796	3596417207	3466694913	3462410463	99.48	99.88	20889032	19417545	202.530	656.241	158	185892	85.27	88.96	22286228	17812111	22286228	17812111	85.49	85.77	22286228	17857081	22286228	17172274	369947895	10.23	1.02	0	4.06	0	0.22	0	0.06	0	0.00	0	2.07	0	20889032	0	202	0	199.86	0	1.76	0	0.01	0	1.44	0	0.01	0	202.64	0	0.52	0	217944	0	21390191	0	867531	0	46307	0	12911	0	0	0	441941	0	5657	0	0	0	53990	0	8781209	0	16002	0	8856858	0	93.60	0	20021501	0	200561	8300266	41.385244389487	21390191.0	20889032.0	217944.0	867531.0	46307.0	12911.0	0.0	441941.0	20021501.0	97.7	1.0	4.1	0.2	0.1	0.0	2.1	93.6	101	101	101.00	38	2160409291	25.4	24.6	24.5	25.5	0.0	32.6	15.4	bulk
655540	SRR1056016	SRP034660	SRS517821	SRX396842	SRA122184	GEO		The GYF domain protein CD2BP2 plays a crucial role in alternative splicing, embryonic development and podocyte integrity	The spliceosome is a multimolecular ribonucleoprotein complex, which catalyzes the removal of introns from pre-mRNA and extends the complexity of genetic information by defining alternative transcripts. Here we analyzed the in vivo function of CD2BP2, which is a marker of early spliceosomal complexes.   Using gene targeting in mice, we show that constitutive or mesoderm- specific ablation of the CD2BP2 gene causes embryonic lethality by E10.5 associated with delayed development, growth retardation and pericard effusion.   Transcriptome analysis in CD2BP2 deficient bone-marrow-derived macrophages (BMM) and podocytes revealed dramatic alterations in the alternative splicing pattern of several mRNAs including VEGFA. Consistent with a previously described critical role of specific VEGFA isoforms for podocyte integrity, mice, which specifically lack CD2BP2flox/flox in this cell type, develop progressive albuminuria followed by lethal kidney failure. We further identified the phosphatase PP1 as a GYF domain independent CD2BP2 interaction partner, suggesting that CD2BP2 acts as an important modulator for spliceosome dephosphorylation, thereby affecting alternative splicing of  physiologically highly relevant transcripts. Overall design: 3x KO vs 3x WT mus m.		GSM1295649: WT Control 2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Tissue was mixed with 700 μL Qiazol®. Samples were homogenized with 5 2.8 diameter ceramic beads for 20 sec, 5000 rpm in a homogenizer (SeqLab). After 5 min incubation at RT, samples were mixed with 140 μL chloroform, incubated for 3 min at RT and centrifuged at 12 000 x g, 15min at 4°C. Samples were transferred into fresh tubes, mixed with same volume of 70% Ethanol and transferred on RNeasy Mini columns (Qiagen). Columns were centrifuged for 15 sec at 8 000 x g at RT. Flow through was mixed with 350 μL RWI buffer and centrifuged.   For DNA depletion, samples were treated with 70 μL RDD-Buffer with 10 μL DNase and incubated for 15 min at RT. Columns were one time washed with 350 μL RWI-buffer and centrifuged for 20 sec at 8 600 x g at RT and again washed with 700 μL RPE buffer, centrifugation lasted 2 min at 8 600 x g. RNA was eluted by applying 30 μL RNase free water onto the column, one min incubation and centrifugation for one min with full speed at RT. RNA concentration was determined at the Nano Drop (peqlab).  Tissue was mixed with 700 μL Qiazol®. Samples were homogenized with 5 2.8 diameter ceramic beads for 20 sec, 5000 rpm in a homogenizer (SeqLab). After 5 min incubation at RT, samples were mixed with 140 μL chloroform, incubated for 3 min at RT and centrifuged at 12 000 x g, 15min at 4°C. Samples were transferred into fresh tubes, mixed with same volume of 70% Ethanol and transferred on RNeasy Mini columns (Qiagen). Columns were centrifuged for 15 sec at 8 000 x g at RT. Flow through was mixed with 350 μL RWI buffer and centrifuged.   For DNA depletion, samples were treated with 70 μL RDD-Buffer with 10 μL DNase and incubated for 15 min at RT. Columns were one time washed with 350 μL RWI-buffer and centrifuged for 20 sec at 8 600 x g at RT and again washed with 700 μL RPE buffer, centrifugation lasted 2 min at 8 600 x g. RNA was eluted by applying 30 μL RNase free water onto the column, one min incubation and centrifugation for one min with full speed at RT. RNA concentration was determined at the Nano Drop (peqlab). RNA quality was estimated (2100 Bioanalyzer, Agilent) and samples with a RIN > 8 were used as input material for the TruSeq RNA Sample Preparation Kit (Illumina). All cDNA fragments were derived from poly(A)+ RNA, subsequently barcoded and sequenced on a HiSeq 2000 instrument (Illumina) with 2 x 100 bp PE chemistry.	Illumina HiSeq 2000	cell type;;Podocytes|genetic background;;C57BL/6|genotype;;Wildtype|source_name;;Podocytes	GEO Accession;;GSM1295649		GSM1295649	WT Control 2	4190954196	20747298	2017-01-03 09:54:06	3169135397	4190954196	20747298	2	20747298	index:0,count:20747298,average:101,stdev:0|index:1,count:20747298,average:101,stdev:0	GSM1295649_r2	GEO			in_mesa	26082520	2.15	2.91	0.03	3495538221	3476531077	3351315427	3346543171	99.46	99.86	20229593	18814718	201.976	652.558	166	179865	85.21	88.91	21588048	17236860	21588048	17236860	85.45	85.73	21588048	17286335	21588048	16620579	359486279	10.28	0.99	0	4.07	0	0.21	0	0.06	0	0.00	0	2.22	0	20229593	0	202	0	199.64	0	1.75	0	0.01	0	1.43	0	0.01	0	132.66	0	0.56	0	205252	0	20747298	0	843540	0	44266	0	12582	0	0	0	460857	0	5321	0	0	0	51539	0	8387250	0	15436	0	8459546	0	93.44	0	19386053	0	198264	7922537	39.959533752976	20747298.0	20229593.0	205252.0	843540.0	44266.0	12582.0	0.0	460857.0	19386053.0	97.5	1.0	4.1	0.2	0.1	0.0	2.2	93.4	101	101	101.00	38	2095477098	25.4	24.6	24.4	25.5	0.0	32.5	15.3	bulk
655548	SRR1056017	SRP034660	SRS517821	SRX396842	SRA122184	GEO		The GYF domain protein CD2BP2 plays a crucial role in alternative splicing, embryonic development and podocyte integrity	The spliceosome is a multimolecular ribonucleoprotein complex, which catalyzes the removal of introns from pre-mRNA and extends the complexity of genetic information by defining alternative transcripts. Here we analyzed the in vivo function of CD2BP2, which is a marker of early spliceosomal complexes.   Using gene targeting in mice, we show that constitutive or mesoderm- specific ablation of the CD2BP2 gene causes embryonic lethality by E10.5 associated with delayed development, growth retardation and pericard effusion.   Transcriptome analysis in CD2BP2 deficient bone-marrow-derived macrophages (BMM) and podocytes revealed dramatic alterations in the alternative splicing pattern of several mRNAs including VEGFA. Consistent with a previously described critical role of specific VEGFA isoforms for podocyte integrity, mice, which specifically lack CD2BP2flox/flox in this cell type, develop progressive albuminuria followed by lethal kidney failure. We further identified the phosphatase PP1 as a GYF domain independent CD2BP2 interaction partner, suggesting that CD2BP2 acts as an important modulator for spliceosome dephosphorylation, thereby affecting alternative splicing of  physiologically highly relevant transcripts. Overall design: 3x KO vs 3x WT mus m.		GSM1295649: WT Control 2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Tissue was mixed with 700 μL Qiazol®. Samples were homogenized with 5 2.8 diameter ceramic beads for 20 sec, 5000 rpm in a homogenizer (SeqLab). After 5 min incubation at RT, samples were mixed with 140 μL chloroform, incubated for 3 min at RT and centrifuged at 12 000 x g, 15min at 4°C. Samples were transferred into fresh tubes, mixed with same volume of 70% Ethanol and transferred on RNeasy Mini columns (Qiagen). Columns were centrifuged for 15 sec at 8 000 x g at RT. Flow through was mixed with 350 μL RWI buffer and centrifuged.   For DNA depletion, samples were treated with 70 μL RDD-Buffer with 10 μL DNase and incubated for 15 min at RT. Columns were one time washed with 350 μL RWI-buffer and centrifuged for 20 sec at 8 600 x g at RT and again washed with 700 μL RPE buffer, centrifugation lasted 2 min at 8 600 x g. RNA was eluted by applying 30 μL RNase free water onto the column, one min incubation and centrifugation for one min with full speed at RT. RNA concentration was determined at the Nano Drop (peqlab).  Tissue was mixed with 700 μL Qiazol®. Samples were homogenized with 5 2.8 diameter ceramic beads for 20 sec, 5000 rpm in a homogenizer (SeqLab). After 5 min incubation at RT, samples were mixed with 140 μL chloroform, incubated for 3 min at RT and centrifuged at 12 000 x g, 15min at 4°C. Samples were transferred into fresh tubes, mixed with same volume of 70% Ethanol and transferred on RNeasy Mini columns (Qiagen). Columns were centrifuged for 15 sec at 8 000 x g at RT. Flow through was mixed with 350 μL RWI buffer and centrifuged.   For DNA depletion, samples were treated with 70 μL RDD-Buffer with 10 μL DNase and incubated for 15 min at RT. Columns were one time washed with 350 μL RWI-buffer and centrifuged for 20 sec at 8 600 x g at RT and again washed with 700 μL RPE buffer, centrifugation lasted 2 min at 8 600 x g. RNA was eluted by applying 30 μL RNase free water onto the column, one min incubation and centrifugation for one min with full speed at RT. RNA concentration was determined at the Nano Drop (peqlab). RNA quality was estimated (2100 Bioanalyzer, Agilent) and samples with a RIN > 8 were used as input material for the TruSeq RNA Sample Preparation Kit (Illumina). All cDNA fragments were derived from poly(A)+ RNA, subsequently barcoded and sequenced on a HiSeq 2000 instrument (Illumina) with 2 x 100 bp PE chemistry.	Illumina HiSeq 2000	cell type;;Podocytes|genetic background;;C57BL/6|genotype;;Wildtype|source_name;;Podocytes	GEO Accession;;GSM1295649		GSM1295649	WT Control 2	4253195446	21055423	2017-01-03 09:54:06	3217047971	4253195446	21055423	2	21055423	index:0,count:21055423,average:101,stdev:0|index:1,count:21055423,average:101,stdev:0	GSM1295649_r3	GEO			in_mesa	26082520	2.17	2.91	0.03	3554835538	3535080412	3407779384	3402638999	99.44	99.85	20552623	19113936	202.164	653.841	158	183020	85.19	88.9	21934558	17508038	21934558	17508038	85.44	85.72	21934558	17560298	21934558	16882134	365607377	10.28	1.02	0	4.08	0	0.21	0	0.06	0	0.00	0	2.12	0	20552623	0	202	0	199.80	0	1.76	0	0.01	0	1.44	0	0.01	0	199.47	0	0.56	0	213985	0	21055423	0	859181	0	44401	0	12735	0	0	0	445664	0	5439	0	0	0	52376	0	8560257	0	15344	0	8633416	0	93.53	0	19693442	0	199279	8085140	40.571961922731	21055423.0	20552623.0	213985.0	859181.0	44401.0	12735.0	0.0	445664.0	19693442.0	97.6	1.0	4.1	0.2	0.1	0.0	2.1	93.5	101	101	101.00	38	2126597723	25.4	24.6	24.4	25.6	0.0	32.6	15.5	bulk
655556	SRR1056018	SRP034660	SRS517821	SRX396842	SRA122184	GEO		The GYF domain protein CD2BP2 plays a crucial role in alternative splicing, embryonic development and podocyte integrity	The spliceosome is a multimolecular ribonucleoprotein complex, which catalyzes the removal of introns from pre-mRNA and extends the complexity of genetic information by defining alternative transcripts. Here we analyzed the in vivo function of CD2BP2, which is a marker of early spliceosomal complexes.   Using gene targeting in mice, we show that constitutive or mesoderm- specific ablation of the CD2BP2 gene causes embryonic lethality by E10.5 associated with delayed development, growth retardation and pericard effusion.   Transcriptome analysis in CD2BP2 deficient bone-marrow-derived macrophages (BMM) and podocytes revealed dramatic alterations in the alternative splicing pattern of several mRNAs including VEGFA. Consistent with a previously described critical role of specific VEGFA isoforms for podocyte integrity, mice, which specifically lack CD2BP2flox/flox in this cell type, develop progressive albuminuria followed by lethal kidney failure. We further identified the phosphatase PP1 as a GYF domain independent CD2BP2 interaction partner, suggesting that CD2BP2 acts as an important modulator for spliceosome dephosphorylation, thereby affecting alternative splicing of  physiologically highly relevant transcripts. Overall design: 3x KO vs 3x WT mus m.		GSM1295649: WT Control 2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Tissue was mixed with 700 μL Qiazol®. Samples were homogenized with 5 2.8 diameter ceramic beads for 20 sec, 5000 rpm in a homogenizer (SeqLab). After 5 min incubation at RT, samples were mixed with 140 μL chloroform, incubated for 3 min at RT and centrifuged at 12 000 x g, 15min at 4°C. Samples were transferred into fresh tubes, mixed with same volume of 70% Ethanol and transferred on RNeasy Mini columns (Qiagen). Columns were centrifuged for 15 sec at 8 000 x g at RT. Flow through was mixed with 350 μL RWI buffer and centrifuged.   For DNA depletion, samples were treated with 70 μL RDD-Buffer with 10 μL DNase and incubated for 15 min at RT. Columns were one time washed with 350 μL RWI-buffer and centrifuged for 20 sec at 8 600 x g at RT and again washed with 700 μL RPE buffer, centrifugation lasted 2 min at 8 600 x g. RNA was eluted by applying 30 μL RNase free water onto the column, one min incubation and centrifugation for one min with full speed at RT. RNA concentration was determined at the Nano Drop (peqlab).  Tissue was mixed with 700 μL Qiazol®. Samples were homogenized with 5 2.8 diameter ceramic beads for 20 sec, 5000 rpm in a homogenizer (SeqLab). After 5 min incubation at RT, samples were mixed with 140 μL chloroform, incubated for 3 min at RT and centrifuged at 12 000 x g, 15min at 4°C. Samples were transferred into fresh tubes, mixed with same volume of 70% Ethanol and transferred on RNeasy Mini columns (Qiagen). Columns were centrifuged for 15 sec at 8 000 x g at RT. Flow through was mixed with 350 μL RWI buffer and centrifuged.   For DNA depletion, samples were treated with 70 μL RDD-Buffer with 10 μL DNase and incubated for 15 min at RT. Columns were one time washed with 350 μL RWI-buffer and centrifuged for 20 sec at 8 600 x g at RT and again washed with 700 μL RPE buffer, centrifugation lasted 2 min at 8 600 x g. RNA was eluted by applying 30 μL RNase free water onto the column, one min incubation and centrifugation for one min with full speed at RT. RNA concentration was determined at the Nano Drop (peqlab). RNA quality was estimated (2100 Bioanalyzer, Agilent) and samples with a RIN > 8 were used as input material for the TruSeq RNA Sample Preparation Kit (Illumina). All cDNA fragments were derived from poly(A)+ RNA, subsequently barcoded and sequenced on a HiSeq 2000 instrument (Illumina) with 2 x 100 bp PE chemistry.	Illumina HiSeq 2000	cell type;;Podocytes|genetic background;;C57BL/6|genotype;;Wildtype|source_name;;Podocytes	GEO Accession;;GSM1295649		GSM1295649	WT Control 2	4369324640	21630320	2017-01-03 09:54:06	3285283667	4369324640	21630320	2	21630320	index:0,count:21630320,average:101,stdev:0|index:1,count:21630320,average:101,stdev:0	GSM1295649_r4	GEO			in_mesa	26082520	2.13	2.89	0.03	3657514295	3637940383	3507166042	3502447613	99.46	99.87	21124509	19636100	202.670	657.064	157	186799	85.27	88.96	22539438	18012245	22539438	18012245	85.49	85.78	22539438	18060230	22539438	17367734	374157846	10.23	1.05	0	4.06	0	0.22	0	0.06	0	0.00	0	2.06	0	21124509	0	202	0	199.86	0	1.76	0	0.01	0	1.44	0	0.01	0	220.59	0	0.51	0	226935	0	21630320	0	877499	0	46743	0	13699	0	0	0	445369	0	5650	0	0	0	54830	0	8895343	0	16177	0	8972000	0	93.60	0	20247010	0	200993	8403004	41.807446030459	21630320.0	21124509.0	226935.0	877499.0	46743.0	13699.0	0.0	445369.0	20247010.0	97.7	1.0	4.1	0.2	0.1	0.0	2.1	93.6	101	101	101.00	38	2184662320	25.4	24.6	24.5	25.5	0.0	32.9	15.9	bulk
655564	SRR1056019	SRP034660	SRS517823	SRX396843	SRA122184	GEO		The GYF domain protein CD2BP2 plays a crucial role in alternative splicing, embryonic development and podocyte integrity	The spliceosome is a multimolecular ribonucleoprotein complex, which catalyzes the removal of introns from pre-mRNA and extends the complexity of genetic information by defining alternative transcripts. Here we analyzed the in vivo function of CD2BP2, which is a marker of early spliceosomal complexes.   Using gene targeting in mice, we show that constitutive or mesoderm- specific ablation of the CD2BP2 gene causes embryonic lethality by E10.5 associated with delayed development, growth retardation and pericard effusion.   Transcriptome analysis in CD2BP2 deficient bone-marrow-derived macrophages (BMM) and podocytes revealed dramatic alterations in the alternative splicing pattern of several mRNAs including VEGFA. Consistent with a previously described critical role of specific VEGFA isoforms for podocyte integrity, mice, which specifically lack CD2BP2flox/flox in this cell type, develop progressive albuminuria followed by lethal kidney failure. We further identified the phosphatase PP1 as a GYF domain independent CD2BP2 interaction partner, suggesting that CD2BP2 acts as an important modulator for spliceosome dephosphorylation, thereby affecting alternative splicing of  physiologically highly relevant transcripts. Overall design: 3x KO vs 3x WT mus m.		GSM1295650: WT Control 3; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Tissue was mixed with 700 μL Qiazol®. Samples were homogenized with 5 2.8 diameter ceramic beads for 20 sec, 5000 rpm in a homogenizer (SeqLab). After 5 min incubation at RT, samples were mixed with 140 μL chloroform, incubated for 3 min at RT and centrifuged at 12 000 x g, 15min at 4°C. Samples were transferred into fresh tubes, mixed with same volume of 70% Ethanol and transferred on RNeasy Mini columns (Qiagen). Columns were centrifuged for 15 sec at 8 000 x g at RT. Flow through was mixed with 350 μL RWI buffer and centrifuged.   For DNA depletion, samples were treated with 70 μL RDD-Buffer with 10 μL DNase and incubated for 15 min at RT. Columns were one time washed with 350 μL RWI-buffer and centrifuged for 20 sec at 8 600 x g at RT and again washed with 700 μL RPE buffer, centrifugation lasted 2 min at 8 600 x g. RNA was eluted by applying 30 μL RNase free water onto the column, one min incubation and centrifugation for one min with full speed at RT. RNA concentration was determined at the Nano Drop (peqlab).  Tissue was mixed with 700 μL Qiazol®. Samples were homogenized with 5 2.8 diameter ceramic beads for 20 sec, 5000 rpm in a homogenizer (SeqLab). After 5 min incubation at RT, samples were mixed with 140 μL chloroform, incubated for 3 min at RT and centrifuged at 12 000 x g, 15min at 4°C. Samples were transferred into fresh tubes, mixed with same volume of 70% Ethanol and transferred on RNeasy Mini columns (Qiagen). Columns were centrifuged for 15 sec at 8 000 x g at RT. Flow through was mixed with 350 μL RWI buffer and centrifuged.   For DNA depletion, samples were treated with 70 μL RDD-Buffer with 10 μL DNase and incubated for 15 min at RT. Columns were one time washed with 350 μL RWI-buffer and centrifuged for 20 sec at 8 600 x g at RT and again washed with 700 μL RPE buffer, centrifugation lasted 2 min at 8 600 x g. RNA was eluted by applying 30 μL RNase free water onto the column, one min incubation and centrifugation for one min with full speed at RT. RNA concentration was determined at the Nano Drop (peqlab). RNA quality was estimated (2100 Bioanalyzer, Agilent) and samples with a RIN > 8 were used as input material for the TruSeq RNA Sample Preparation Kit (Illumina). All cDNA fragments were derived from poly(A)+ RNA, subsequently barcoded and sequenced on a HiSeq 2000 instrument (Illumina) with 2 x 100 bp PE chemistry.	Illumina HiSeq 2000	cell type;;Podocytes|genetic background;;C57BL/6|genotype;;Wildtype|source_name;;Podocytes	GEO Accession;;GSM1295650		GSM1295650	WT Control 3	5351954044	26494822	2017-01-03 09:54:06	4005925828	5351954044	26494822	2	26494822	index:0,count:26494822,average:101,stdev:0|index:1,count:26494822,average:101,stdev:0	GSM1295650_r1	GEO			in_mesa	26082520	2.06	2.9	0.03	4455343508	4437645435	4273420695	4272296397	99.6	99.97	25886786	24096943	200.647	637.452	157	231544	84.95	88.61	27589567	21990564	27589567	21990564	85.14	85.38	27589567	22041164	27589567	21187959	474852781	10.66	1.01	0	4.04	0	0.18	0	0.07	0	0.00	0	2.04	0	25886786	0	202	0	199.93	0	1.70	0	0.01	0	1.39	0	0.01	0	227.10	0	0.49	0	266618	0	26494822	0	1070074	0	46822	0	19528	0	0	0	541686	0	6870	0	0	0	67604	0	10992733	0	18875	0	11086082	0	93.67	0	24816712	0	212149	10337258	48.726404555289	26494822.0	25886786.0	266618.0	1070074.0	46822.0	19528.0	0.0	541686.0	24816712.0	97.7	1.0	4.0	0.2	0.1	0.0	2.0	93.7	101	101	101.00	38	2675977022	25.3	24.7	24.6	25.4	0.0	32.9	15.7	bulk
655620	SRR1056020	SRP034660	SRS517823	SRX396843	SRA122184	GEO		The GYF domain protein CD2BP2 plays a crucial role in alternative splicing, embryonic development and podocyte integrity	The spliceosome is a multimolecular ribonucleoprotein complex, which catalyzes the removal of introns from pre-mRNA and extends the complexity of genetic information by defining alternative transcripts. Here we analyzed the in vivo function of CD2BP2, which is a marker of early spliceosomal complexes.   Using gene targeting in mice, we show that constitutive or mesoderm- specific ablation of the CD2BP2 gene causes embryonic lethality by E10.5 associated with delayed development, growth retardation and pericard effusion.   Transcriptome analysis in CD2BP2 deficient bone-marrow-derived macrophages (BMM) and podocytes revealed dramatic alterations in the alternative splicing pattern of several mRNAs including VEGFA. Consistent with a previously described critical role of specific VEGFA isoforms for podocyte integrity, mice, which specifically lack CD2BP2flox/flox in this cell type, develop progressive albuminuria followed by lethal kidney failure. We further identified the phosphatase PP1 as a GYF domain independent CD2BP2 interaction partner, suggesting that CD2BP2 acts as an important modulator for spliceosome dephosphorylation, thereby affecting alternative splicing of  physiologically highly relevant transcripts. Overall design: 3x KO vs 3x WT mus m.		GSM1295650: WT Control 3; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Tissue was mixed with 700 μL Qiazol®. Samples were homogenized with 5 2.8 diameter ceramic beads for 20 sec, 5000 rpm in a homogenizer (SeqLab). After 5 min incubation at RT, samples were mixed with 140 μL chloroform, incubated for 3 min at RT and centrifuged at 12 000 x g, 15min at 4°C. Samples were transferred into fresh tubes, mixed with same volume of 70% Ethanol and transferred on RNeasy Mini columns (Qiagen). Columns were centrifuged for 15 sec at 8 000 x g at RT. Flow through was mixed with 350 μL RWI buffer and centrifuged.   For DNA depletion, samples were treated with 70 μL RDD-Buffer with 10 μL DNase and incubated for 15 min at RT. Columns were one time washed with 350 μL RWI-buffer and centrifuged for 20 sec at 8 600 x g at RT and again washed with 700 μL RPE buffer, centrifugation lasted 2 min at 8 600 x g. RNA was eluted by applying 30 μL RNase free water onto the column, one min incubation and centrifugation for one min with full speed at RT. RNA concentration was determined at the Nano Drop (peqlab).  Tissue was mixed with 700 μL Qiazol®. Samples were homogenized with 5 2.8 diameter ceramic beads for 20 sec, 5000 rpm in a homogenizer (SeqLab). After 5 min incubation at RT, samples were mixed with 140 μL chloroform, incubated for 3 min at RT and centrifuged at 12 000 x g, 15min at 4°C. Samples were transferred into fresh tubes, mixed with same volume of 70% Ethanol and transferred on RNeasy Mini columns (Qiagen). Columns were centrifuged for 15 sec at 8 000 x g at RT. Flow through was mixed with 350 μL RWI buffer and centrifuged.   For DNA depletion, samples were treated with 70 μL RDD-Buffer with 10 μL DNase and incubated for 15 min at RT. Columns were one time washed with 350 μL RWI-buffer and centrifuged for 20 sec at 8 600 x g at RT and again washed with 700 μL RPE buffer, centrifugation lasted 2 min at 8 600 x g. RNA was eluted by applying 30 μL RNase free water onto the column, one min incubation and centrifugation for one min with full speed at RT. RNA concentration was determined at the Nano Drop (peqlab). RNA quality was estimated (2100 Bioanalyzer, Agilent) and samples with a RIN > 8 were used as input material for the TruSeq RNA Sample Preparation Kit (Illumina). All cDNA fragments were derived from poly(A)+ RNA, subsequently barcoded and sequenced on a HiSeq 2000 instrument (Illumina) with 2 x 100 bp PE chemistry.	Illumina HiSeq 2000	cell type;;Podocytes|genetic background;;C57BL/6|genotype;;Wildtype|source_name;;Podocytes	GEO Accession;;GSM1295650		GSM1295650	WT Control 3	5173724394	25612497	2017-01-03 09:54:06	3896233844	5173724394	25612497	2	25612497	index:0,count:25612497,average:101,stdev:0|index:1,count:25612497,average:101,stdev:0	GSM1295650_r2	GEO			in_mesa	26082520	2.09	2.92	0.03	4295063776	4277159166	4118955569	4117263948	99.58	99.96	24989285	23273238	200.132	634.815	158	224577	84.88	88.56	26640529	21211638	26640529	21211638	85.09	85.32	26640529	21263376	26640529	20436937	460379683	10.72	0.98	0	4.05	0	0.18	0	0.07	0	0.00	0	2.19	0	24989285	0	202	0	199.73	0	1.70	0	0.01	0	1.40	0	0.01	0	229.37	0	0.53	0	252086	0	25612497	0	1036902	0	44831	0	18657	0	0	0	559724	0	6403	0	0	0	63804	0	10463742	0	18155	0	10552104	0	93.52	0	23952383	0	210069	9838247	46.833407118613	25612497.0	24989285.0	252086.0	1036902.0	44831.0	18657.0	0.0	559724.0	23952383.0	97.6	1.0	4.0	0.2	0.1	0.0	2.2	93.5	101	101	101.00	38	2586862197	25.3	24.7	24.5	25.5	0.0	32.7	15.6	bulk
655628	SRR1056021	SRP034660	SRS517823	SRX396843	SRA122184	GEO		The GYF domain protein CD2BP2 plays a crucial role in alternative splicing, embryonic development and podocyte integrity	The spliceosome is a multimolecular ribonucleoprotein complex, which catalyzes the removal of introns from pre-mRNA and extends the complexity of genetic information by defining alternative transcripts. Here we analyzed the in vivo function of CD2BP2, which is a marker of early spliceosomal complexes.   Using gene targeting in mice, we show that constitutive or mesoderm- specific ablation of the CD2BP2 gene causes embryonic lethality by E10.5 associated with delayed development, growth retardation and pericard effusion.   Transcriptome analysis in CD2BP2 deficient bone-marrow-derived macrophages (BMM) and podocytes revealed dramatic alterations in the alternative splicing pattern of several mRNAs including VEGFA. Consistent with a previously described critical role of specific VEGFA isoforms for podocyte integrity, mice, which specifically lack CD2BP2flox/flox in this cell type, develop progressive albuminuria followed by lethal kidney failure. We further identified the phosphatase PP1 as a GYF domain independent CD2BP2 interaction partner, suggesting that CD2BP2 acts as an important modulator for spliceosome dephosphorylation, thereby affecting alternative splicing of  physiologically highly relevant transcripts. Overall design: 3x KO vs 3x WT mus m.		GSM1295650: WT Control 3; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Tissue was mixed with 700 μL Qiazol®. Samples were homogenized with 5 2.8 diameter ceramic beads for 20 sec, 5000 rpm in a homogenizer (SeqLab). After 5 min incubation at RT, samples were mixed with 140 μL chloroform, incubated for 3 min at RT and centrifuged at 12 000 x g, 15min at 4°C. Samples were transferred into fresh tubes, mixed with same volume of 70% Ethanol and transferred on RNeasy Mini columns (Qiagen). Columns were centrifuged for 15 sec at 8 000 x g at RT. Flow through was mixed with 350 μL RWI buffer and centrifuged.   For DNA depletion, samples were treated with 70 μL RDD-Buffer with 10 μL DNase and incubated for 15 min at RT. Columns were one time washed with 350 μL RWI-buffer and centrifuged for 20 sec at 8 600 x g at RT and again washed with 700 μL RPE buffer, centrifugation lasted 2 min at 8 600 x g. RNA was eluted by applying 30 μL RNase free water onto the column, one min incubation and centrifugation for one min with full speed at RT. RNA concentration was determined at the Nano Drop (peqlab).  Tissue was mixed with 700 μL Qiazol®. Samples were homogenized with 5 2.8 diameter ceramic beads for 20 sec, 5000 rpm in a homogenizer (SeqLab). After 5 min incubation at RT, samples were mixed with 140 μL chloroform, incubated for 3 min at RT and centrifuged at 12 000 x g, 15min at 4°C. Samples were transferred into fresh tubes, mixed with same volume of 70% Ethanol and transferred on RNeasy Mini columns (Qiagen). Columns were centrifuged for 15 sec at 8 000 x g at RT. Flow through was mixed with 350 μL RWI buffer and centrifuged.   For DNA depletion, samples were treated with 70 μL RDD-Buffer with 10 μL DNase and incubated for 15 min at RT. Columns were one time washed with 350 μL RWI-buffer and centrifuged for 20 sec at 8 600 x g at RT and again washed with 700 μL RPE buffer, centrifugation lasted 2 min at 8 600 x g. RNA was eluted by applying 30 μL RNase free water onto the column, one min incubation and centrifugation for one min with full speed at RT. RNA concentration was determined at the Nano Drop (peqlab). RNA quality was estimated (2100 Bioanalyzer, Agilent) and samples with a RIN > 8 were used as input material for the TruSeq RNA Sample Preparation Kit (Illumina). All cDNA fragments were derived from poly(A)+ RNA, subsequently barcoded and sequenced on a HiSeq 2000 instrument (Illumina) with 2 x 100 bp PE chemistry.	Illumina HiSeq 2000	cell type;;Podocytes|genetic background;;C57BL/6|genotype;;Wildtype|source_name;;Podocytes	GEO Accession;;GSM1295650		GSM1295650	WT Control 3	5234420950	25912975	2017-01-03 09:54:06	3942048279	5234420950	25912975	2	25912975	index:0,count:25912975,average:101,stdev:0|index:1,count:25912975,average:101,stdev:0	GSM1295650_r3	GEO			in_mesa	26082520	2.1	2.91	0.03	4354135475	4335837609	4175145345	4173253426	99.58	99.95	25307398	23567253	200.401	635.295	157	225854	84.85	88.54	26978808	21474410	26978808	21474410	85.08	85.31	26978808	21530890	26978808	20691676	467034915	10.73	1.01	0	4.06	0	0.18	0	0.07	0	0.00	0	2.09	0	25307398	0	202	0	199.87	0	1.70	0	0.01	0	1.39	0	0.01	0	130.47	0	0.53	0	260439	0	25912975	0	1052918	0	45369	0	18915	0	0	0	541293	0	6793	0	0	0	64512	0	10647867	0	18786	0	10737958	0	93.60	0	24254480	0	210589	10006180	47.515207347012	25912975.0	25307398.0	260439.0	1052918.0	45369.0	18915.0	0.0	541293.0	24254480.0	97.7	1.0	4.1	0.2	0.1	0.0	2.1	93.6	101	101	101.00	38	2617210475	25.4	24.7	24.5	25.5	0.0	32.8	15.7	bulk
655637	SRR1056022	SRP034660	SRS517823	SRX396843	SRA122184	GEO		The GYF domain protein CD2BP2 plays a crucial role in alternative splicing, embryonic development and podocyte integrity	The spliceosome is a multimolecular ribonucleoprotein complex, which catalyzes the removal of introns from pre-mRNA and extends the complexity of genetic information by defining alternative transcripts. Here we analyzed the in vivo function of CD2BP2, which is a marker of early spliceosomal complexes.   Using gene targeting in mice, we show that constitutive or mesoderm- specific ablation of the CD2BP2 gene causes embryonic lethality by E10.5 associated with delayed development, growth retardation and pericard effusion.   Transcriptome analysis in CD2BP2 deficient bone-marrow-derived macrophages (BMM) and podocytes revealed dramatic alterations in the alternative splicing pattern of several mRNAs including VEGFA. Consistent with a previously described critical role of specific VEGFA isoforms for podocyte integrity, mice, which specifically lack CD2BP2flox/flox in this cell type, develop progressive albuminuria followed by lethal kidney failure. We further identified the phosphatase PP1 as a GYF domain independent CD2BP2 interaction partner, suggesting that CD2BP2 acts as an important modulator for spliceosome dephosphorylation, thereby affecting alternative splicing of  physiologically highly relevant transcripts. Overall design: 3x KO vs 3x WT mus m.		GSM1295650: WT Control 3; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Tissue was mixed with 700 μL Qiazol®. Samples were homogenized with 5 2.8 diameter ceramic beads for 20 sec, 5000 rpm in a homogenizer (SeqLab). After 5 min incubation at RT, samples were mixed with 140 μL chloroform, incubated for 3 min at RT and centrifuged at 12 000 x g, 15min at 4°C. Samples were transferred into fresh tubes, mixed with same volume of 70% Ethanol and transferred on RNeasy Mini columns (Qiagen). Columns were centrifuged for 15 sec at 8 000 x g at RT. Flow through was mixed with 350 μL RWI buffer and centrifuged.   For DNA depletion, samples were treated with 70 μL RDD-Buffer with 10 μL DNase and incubated for 15 min at RT. Columns were one time washed with 350 μL RWI-buffer and centrifuged for 20 sec at 8 600 x g at RT and again washed with 700 μL RPE buffer, centrifugation lasted 2 min at 8 600 x g. RNA was eluted by applying 30 μL RNase free water onto the column, one min incubation and centrifugation for one min with full speed at RT. RNA concentration was determined at the Nano Drop (peqlab).  Tissue was mixed with 700 μL Qiazol®. Samples were homogenized with 5 2.8 diameter ceramic beads for 20 sec, 5000 rpm in a homogenizer (SeqLab). After 5 min incubation at RT, samples were mixed with 140 μL chloroform, incubated for 3 min at RT and centrifuged at 12 000 x g, 15min at 4°C. Samples were transferred into fresh tubes, mixed with same volume of 70% Ethanol and transferred on RNeasy Mini columns (Qiagen). Columns were centrifuged for 15 sec at 8 000 x g at RT. Flow through was mixed with 350 μL RWI buffer and centrifuged.   For DNA depletion, samples were treated with 70 μL RDD-Buffer with 10 μL DNase and incubated for 15 min at RT. Columns were one time washed with 350 μL RWI-buffer and centrifuged for 20 sec at 8 600 x g at RT and again washed with 700 μL RPE buffer, centrifugation lasted 2 min at 8 600 x g. RNA was eluted by applying 30 μL RNase free water onto the column, one min incubation and centrifugation for one min with full speed at RT. RNA concentration was determined at the Nano Drop (peqlab). RNA quality was estimated (2100 Bioanalyzer, Agilent) and samples with a RIN > 8 were used as input material for the TruSeq RNA Sample Preparation Kit (Illumina). All cDNA fragments were derived from poly(A)+ RNA, subsequently barcoded and sequenced on a HiSeq 2000 instrument (Illumina) with 2 x 100 bp PE chemistry.	Illumina HiSeq 2000	cell type;;Podocytes|genetic background;;C57BL/6|genotype;;Wildtype|source_name;;Podocytes	GEO Accession;;GSM1295650		GSM1295650	WT Control 3	5380795402	26637601	2017-01-03 09:54:06	4026069816	5380795402	26637601	2	26637601	index:0,count:26637601,average:101,stdev:0|index:1,count:26637601,average:101,stdev:0	GSM1295650_r4	GEO			in_mesa	26082520	2.07	2.9	0.03	4482107151	4463758474	4299268929	4297612724	99.59	99.96	26027030	24225989	200.824	638.129	166	231373	84.94	88.6	27737092	22107523	27737092	22107523	85.14	85.37	27737092	22158542	27737092	21301644	478389248	10.67	1.04	0	4.04	0	0.18	0	0.08	0	0.00	0	2.04	0	26027030	0	202	0	199.93	0	1.70	0	0.01	0	1.40	0	0.01	0	242.77	0	0.48	0	276339	0	26637601	0	1075005	0	47258	0	20000	0	0	0	543313	0	7092	0	0	0	67745	0	11056751	0	19518	0	11151106	0	93.67	0	24952025	0	212824	10396303	48.849298011502	26637601.0	26027030.0	276339.0	1075005.0	47258.0	20000.0	0.0	543313.0	24952025.0	97.7	1.0	4.0	0.2	0.1	0.0	2.0	93.7	101	101	101.00	38	2690397701	25.3	24.7	24.5	25.5	0.0	33.1	16.2	bulk
1385003	SRR1068222	SRP034891	SRS523971	SRX404377	SRA122965	GEO		Deep sequencing of the murine olfactory receptor neuron transcriptome	The recent development of next-generation sequencing (NGS) techniques encouraged us to assess the transcriptome of the murine OE. We analyzed RNA from OEs of female and male adult mice and from fluorescence-activated cell sorting (FACS)-sorted olfactory receptor neurons (ORNs) obtained from transgenic OMP-GFP mice Overall design: The Illumina RNA-Seq protocol was utilized to generate up to 86 million reads per transcriptome.		GSM1300902: C57BL6/J female OE; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Olfactory Epithelia were prepared and pooled from eight individuals for each condition. ORNs were obtained from OMP-GFP mice and enriched by FACS sorting. Subsequently RNA was isolated using RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer´s protocol including the optional on-column DNaseI digestion. Libraries for NGS sequencing were prepared from RNA and subjected to DSN normalization by standard Illumina protocols	Illumina HiSeq 2000	gender;;female|genotype/variation;;wildtype|source_name;;Olfactory Epithelium|strain;;C57BL/6J|tissue/cell type;;Olfactory Epithelium (OE)	GEO Accession;;GSM1300902		GSM1300902	C57BL6/J female OE	8726821776	43202088	2015-01-21 16:03:03	5786300821	8726821776	43202088	2	43202088	index:0,count:43202088,average:101,stdev:0|index:1,count:43202088,average:101,stdev:0	GSM1300902_r1	GEO					3.65	9.09	0.03	6495792246	6389957429	5990475487	5938971824	98.37	99.14	41550810	38439469	189.625	663.362	135	409676	85.13	92.44	46467371	35373973	46467371	35373973	87.42	87.97	46467371	36322920	46467371	33664458	332088199	5.11	1.21	0	7.60	0	0.18	0	0.06	0	0.00	0	3.58	0	41550810	0	202	0	199.67	0	2.10	0	0.01	0	1.77	0	0.01	0	190.13	0	0.28	0	521484	0	43202088	0	3283007	0	79091	0	27672	0	0	0	1544515	0	10367	0	0	0	117211	0	21633670	0	41544	0	21802792	0	88.58	0	38267803	0	262250	20679252	78.853201143947	43202088.0	41550810.0	521484.0	3283007.0	79091.0	27672.0	0.0	1544515.0	38267803.0	96.2	1.2	7.6	0.2	0.1	0.0	3.6	88.6	101	101	101.00	38	4363410888	25.1	24.8	24.7	25.3	0.0	35.6	18.7	bulk
1385051	SRR1068225	SRP034891	SRS523973	SRX404379	SRA122965	GEO		Deep sequencing of the murine olfactory receptor neuron transcriptome	The recent development of next-generation sequencing (NGS) techniques encouraged us to assess the transcriptome of the murine OE. We analyzed RNA from OEs of female and male adult mice and from fluorescence-activated cell sorting (FACS)-sorted olfactory receptor neurons (ORNs) obtained from transgenic OMP-GFP mice Overall design: The Illumina RNA-Seq protocol was utilized to generate up to 86 million reads per transcriptome.		GSM1300904: FACS-sorted ORNs (heterozygous); Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Olfactory Epithelia were prepared and pooled from eight individuals for each condition. ORNs were obtained from OMP-GFP mice and enriched by FACS sorting. Subsequently RNA was isolated using RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer´s protocol including the optional on-column DNaseI digestion. Libraries for NGS sequencing were prepared from RNA and subjected to DSN normalization by standard Illumina protocols	Illumina HiSeq 2000	cell type;;FACS-sorted olfactory receptor neurons (ORNs)|genotype/variation;;transgenic OMP-GFP mice, heterozygous|source_name;;Olfactory Receptor Neurons|strain;;C57BL/6J|tissue/cell type;;Olfactory Epithelium (OE)	GEO Accession;;GSM1300904		GSM1300904	FACS-sorted ORNs (heterozygous)	5882157786	29119593	2015-01-21 16:03:03	4281914636	5882157786	29119593	2	29119593	index:0,count:29119593,average:101,stdev:0|index:1,count:29119593,average:101,stdev:0	GSM1300904_r1	GEO					2.31	0.84	0.02	3474583730	3206882499	3124132123	2954506128	92.3	94.57	24573167	24387186	146.624	219.900	124	369746	47.7	53.51	29585754	11720680	29585754	11720680	28.02	29.59	29585754	6884549	29585754	6482381	742598248	21.37	1.14	0	9.16	0	0.17	0	0.09	0	0.00	0	15.35	0	24573167	0	202	0	196.03	0	4.26	0	0.06	0	2.74	0	0.10	0	149.12	0	1.14	0	332908	0	29119593	0	2668316	0	48682	0	26882	0	0	0	4470862	0	740	0	0	0	8352	0	1049322	0	20920	0	1079334	0	75.22	0	21904851	0	120846	873488	7.228108501729	29119593.0	24573167.0	332908.0	2668316.0	48682.0	26882.0	0.0	4470862.0	21904851.0	84.4	1.1	9.2	0.2	0.1	0.0	15.4	75.2	101	101	101.00	38	2941078893	22.7	27.4	27.5	22.5	0.0	33.4	20.1	bulk
328135	SRR1177071	SRP038980	SRS561963	SRX476260	SRA142452	GEO		Systematic analysis of the pro and anti-inflammatory activation of mouse myeloid cells	Inflammation is a fundamental physiological process and a key line of defense against pathogen invasion. Inflammation is exquisitely controlled: Too high and inflammation can be dangerous to the organism, but too low and the invading pathogen can escape suppression. Multiple opposing molecules initiate either a pro or anti inflammatory program, of particular interest is the pro-inflammatory bacterial endotoxins and an opposing anti-inflammatory pathway involving IL-10 and STAT3. Much work has been expended in understanding these two pathways in macrophages, key cells in the myeloid system. But other cells of the myeloid system also show a response to endotoxin and IL-10. These myeloid cell types have been less well explored. With the aim to understand similarities and differences amongst myeloid cells we performed RNA-seq analysis on 5 cells from the myeloid system: Macrophages, Neutrophils, splenic dendritic cells, mast cells and eosinophils. We treated the cells with IL-10 or LPS (endotoxin), either separately or in combination. Although the 5 cell types show much similarity in the outcome of the pro inflammatory response, the broad outline of their pro and anti-inflammatory response is highly divergent between the 5 myeloid cell types. Overall design: RNA-seq data from 5 myeloid cell types, treated with IL-10, LPS or both in combination. Samples are in biological duplicate.		GSM1335263: Splenic dendritic cell -IL10 -LPS replicate 2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			TRIzol RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2000	source_name;;spleen-purified dendritic cells|strain;;C57Bl6cJ|treatment;;None	GEO Accession;;GSM1335263		GSM1335263	Splenic dendritic cell -IL10 -LPS replicate 2	4654989360	25861052	2015-07-22 17:07:11	3274167741	4654989360	25861052	2	25861052	index:0,count:25861052,average:90,stdev:0|index:1,count:25861052,average:90,stdev:0	GSM1335263_r1	GEO			in_mesa	25765318	2.49	3.06	0.13	3928001875	3917994403	3678556735	3686088652	99.75	100.2	25575920	24352304	177.829	436.379	146	321298	83.98	89.77	28282010	21478359	28282010	21478359	85.47	85.87	28282010	21860351	28282010	20545302	374872685	9.54	0.98	0	6.38	0	0.29	0	0.10	0	0.00	0	0.72	0	25575920	0	180	0	178.57	0	1.48	0	0.01	0	1.18	0	0.01	0	381.56	0	0.19	0	254671	0	25861052	0	1650976	0	74299	0	25645	0	0	0	185188	0	5528	0	0	0	63376	0	9233418	0	19808	0	9322130	0	92.51	0	23924944	0	187161	8696370	46.464648083735	25861052.0	25575920.0	254671.0	1650976.0	74299.0	25645.0	0.0	185188.0	23924944.0	98.9	1.0	6.4	0.3	0.1	0.0	0.7	92.5	90	90	90.00	38	2327494680	25.1	24.8	25.0	25.2	0.0	35.7	22.7	bulk
328139	SRR1177072	SRP038980	SRS561964	SRX476261	SRA142452	GEO		Systematic analysis of the pro and anti-inflammatory activation of mouse myeloid cells	Inflammation is a fundamental physiological process and a key line of defense against pathogen invasion. Inflammation is exquisitely controlled: Too high and inflammation can be dangerous to the organism, but too low and the invading pathogen can escape suppression. Multiple opposing molecules initiate either a pro or anti inflammatory program, of particular interest is the pro-inflammatory bacterial endotoxins and an opposing anti-inflammatory pathway involving IL-10 and STAT3. Much work has been expended in understanding these two pathways in macrophages, key cells in the myeloid system. But other cells of the myeloid system also show a response to endotoxin and IL-10. These myeloid cell types have been less well explored. With the aim to understand similarities and differences amongst myeloid cells we performed RNA-seq analysis on 5 cells from the myeloid system: Macrophages, Neutrophils, splenic dendritic cells, mast cells and eosinophils. We treated the cells with IL-10 or LPS (endotoxin), either separately or in combination. Although the 5 cell types show much similarity in the outcome of the pro inflammatory response, the broad outline of their pro and anti-inflammatory response is highly divergent between the 5 myeloid cell types. Overall design: RNA-seq data from 5 myeloid cell types, treated with IL-10, LPS or both in combination. Samples are in biological duplicate.		GSM1335264: Splenic dendritic cell -IL10 +LPS replicate 1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			TRIzol RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2000	source_name;;spleen-purified dendritic cells|strain;;C57Bl6cJ|treatment;;LPS	GEO Accession;;GSM1335264		GSM1335264	Splenic dendritic cell -IL10 +LPS replicate 1	4780771380	26559841	2015-07-22 17:07:11	3349145747	4780771380	26559841	2	26559841	index:0,count:26559841,average:90,stdev:0|index:1,count:26559841,average:90,stdev:0	GSM1335264_r1	GEO			in_mesa	25765318	2.16	2.93	0.13	4028172809	4014221757	3785957636	3791674278	99.65	100.15	26183611	24853779	180.175	449.496	146	307363	83.13	88.55	28780978	21765926	28780978	21765926	84.11	84.52	28780978	22022288	28780978	20775539	418233902	10.38	1.08	0	6.03	0	0.31	0	0.11	0	0.00	0	1.00	0	26183611	0	180	0	178.52	0	1.60	0	0.01	0	1.28	0	0.01	0	294.20	0	0.17	0	287461	0	26559841	0	1602097	0	82369	0	28870	0	0	0	264991	0	4953	0	0	0	61935	0	9085514	0	19155	0	9171557	0	92.55	0	24581514	0	176642	8563472	48.479251820065	26559841.0	26183611.0	287461.0	1602097.0	82369.0	28870.0	0.0	264991.0	24581514.0	98.6	1.1	6.0	0.3	0.1	0.0	1.0	92.6	90	90	90.00	38	2390385690	25.1	24.8	24.9	25.2	0.0	35.8	22.8	bulk
655892	SRR1177042	SRP038980	SRS561934	SRX476231	SRA142452	GEO		Systematic analysis of the pro and anti-inflammatory activation of mouse myeloid cells	Inflammation is a fundamental physiological process and a key line of defense against pathogen invasion. Inflammation is exquisitely controlled: Too high and inflammation can be dangerous to the organism, but too low and the invading pathogen can escape suppression. Multiple opposing molecules initiate either a pro or anti inflammatory program, of particular interest is the pro-inflammatory bacterial endotoxins and an opposing anti-inflammatory pathway involving IL-10 and STAT3. Much work has been expended in understanding these two pathways in macrophages, key cells in the myeloid system. But other cells of the myeloid system also show a response to endotoxin and IL-10. These myeloid cell types have been less well explored. With the aim to understand similarities and differences amongst myeloid cells we performed RNA-seq analysis on 5 cells from the myeloid system: Macrophages, Neutrophils, splenic dendritic cells, mast cells and eosinophils. We treated the cells with IL-10 or LPS (endotoxin), either separately or in combination. Although the 5 cell types show much similarity in the outcome of the pro inflammatory response, the broad outline of their pro and anti-inflammatory response is highly divergent between the 5 myeloid cell types. Overall design: RNA-seq data from 5 myeloid cell types, treated with IL-10, LPS or both in combination. Samples are in biological duplicate.		GSM1335234: Eosinophils -IL-10 -LPS replicate 1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			TRIzol RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2000	source_name;;Bone marrow-derived Eosinophils|strain;;C57Bl6cJ|treatment;;None	GEO Accession;;GSM1335234		GSM1335234	Eosinophils -IL-10 -LPS replicate 1	8976486060	49869367	2015-07-22 17:07:11	6038218602	8976486060	49869367	2	49869367	index:0,count:49869367,average:90,stdev:0|index:1,count:49869367,average:90,stdev:0	GSM1335234_r1	GEO			in_mesa	25765318	3.22	2.96	0.06	8391688886	8356389260	7766894233	7776487278	99.58	100.12	48815839	46361793	209.893	466.363	198	937617	81.4	88.04	54989309	39736730	54989309	39736730	83.84	84.14	54989309	40927293	54989309	37978473	916031841	10.92	1.32	0	7.38	0	0.40	0	0.11	0	0.00	0	1.61	0	48815839	0	180	0	178.54	0	1.82	0	0.00	0	1.23	0	0.00	0	381.17	0	0.12	0	655860	0	49869367	0	3680414	0	198305	0	54153	0	0	0	801070	0	28505	0	0	0	78878	0	15412380	0	27644	0	15547407	0	90.51	0	45135425	0	167721	15643635	93.271772765486	49869367.0	48815839.0	655860.0	3680414.0	198305.0	54153.0	0.0	801070.0	45135425.0	97.9	1.3	7.4	0.4	0.1	0.0	1.6	90.5	90	90	90.00	38	4488243030	24.9	24.2	26.0	24.9	0.0	36.5	26.0	bulk
655900	SRR1177043	SRP038980	SRS561935	SRX476232	SRA142452	GEO		Systematic analysis of the pro and anti-inflammatory activation of mouse myeloid cells	Inflammation is a fundamental physiological process and a key line of defense against pathogen invasion. Inflammation is exquisitely controlled: Too high and inflammation can be dangerous to the organism, but too low and the invading pathogen can escape suppression. Multiple opposing molecules initiate either a pro or anti inflammatory program, of particular interest is the pro-inflammatory bacterial endotoxins and an opposing anti-inflammatory pathway involving IL-10 and STAT3. Much work has been expended in understanding these two pathways in macrophages, key cells in the myeloid system. But other cells of the myeloid system also show a response to endotoxin and IL-10. These myeloid cell types have been less well explored. With the aim to understand similarities and differences amongst myeloid cells we performed RNA-seq analysis on 5 cells from the myeloid system: Macrophages, Neutrophils, splenic dendritic cells, mast cells and eosinophils. We treated the cells with IL-10 or LPS (endotoxin), either separately or in combination. Although the 5 cell types show much similarity in the outcome of the pro inflammatory response, the broad outline of their pro and anti-inflammatory response is highly divergent between the 5 myeloid cell types. Overall design: RNA-seq data from 5 myeloid cell types, treated with IL-10, LPS or both in combination. Samples are in biological duplicate.		GSM1335235: Eosinophils -IL-10 -LPS replicate 2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			TRIzol RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2000	source_name;;Bone marrow-derived Eosinophils|strain;;C57Bl6cJ|treatment;;None	GEO Accession;;GSM1335235		GSM1335235	Eosinophils -IL-10 -LPS replicate 2	8680590540	48225503	2015-07-22 17:07:11	5926015426	8680590540	48225503	2	48225503	index:0,count:48225503,average:90,stdev:0|index:1,count:48225503,average:90,stdev:0	GSM1335235_r1	GEO			in_mesa	25765318	3.49	2.95	0.07	8133313680	8113094927	7535163115	7552801016	99.75	100.23	47297241	43998240	222.885	567.129	209	909472	82.91	89.58	53208427	39214302	53208427	39214302	85.6	85.93	53208427	40485374	53208427	37616099	811962191	9.98	1.41	0	7.30	0	0.40	0	0.11	0	0.00	0	1.42	0	47297241	0	180	0	178.49	0	1.66	0	0.00	0	1.18	0	0.00	0	398.19	0	0.12	0	680903	0	48225503	0	3519788	0	194286	0	51106	0	0	0	682870	0	32343	0	0	0	94443	0	16356747	0	28854	0	16512387	0	90.78	0	43777453	0	180197	16582335	92.023368868516	48225503.0	47297241.0	680903.0	3519788.0	194286.0	51106.0	0.0	682870.0	43777453.0	98.1	1.4	7.3	0.4	0.1	0.0	1.4	90.8	90	90	90.00	38	4340295270	24.8	24.3	26.0	24.9	0.0	36.3	25.6	bulk
655908	SRR1177044	SRP038980	SRS561937	SRX476233	SRA142452	GEO		Systematic analysis of the pro and anti-inflammatory activation of mouse myeloid cells	Inflammation is a fundamental physiological process and a key line of defense against pathogen invasion. Inflammation is exquisitely controlled: Too high and inflammation can be dangerous to the organism, but too low and the invading pathogen can escape suppression. Multiple opposing molecules initiate either a pro or anti inflammatory program, of particular interest is the pro-inflammatory bacterial endotoxins and an opposing anti-inflammatory pathway involving IL-10 and STAT3. Much work has been expended in understanding these two pathways in macrophages, key cells in the myeloid system. But other cells of the myeloid system also show a response to endotoxin and IL-10. These myeloid cell types have been less well explored. With the aim to understand similarities and differences amongst myeloid cells we performed RNA-seq analysis on 5 cells from the myeloid system: Macrophages, Neutrophils, splenic dendritic cells, mast cells and eosinophils. We treated the cells with IL-10 or LPS (endotoxin), either separately or in combination. Although the 5 cell types show much similarity in the outcome of the pro inflammatory response, the broad outline of their pro and anti-inflammatory response is highly divergent between the 5 myeloid cell types. Overall design: RNA-seq data from 5 myeloid cell types, treated with IL-10, LPS or both in combination. Samples are in biological duplicate.		GSM1335236: Eosinophils -IL-10 +LPS replicate 1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			TRIzol RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2000	source_name;;Bone marrow-derived Eosinophils|strain;;C57Bl6cJ|treatment;;LPS	GEO Accession;;GSM1335236		GSM1335236	Eosinophils -IL-10 +LPS replicate 1	8216054100	45644745	2015-07-22 17:07:11	5593551578	8216054100	45644745	2	45644745	index:0,count:45644745,average:90,stdev:0|index:1,count:45644745,average:90,stdev:0	GSM1335236_r1	GEO			in_mesa	25765318	3.35	3.03	0.06	7717630441	7693287263	7178143960	7191936007	99.68	100.19	44827777	42529111	206.909	465.277	195	795200	83.06	89.38	50097741	37235268	50097741	37235268	85.27	85.59	50097741	38224926	50097741	35654587	756742012	9.81	1.18	0	6.95	0	0.38	0	0.11	0	0.00	0	1.30	0	44827777	0	180	0	178.62	0	1.61	0	0.00	0	1.19	0	0.00	0	329.30	0	0.12	0	539517	0	45644745	0	3170426	0	173592	0	48600	0	0	0	594776	0	28921	0	0	0	80882	0	15389960	0	25412	0	15525175	0	91.26	0	41657351	0	173159	15616389	90.185257480119	45644745.0	44827777.0	539517.0	3170426.0	173592.0	48600.0	0.0	594776.0	41657351.0	98.2	1.2	6.9	0.4	0.1	0.0	1.3	91.3	90	90	90.00	38	4108027050	24.8	24.4	26.1	24.8	0.0	36.4	25.7	bulk
655917	SRR1177045	SRP038980	SRS561936	SRX476234	SRA142452	GEO		Systematic analysis of the pro and anti-inflammatory activation of mouse myeloid cells	Inflammation is a fundamental physiological process and a key line of defense against pathogen invasion. Inflammation is exquisitely controlled: Too high and inflammation can be dangerous to the organism, but too low and the invading pathogen can escape suppression. Multiple opposing molecules initiate either a pro or anti inflammatory program, of particular interest is the pro-inflammatory bacterial endotoxins and an opposing anti-inflammatory pathway involving IL-10 and STAT3. Much work has been expended in understanding these two pathways in macrophages, key cells in the myeloid system. But other cells of the myeloid system also show a response to endotoxin and IL-10. These myeloid cell types have been less well explored. With the aim to understand similarities and differences amongst myeloid cells we performed RNA-seq analysis on 5 cells from the myeloid system: Macrophages, Neutrophils, splenic dendritic cells, mast cells and eosinophils. We treated the cells with IL-10 or LPS (endotoxin), either separately or in combination. Although the 5 cell types show much similarity in the outcome of the pro inflammatory response, the broad outline of their pro and anti-inflammatory response is highly divergent between the 5 myeloid cell types. Overall design: RNA-seq data from 5 myeloid cell types, treated with IL-10, LPS or both in combination. Samples are in biological duplicate.		GSM1335237: Eosinophils -IL-10 +LPS replicate 2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			TRIzol RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2000	source_name;;Bone marrow-derived Eosinophils|strain;;C57Bl6cJ|treatment;;LPS	GEO Accession;;GSM1335237		GSM1335237	Eosinophils -IL-10 +LPS replicate 2	6451308720	35840604	2015-07-22 17:07:11	4389529318	6451308720	35840604	2	35840604	index:0,count:35840604,average:90,stdev:0|index:1,count:35840604,average:90,stdev:0	GSM1335237_r1	GEO			in_mesa	25765318	3.44	2.98	0.07	6289459881	6272423439	5824620200	5838792321	99.73	100.24	35313522	32983794	230.819	529.740	205	867653	83.09	89.72	39629801	29343388	39629801	29343388	85.67	86.04	39629801	30252001	39629801	28140515	614106890	9.76	1.33	0	7.28	0	0.38	0	0.11	0	0.00	0	0.98	0	35313522	0	180	0	178.68	0	1.65	0	0.00	0	1.21	0	0.00	0	146.45	0	0.12	0	475159	0	35840604	0	2608246	0	136723	0	38459	0	0	0	351900	0	22634	0	0	0	68026	0	11818501	0	19675	0	11928836	0	91.25	0	32705276	0	162779	12262082	75.329630972054	35840604.0	35313522.0	475159.0	2608246.0	136723.0	38459.0	0.0	351900.0	32705276.0	98.5	1.3	7.3	0.4	0.1	0.0	1.0	91.3	90	90	90.00	38	3225654360	24.8	24.3	25.9	24.9	0.0	36.4	25.7	bulk
655924	SRR1177046	SRP038980	SRS561938	SRX476235	SRA142452	GEO		Systematic analysis of the pro and anti-inflammatory activation of mouse myeloid cells	Inflammation is a fundamental physiological process and a key line of defense against pathogen invasion. Inflammation is exquisitely controlled: Too high and inflammation can be dangerous to the organism, but too low and the invading pathogen can escape suppression. Multiple opposing molecules initiate either a pro or anti inflammatory program, of particular interest is the pro-inflammatory bacterial endotoxins and an opposing anti-inflammatory pathway involving IL-10 and STAT3. Much work has been expended in understanding these two pathways in macrophages, key cells in the myeloid system. But other cells of the myeloid system also show a response to endotoxin and IL-10. These myeloid cell types have been less well explored. With the aim to understand similarities and differences amongst myeloid cells we performed RNA-seq analysis on 5 cells from the myeloid system: Macrophages, Neutrophils, splenic dendritic cells, mast cells and eosinophils. We treated the cells with IL-10 or LPS (endotoxin), either separately or in combination. Although the 5 cell types show much similarity in the outcome of the pro inflammatory response, the broad outline of their pro and anti-inflammatory response is highly divergent between the 5 myeloid cell types. Overall design: RNA-seq data from 5 myeloid cell types, treated with IL-10, LPS or both in combination. Samples are in biological duplicate.		GSM1335238: PEC macrophage -IL10 -LPS replicate 1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			TRIzol RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2000	source_name;;Peritoneal exudate cells (adherent cells)|strain;;C57Bl6cJ|treatment;;None	GEO Accession;;GSM1335238		GSM1335238	PEC macrophage -IL10 -LPS replicate 1	2400000120	13333334	2015-07-22 17:07:11	1450873676	2400000120	13333334	2	13333334	index:0,count:13333334,average:90,stdev:0|index:1,count:13333334,average:90,stdev:0	GSM1335238_r1	GEO			in_mesa	25765318	3.26	2.5	0.03	2301617529	2329878819	2151331912	2183757747	101.23	101.51	13082901	12056145	211.832	557.444	190	383579	91.52	97.89	14355101	11973161	14355101	11973161	92.6	93.12	14355101	12114589	14355101	11389711	43526348	1.89	1.05	0	6.38	0	0.28	0	0.02	0	0.00	0	1.58	0	13082901	0	180	0	177.36	0	1.60	0	0.00	0	1.34	0	0.00	0	296.30	0	0.64	0	140134	0	13333334	0	851178	0	37290	0	2894	0	0	0	210249	0	8004	0	0	0	32833	0	6052218	0	6264	0	6099319	0	91.74	0	12231723	0	132401	6212117	46.918958316025	13333334.0	13082901.0	140134.0	851178.0	37290.0	2894.0	0.0	210249.0	12231723.0	98.1	1.1	6.4	0.3	0.0	0.0	1.6	91.7	90	90	90.00	37	1200000060	23.8	25.3	27.0	24.0	0.0	32.8	14.5	bulk
655933	SRR1177047	SRP038980	SRS561940	SRX476236	SRA142452	GEO		Systematic analysis of the pro and anti-inflammatory activation of mouse myeloid cells	Inflammation is a fundamental physiological process and a key line of defense against pathogen invasion. Inflammation is exquisitely controlled: Too high and inflammation can be dangerous to the organism, but too low and the invading pathogen can escape suppression. Multiple opposing molecules initiate either a pro or anti inflammatory program, of particular interest is the pro-inflammatory bacterial endotoxins and an opposing anti-inflammatory pathway involving IL-10 and STAT3. Much work has been expended in understanding these two pathways in macrophages, key cells in the myeloid system. But other cells of the myeloid system also show a response to endotoxin and IL-10. These myeloid cell types have been less well explored. With the aim to understand similarities and differences amongst myeloid cells we performed RNA-seq analysis on 5 cells from the myeloid system: Macrophages, Neutrophils, splenic dendritic cells, mast cells and eosinophils. We treated the cells with IL-10 or LPS (endotoxin), either separately or in combination. Although the 5 cell types show much similarity in the outcome of the pro inflammatory response, the broad outline of their pro and anti-inflammatory response is highly divergent between the 5 myeloid cell types. Overall design: RNA-seq data from 5 myeloid cell types, treated with IL-10, LPS or both in combination. Samples are in biological duplicate.		GSM1335239: PEC macrophage -IL10 -LPS replicate 2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			TRIzol RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2000	source_name;;Peritoneal exudate cells (adherent cells)|strain;;C57Bl6cJ|treatment;;None	GEO Accession;;GSM1335239		GSM1335239	PEC macrophage -IL10 -LPS replicate 2	4297953648	23911641	2015-03-25 16:42:21	2964061714	4297953648	23911641	2	23911641	index:0,count:23911641,average:89.87,stdev:2.20|index:1,count:23911641,average:89.87,stdev:2.20	GSM1335239_r1	GEO			in_mesa	25765318	3.97	2.8	0.07	4179649106	4200270886	3913081400	3948757540	100.49	100.91	23663320	22358728	203.636	454.782	190	691244	88.05	94.06	25956820	20836237	25956820	20836237	89.48	89.99	25956820	21174600	25956820	19934962	229494742	5.49	0.51	0	6.32	0	0.23	0	0.05	0	0.00	0	0.77	0	23663374	0	179	0	178.42	0	1.61	0	0.00	0	1.22	0	0.00	0	137.95	0	0.26	0	122113	0	23911641	0	1512078	0	53817	0	11100	0	0	0	183350	0	7990	0	0	0	51578	0	9053777	0	13669	0	9127014	0	92.64	0	22151296	0	159580	9299278	58.273455320216	23911641.0	23663374.0	122113.0	1512078.0	53817.0	11100.0	0.0	183350.0	22151296.0	99.0	0.5	6.3	0.2	0.0	0.0	0.8	92.6	30	90	89.87	38	2148974383	24.6	24.5	25.6	25.2	0.0	35.7	19.8	bulk
655940	SRR1177048	SRP038980	SRS561939	SRX476237	SRA142452	GEO		Systematic analysis of the pro and anti-inflammatory activation of mouse myeloid cells	Inflammation is a fundamental physiological process and a key line of defense against pathogen invasion. Inflammation is exquisitely controlled: Too high and inflammation can be dangerous to the organism, but too low and the invading pathogen can escape suppression. Multiple opposing molecules initiate either a pro or anti inflammatory program, of particular interest is the pro-inflammatory bacterial endotoxins and an opposing anti-inflammatory pathway involving IL-10 and STAT3. Much work has been expended in understanding these two pathways in macrophages, key cells in the myeloid system. But other cells of the myeloid system also show a response to endotoxin and IL-10. These myeloid cell types have been less well explored. With the aim to understand similarities and differences amongst myeloid cells we performed RNA-seq analysis on 5 cells from the myeloid system: Macrophages, Neutrophils, splenic dendritic cells, mast cells and eosinophils. We treated the cells with IL-10 or LPS (endotoxin), either separately or in combination. Although the 5 cell types show much similarity in the outcome of the pro inflammatory response, the broad outline of their pro and anti-inflammatory response is highly divergent between the 5 myeloid cell types. Overall design: RNA-seq data from 5 myeloid cell types, treated with IL-10, LPS or both in combination. Samples are in biological duplicate.		GSM1335240: PEC macrophage -IL10 +LPS replicate 1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			TRIzol RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2000	source_name;;Peritoneal exudate cells (adherent cells)|strain;;C57Bl6cJ|treatment;;LPS	GEO Accession;;GSM1335240		GSM1335240	PEC macrophage -IL10 +LPS replicate 1	1238000040	6877778	2015-07-22 17:07:11	740250251	1238000040	6877778	2	6877778	index:0,count:6877778,average:90,stdev:0|index:1,count:6877778,average:90,stdev:0	GSM1335240_r1	GEO			in_mesa	25765318	2.58	2.82	0.06	1194944045	1195841328	1123561379	1129296137	100.08	100.51	6748039	6161104	221.767	632.117	198	221480	87.74	93.3	7381464	5920573	7381464	5920573	89.03	89.62	7381464	6007791	7381464	5687210	70630201	5.91	1.09	0	5.85	0	0.25	0	0.07	0	0.00	0	1.56	0	6748039	0	180	0	177.79	0	1.79	0	0.00	0	1.30	0	0.00	0	266.24	0	0.49	0	75222	0	6877778	0	402043	0	17336	0	4879	0	0	0	107524	0	2793	0	0	0	17919	0	2763227	0	4231	0	2788170	0	92.27	0	6345996	0	120666	2863717	23.732592445262	6877778.0	6748039.0	75222.0	402043.0	17336.0	4879.0	0.0	107524.0	6345996.0	98.1	1.1	5.8	0.3	0.1	0.0	1.6	92.3	90	90	90.00	38	619000020	24.5	24.7	25.7	25.1	0.0	34.5	16.2	bulk
655948	SRR1177049	SRP038980	SRS561941	SRX476238	SRA142452	GEO		Systematic analysis of the pro and anti-inflammatory activation of mouse myeloid cells	Inflammation is a fundamental physiological process and a key line of defense against pathogen invasion. Inflammation is exquisitely controlled: Too high and inflammation can be dangerous to the organism, but too low and the invading pathogen can escape suppression. Multiple opposing molecules initiate either a pro or anti inflammatory program, of particular interest is the pro-inflammatory bacterial endotoxins and an opposing anti-inflammatory pathway involving IL-10 and STAT3. Much work has been expended in understanding these two pathways in macrophages, key cells in the myeloid system. But other cells of the myeloid system also show a response to endotoxin and IL-10. These myeloid cell types have been less well explored. With the aim to understand similarities and differences amongst myeloid cells we performed RNA-seq analysis on 5 cells from the myeloid system: Macrophages, Neutrophils, splenic dendritic cells, mast cells and eosinophils. We treated the cells with IL-10 or LPS (endotoxin), either separately or in combination. Although the 5 cell types show much similarity in the outcome of the pro inflammatory response, the broad outline of their pro and anti-inflammatory response is highly divergent between the 5 myeloid cell types. Overall design: RNA-seq data from 5 myeloid cell types, treated with IL-10, LPS or both in combination. Samples are in biological duplicate.		GSM1335241: PEC macrophage -IL10 +LPS replicate 2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			TRIzol RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2000	source_name;;Peritoneal exudate cells (adherent cells)|strain;;C57Bl6cJ|treatment;;LPS	GEO Accession;;GSM1335241		GSM1335241	PEC macrophage -IL10 +LPS replicate 2	4320728128	24011045	2015-03-25 16:42:21	2973709119	4320728128	24011045	2	24011045	index:0,count:24011045,average:89.97,stdev:0.96|index:1,count:24011045,average:89.97,stdev:0.96	GSM1335241_r1	GEO			in_mesa	25765318	3.56	2.3	0.1	4172840877	4157496418	3924213884	3930642407	99.63	100.16	23761660	22694246	197.157	407.567	184	637782	87.52	93.07	25931951	20796022	25931951	20796022	89.12	89.79	25931951	21176924	25931951	20063367	256446304	6.15	0.51	0	5.90	0	0.20	0	0.08	0	0.00	0	0.76	0	23761704	0	179	0	178.67	0	1.57	0	0.00	0	1.22	0	0.00	0	338.98	0	0.25	0	121262	0	24011045	0	1416055	0	48556	0	18294	0	0	0	182491	0	6827	0	0	0	45634	0	8556381	0	14458	0	8623300	0	93.06	0	22345649	0	151416	8927304	58.958789031542	24011045.0	23761704.0	121262.0	1416055.0	48556.0	18294.0	0.0	182491.0	22345649.0	99.0	0.5	5.9	0.2	0.1	0.0	0.8	93.1	30	90	89.97	38	2160358910	25.0	24.1	25.5	25.4	0.0	35.7	19.9	bulk
656004	SRR1177050	SRP038980	SRS561942	SRX476239	SRA142452	GEO		Systematic analysis of the pro and anti-inflammatory activation of mouse myeloid cells	Inflammation is a fundamental physiological process and a key line of defense against pathogen invasion. Inflammation is exquisitely controlled: Too high and inflammation can be dangerous to the organism, but too low and the invading pathogen can escape suppression. Multiple opposing molecules initiate either a pro or anti inflammatory program, of particular interest is the pro-inflammatory bacterial endotoxins and an opposing anti-inflammatory pathway involving IL-10 and STAT3. Much work has been expended in understanding these two pathways in macrophages, key cells in the myeloid system. But other cells of the myeloid system also show a response to endotoxin and IL-10. These myeloid cell types have been less well explored. With the aim to understand similarities and differences amongst myeloid cells we performed RNA-seq analysis on 5 cells from the myeloid system: Macrophages, Neutrophils, splenic dendritic cells, mast cells and eosinophils. We treated the cells with IL-10 or LPS (endotoxin), either separately or in combination. Although the 5 cell types show much similarity in the outcome of the pro inflammatory response, the broad outline of their pro and anti-inflammatory response is highly divergent between the 5 myeloid cell types. Overall design: RNA-seq data from 5 myeloid cell types, treated with IL-10, LPS or both in combination. Samples are in biological duplicate.		GSM1335242: PEC macrophage +IL10 -LPS replicate 1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			TRIzol RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2000	source_name;;Peritoneal exudate cells (adherent cells)|strain;;C57Bl6cJ|treatment;;IL10	GEO Accession;;GSM1335242		GSM1335242	PEC macrophage +IL10 -LPS replicate 1	2400000120	13333334	2015-07-22 17:07:11	1572403190	2400000120	13333334	2	13333334	index:0,count:13333334,average:90,stdev:0|index:1,count:13333334,average:90,stdev:0	GSM1335242_r1	GEO			in_mesa	25765318	2.92	2.51	0.04	2277196669	2300097790	2137687466	2166134788	101.01	101.33	13149589	12235150	202.478	515.122	184	376653	91.67	97.64	14363033	12054253	14363033	12054253	92.5	93.04	14363033	12162757	14363033	11486228	47539022	2.09	0.93	0	6.03	0	0.26	0	0.02	0	0.00	0	1.10	0	13149589	0	180	0	176.96	0	1.59	0	0.00	0	1.27	0	0.00	0	266.67	0	0.85	0	123997	0	13333334	0	803709	0	34787	0	2469	0	0	0	146489	0	7108	0	0	0	32202	0	5935213	0	6398	0	5980921	0	92.59	0	12345880	0	131906	6074222	46.049626248995	13333334.0	13149589.0	123997.0	803709.0	34787.0	2469.0	0.0	146489.0	12345880.0	98.6	0.9	6.0	0.3	0.0	0.0	1.1	92.6	90	90	90.00	37	1200000060	23.8	25.4	26.8	24.0	0.0	31.0	13.3	bulk
656012	SRR1177051	SRP038980	SRS561943	SRX476240	SRA142452	GEO		Systematic analysis of the pro and anti-inflammatory activation of mouse myeloid cells	Inflammation is a fundamental physiological process and a key line of defense against pathogen invasion. Inflammation is exquisitely controlled: Too high and inflammation can be dangerous to the organism, but too low and the invading pathogen can escape suppression. Multiple opposing molecules initiate either a pro or anti inflammatory program, of particular interest is the pro-inflammatory bacterial endotoxins and an opposing anti-inflammatory pathway involving IL-10 and STAT3. Much work has been expended in understanding these two pathways in macrophages, key cells in the myeloid system. But other cells of the myeloid system also show a response to endotoxin and IL-10. These myeloid cell types have been less well explored. With the aim to understand similarities and differences amongst myeloid cells we performed RNA-seq analysis on 5 cells from the myeloid system: Macrophages, Neutrophils, splenic dendritic cells, mast cells and eosinophils. We treated the cells with IL-10 or LPS (endotoxin), either separately or in combination. Although the 5 cell types show much similarity in the outcome of the pro inflammatory response, the broad outline of their pro and anti-inflammatory response is highly divergent between the 5 myeloid cell types. Overall design: RNA-seq data from 5 myeloid cell types, treated with IL-10, LPS or both in combination. Samples are in biological duplicate.		GSM1335243: PEC macrophage +IL10 -LPS replicate 2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			TRIzol RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2000	source_name;;Peritoneal exudate cells (adherent cells)|strain;;C57Bl6cJ|treatment;;IL10	GEO Accession;;GSM1335243		GSM1335243	PEC macrophage +IL10 -LPS replicate 2	4289942009	23862473	2015-03-25 16:42:21	2954123668	4289942009	23862473	2	23862473	index:0,count:23862473,average:89.89,stdev:2.05|index:1,count:23862473,average:89.89,stdev:2.05	GSM1335243_r1	GEO			in_mesa	25765318	3.59	2.7	0.07	4167506824	4188355745	3909754620	3944324197	100.5	100.88	23624263	22173765	206.647	479.776	184	547659	88.51	94.35	25846359	20909413	25846359	20909413	89.87	90.38	25846359	21230068	25846359	20028569	219697034	5.27	0.50	0	6.13	0	0.22	0	0.05	0	0.00	0	0.73	0	23624317	0	179	0	178.41	0	1.63	0	0.00	0	1.23	0	0.00	0	284.45	0	0.27	0	119761	0	23862473	0	1463251	0	52764	0	10786	0	0	0	174606	0	9355	0	0	0	55050	0	9485277	0	13964	0	9563646	0	92.87	0	22161066	0	160335	9768858	60.927794929367	23862473.0	23624317.0	119761.0	1463251.0	52764.0	10786.0	0.0	174606.0	22161066.0	99.0	0.5	6.1	0.2	0.0	0.0	0.7	92.9	30	90	89.89	38	2144967993	24.5	24.6	25.7	25.2	0.0	35.7	19.7	bulk
656020	SRR1177052	SRP038980	SRS561944	SRX476241	SRA142452	GEO		Systematic analysis of the pro and anti-inflammatory activation of mouse myeloid cells	Inflammation is a fundamental physiological process and a key line of defense against pathogen invasion. Inflammation is exquisitely controlled: Too high and inflammation can be dangerous to the organism, but too low and the invading pathogen can escape suppression. Multiple opposing molecules initiate either a pro or anti inflammatory program, of particular interest is the pro-inflammatory bacterial endotoxins and an opposing anti-inflammatory pathway involving IL-10 and STAT3. Much work has been expended in understanding these two pathways in macrophages, key cells in the myeloid system. But other cells of the myeloid system also show a response to endotoxin and IL-10. These myeloid cell types have been less well explored. With the aim to understand similarities and differences amongst myeloid cells we performed RNA-seq analysis on 5 cells from the myeloid system: Macrophages, Neutrophils, splenic dendritic cells, mast cells and eosinophils. We treated the cells with IL-10 or LPS (endotoxin), either separately or in combination. Although the 5 cell types show much similarity in the outcome of the pro inflammatory response, the broad outline of their pro and anti-inflammatory response is highly divergent between the 5 myeloid cell types. Overall design: RNA-seq data from 5 myeloid cell types, treated with IL-10, LPS or both in combination. Samples are in biological duplicate.		GSM1335244: PEC macrophage +IL10 +LPS replicate 1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			TRIzol RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2000	source_name;;Peritoneal exudate cells (adherent cells)|strain;;C57Bl6cJ|treatment;;IL10, LPS	GEO Accession;;GSM1335244		GSM1335244	PEC macrophage +IL10 +LPS replicate 1	1238000040	6877778	2015-07-22 17:07:11	776528235	1238000040	6877778	2	6877778	index:0,count:6877778,average:90,stdev:0|index:1,count:6877778,average:90,stdev:0	GSM1335244_r1	GEO			in_mesa	25765318	2.18	2.88	0.07	1197347441	1194539570	1127974864	1130444154	99.77	100.22	6746485	5966910	240.678	757.833	211	204068	88.73	94.16	7372699	5985990	7372699	5985990	90.22	90.87	7372699	6086547	7372699	5776867	62797961	5.24	0.70	0	5.66	0	0.26	0	0.07	0	0.00	0	1.58	0	6746485	0	180	0	177.57	0	1.55	0	0.00	0	1.23	0	0.00	0	330.13	0	0.62	0	48232	0	6877778	0	388986	0	17800	0	5143	0	0	0	108350	0	3612	0	0	0	17912	0	2886655	0	3610	0	2911789	0	92.44	0	6357499	0	120742	2998554	24.834390684269	6877778.0	6746485.0	48232.0	388986.0	17800.0	5143.0	0.0	108350.0	6357499.0	98.1	0.7	5.7	0.3	0.1	0.0	1.6	92.4	90	90	90.00	38	619000020	24.4	24.7	25.8	25.1	0.0	34.9	17.1	bulk
656028	SRR1177053	SRP038980	SRS561945	SRX476242	SRA142452	GEO		Systematic analysis of the pro and anti-inflammatory activation of mouse myeloid cells	Inflammation is a fundamental physiological process and a key line of defense against pathogen invasion. Inflammation is exquisitely controlled: Too high and inflammation can be dangerous to the organism, but too low and the invading pathogen can escape suppression. Multiple opposing molecules initiate either a pro or anti inflammatory program, of particular interest is the pro-inflammatory bacterial endotoxins and an opposing anti-inflammatory pathway involving IL-10 and STAT3. Much work has been expended in understanding these two pathways in macrophages, key cells in the myeloid system. But other cells of the myeloid system also show a response to endotoxin and IL-10. These myeloid cell types have been less well explored. With the aim to understand similarities and differences amongst myeloid cells we performed RNA-seq analysis on 5 cells from the myeloid system: Macrophages, Neutrophils, splenic dendritic cells, mast cells and eosinophils. We treated the cells with IL-10 or LPS (endotoxin), either separately or in combination. Although the 5 cell types show much similarity in the outcome of the pro inflammatory response, the broad outline of their pro and anti-inflammatory response is highly divergent between the 5 myeloid cell types. Overall design: RNA-seq data from 5 myeloid cell types, treated with IL-10, LPS or both in combination. Samples are in biological duplicate.		GSM1335245: PEC macrophage +IL10 +LPS replicate 2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			TRIzol RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2000	source_name;;Peritoneal exudate cells (adherent cells)|strain;;C57Bl6cJ|treatment;;IL10, LPS	GEO Accession;;GSM1335245		GSM1335245	PEC macrophage +IL10 +LPS replicate 2	4583825100	25465695	2015-07-22 17:07:11	3088984894	4583825100	25465695	2	25465695	index:0,count:25465695,average:90,stdev:0|index:1,count:25465695,average:90,stdev:0	GSM1335245_r1	GEO			in_mesa	25765318	2.89	2.53	0.09	4504828451	4485949727	4231279888	4238397325	99.58	100.17	25247953	23546808	215.924	509.422	198	849073	87.9	93.57	27659191	22192089	27659191	22192089	89.48	90.21	27659191	22592964	27659191	21394502	255371700	5.67	0.48	0	6.01	0	0.22	0	0.08	0	0.00	0	0.55	0	25247953	0	180	0	178.92	0	1.69	0	0.00	0	1.20	0	0.00	0	295.73	0	0.16	0	122920	0	25465695	0	1530979	0	57142	0	20734	0	0	0	139866	0	9309	0	0	0	50552	0	10028431	0	16021	0	10104313	0	93.13	0	23716974	0	155714	10453732	67.134181897581	25465695.0	25247953.0	122920.0	1530979.0	57142.0	20734.0	0.0	139866.0	23716974.0	99.1	0.5	6.0	0.2	0.1	0.0	0.5	93.1	90	90	90.00	38	2291912550	24.9	24.2	25.3	25.6	0.0	36.4	23.4	bulk
656036	SRR1177054	SRP038980	SRS561946	SRX476243	SRA142452	GEO		Systematic analysis of the pro and anti-inflammatory activation of mouse myeloid cells	Inflammation is a fundamental physiological process and a key line of defense against pathogen invasion. Inflammation is exquisitely controlled: Too high and inflammation can be dangerous to the organism, but too low and the invading pathogen can escape suppression. Multiple opposing molecules initiate either a pro or anti inflammatory program, of particular interest is the pro-inflammatory bacterial endotoxins and an opposing anti-inflammatory pathway involving IL-10 and STAT3. Much work has been expended in understanding these two pathways in macrophages, key cells in the myeloid system. But other cells of the myeloid system also show a response to endotoxin and IL-10. These myeloid cell types have been less well explored. With the aim to understand similarities and differences amongst myeloid cells we performed RNA-seq analysis on 5 cells from the myeloid system: Macrophages, Neutrophils, splenic dendritic cells, mast cells and eosinophils. We treated the cells with IL-10 or LPS (endotoxin), either separately or in combination. Although the 5 cell types show much similarity in the outcome of the pro inflammatory response, the broad outline of their pro and anti-inflammatory response is highly divergent between the 5 myeloid cell types. Overall design: RNA-seq data from 5 myeloid cell types, treated with IL-10, LPS or both in combination. Samples are in biological duplicate.		GSM1335246: Mast cell -IL10 -LPS replicate 1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			TRIzol RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2000	source_name;;Bone marrow-derived mast cell|strain;;C57Bl6cJ|treatment;;None	GEO Accession;;GSM1335246		GSM1335246	Mast cell -IL10 -LPS replicate 1	5259898980	29221661	2015-07-22 17:07:11	3546906412	5259898980	29221661	2	29221661	index:0,count:29221661,average:90,stdev:0|index:1,count:29221661,average:90,stdev:0	GSM1335246_r1	GEO			in_mesa	25765318	1.89	2.66	0.09	4947823308	4847823328	4760863489	4688804042	97.98	98.49	28625563	26241964	225.957	699.380	212	525378	79.04	82.22	30659299	22625601	30659299	22625601	78.8	79.15	30659299	22557263	30659299	21781926	809364446	16.36	1.46	0	3.78	0	0.34	0	0.20	0	0.00	0	1.50	0	28625563	0	180	0	178.59	0	1.47	0	0.00	0	1.16	0	0.00	0	339.35	0	0.12	0	426291	0	29221661	0	1106036	0	100746	0	58147	0	0	0	437205	0	8502	0	0	0	74053	0	9777712	0	18660	0	9878927	0	94.18	0	27519527	0	187999	9776107	52.000845749180	29221661.0	28625563.0	426291.0	1106036.0	100746.0	58147.0	0.0	437205.0	27519527.0	98.0	1.5	3.8	0.3	0.2	0.0	1.5	94.2	90	90	90.00	38	2629949490	25.0	24.2	25.7	25.0	0.0	36.5	25.8	bulk
656044	SRR1177055	SRP038980	SRS561947	SRX476244	SRA142452	GEO		Systematic analysis of the pro and anti-inflammatory activation of mouse myeloid cells	Inflammation is a fundamental physiological process and a key line of defense against pathogen invasion. Inflammation is exquisitely controlled: Too high and inflammation can be dangerous to the organism, but too low and the invading pathogen can escape suppression. Multiple opposing molecules initiate either a pro or anti inflammatory program, of particular interest is the pro-inflammatory bacterial endotoxins and an opposing anti-inflammatory pathway involving IL-10 and STAT3. Much work has been expended in understanding these two pathways in macrophages, key cells in the myeloid system. But other cells of the myeloid system also show a response to endotoxin and IL-10. These myeloid cell types have been less well explored. With the aim to understand similarities and differences amongst myeloid cells we performed RNA-seq analysis on 5 cells from the myeloid system: Macrophages, Neutrophils, splenic dendritic cells, mast cells and eosinophils. We treated the cells with IL-10 or LPS (endotoxin), either separately or in combination. Although the 5 cell types show much similarity in the outcome of the pro inflammatory response, the broad outline of their pro and anti-inflammatory response is highly divergent between the 5 myeloid cell types. Overall design: RNA-seq data from 5 myeloid cell types, treated with IL-10, LPS or both in combination. Samples are in biological duplicate.		GSM1335247: Mast cell -IL10 -LPS replicate 2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			TRIzol RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2000	source_name;;Bone marrow-derived mast cell|strain;;C57Bl6cJ|treatment;;None	GEO Accession;;GSM1335247		GSM1335247	Mast cell -IL10 -LPS replicate 2	6011596440	33397758	2015-07-22 17:07:11	4273371204	6011596440	33397758	2	33397758	index:0,count:33397758,average:90,stdev:0|index:1,count:33397758,average:90,stdev:0	GSM1335247_r1	GEO			in_mesa	25765318	3.4	2.76	0.11	5000115066	4977141077	4665181394	4668266228	99.54	100.07	32990864	31204570	176.535	458.007	136	357779	82.56	88.59	36740181	27236895	36740181	27236895	84.38	84.81	36740181	27836652	36740181	26073650	543041569	10.86	0.78	0	6.72	0	0.46	0	0.13	0	0.00	0	0.63	0	32990864	0	180	0	178.77	0	1.40	0	0.00	0	1.14	0	0.01	0	440.41	0	0.18	0	259393	0	33397758	0	2245573	0	153405	0	42246	0	0	0	211243	0	7894	0	0	0	90258	0	12228905	0	22925	0	12349982	0	92.06	0	30745291	0	188012	11369917	60.474421845414	33397758.0	32990864.0	259393.0	2245573.0	153405.0	42246.0	0.0	211243.0	30745291.0	98.8	0.8	6.7	0.5	0.1	0.0	0.6	92.1	90	90	90.00	38	3005798220	25.4	24.5	24.5	25.6	0.0	35.8	23.2	bulk
656053	SRR1177056	SRP038980	SRS561948	SRX476245	SRA142452	GEO		Systematic analysis of the pro and anti-inflammatory activation of mouse myeloid cells	Inflammation is a fundamental physiological process and a key line of defense against pathogen invasion. Inflammation is exquisitely controlled: Too high and inflammation can be dangerous to the organism, but too low and the invading pathogen can escape suppression. Multiple opposing molecules initiate either a pro or anti inflammatory program, of particular interest is the pro-inflammatory bacterial endotoxins and an opposing anti-inflammatory pathway involving IL-10 and STAT3. Much work has been expended in understanding these two pathways in macrophages, key cells in the myeloid system. But other cells of the myeloid system also show a response to endotoxin and IL-10. These myeloid cell types have been less well explored. With the aim to understand similarities and differences amongst myeloid cells we performed RNA-seq analysis on 5 cells from the myeloid system: Macrophages, Neutrophils, splenic dendritic cells, mast cells and eosinophils. We treated the cells with IL-10 or LPS (endotoxin), either separately or in combination. Although the 5 cell types show much similarity in the outcome of the pro inflammatory response, the broad outline of their pro and anti-inflammatory response is highly divergent between the 5 myeloid cell types. Overall design: RNA-seq data from 5 myeloid cell types, treated with IL-10, LPS or both in combination. Samples are in biological duplicate.		GSM1335248: Mast cell -IL10 +LPS replicate 1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			TRIzol RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2000	source_name;;Bone marrow-derived mast cell|strain;;C57Bl6cJ|treatment;;LPS	GEO Accession;;GSM1335248		GSM1335248	Mast cell -IL10 +LPS replicate 1	6024723660	33470687	2015-07-22 17:07:11	4144975185	6024723660	33470687	2	33470687	index:0,count:33470687,average:90,stdev:0|index:1,count:33470687,average:90,stdev:0	GSM1335248_r1	GEO			in_mesa	25765318	4.7	2.45	0.17	5640931390	5519156413	5281999823	5204104884	97.84	98.53	32808613	30345729	217.242	630.937	205	625115	79.42	84.88	36257756	26058014	36257756	26058014	81.25	81.65	36257756	26657908	36257756	25066524	748241112	13.26	1.24	0	6.30	0	0.37	0	0.17	0	0.00	0	1.44	0	32808613	0	180	0	178.56	0	1.58	0	0.00	0	1.18	0	0.00	0	352.32	0	0.12	0	414742	0	33470687	0	2107912	0	124264	0	55605	0	0	0	482205	0	11981	0	0	0	90968	0	10976858	0	19775	0	11099582	0	91.72	0	30700701	0	178717	10965378	61.356099307844	33470687.0	32808613.0	414742.0	2107912.0	124264.0	55605.0	0.0	482205.0	30700701.0	98.0	1.2	6.3	0.4	0.2	0.0	1.4	91.7	90	90	90.00	38	3012361830	25.2	23.9	25.4	25.3	0.2	36.2	24.3	bulk
656061	SRR1177057	SRP038980	SRS561949	SRX476246	SRA142452	GEO		Systematic analysis of the pro and anti-inflammatory activation of mouse myeloid cells	Inflammation is a fundamental physiological process and a key line of defense against pathogen invasion. Inflammation is exquisitely controlled: Too high and inflammation can be dangerous to the organism, but too low and the invading pathogen can escape suppression. Multiple opposing molecules initiate either a pro or anti inflammatory program, of particular interest is the pro-inflammatory bacterial endotoxins and an opposing anti-inflammatory pathway involving IL-10 and STAT3. Much work has been expended in understanding these two pathways in macrophages, key cells in the myeloid system. But other cells of the myeloid system also show a response to endotoxin and IL-10. These myeloid cell types have been less well explored. With the aim to understand similarities and differences amongst myeloid cells we performed RNA-seq analysis on 5 cells from the myeloid system: Macrophages, Neutrophils, splenic dendritic cells, mast cells and eosinophils. We treated the cells with IL-10 or LPS (endotoxin), either separately or in combination. Although the 5 cell types show much similarity in the outcome of the pro inflammatory response, the broad outline of their pro and anti-inflammatory response is highly divergent between the 5 myeloid cell types. Overall design: RNA-seq data from 5 myeloid cell types, treated with IL-10, LPS or both in combination. Samples are in biological duplicate.		GSM1335249: Mast cell -IL10 +LPS replicate 2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			TRIzol RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2000	source_name;;Bone marrow-derived mast cell|strain;;C57Bl6cJ|treatment;;LPS	GEO Accession;;GSM1335249		GSM1335249	Mast cell -IL10 +LPS replicate 2	5752032840	31955738	2015-07-22 17:07:11	4119476623	5752032840	31955738	2	31955738	index:0,count:31955738,average:90,stdev:0|index:1,count:31955738,average:90,stdev:0	GSM1335249_r1	GEO			in_mesa	25765318	3.31	2.9	0.12	4804143568	4788018812	4481563595	4488670440	99.66	100.16	31574484	29846993	176.854	451.333	136	346198	83.95	90.09	35206377	26506625	35206377	26506625	85.85	86.32	35206377	27105166	35206377	25397939	449524182	9.36	0.88	0	6.74	0	0.46	0	0.10	0	0.00	0	0.64	0	31574484	0	180	0	178.68	0	1.42	0	0.00	0	1.15	0	0.01	0	310.08	0	0.19	0	281178	0	31955738	0	2152504	0	145557	0	31484	0	0	0	204213	0	7402	0	0	0	90179	0	12137807	0	21758	0	12257146	0	92.07	0	29421980	0	178823	11322717	63.318012783590	31955738.0	31574484.0	281178.0	2152504.0	145557.0	31484.0	0.0	204213.0	29421980.0	98.8	0.9	6.7	0.5	0.1	0.0	0.6	92.1	90	90	90.00	38	2876016420	25.4	24.6	24.6	25.5	0.0	35.6	22.9	bulk
656069	SRR1177058	SRP038980	SRS561950	SRX476247	SRA142452	GEO		Systematic analysis of the pro and anti-inflammatory activation of mouse myeloid cells	Inflammation is a fundamental physiological process and a key line of defense against pathogen invasion. Inflammation is exquisitely controlled: Too high and inflammation can be dangerous to the organism, but too low and the invading pathogen can escape suppression. Multiple opposing molecules initiate either a pro or anti inflammatory program, of particular interest is the pro-inflammatory bacterial endotoxins and an opposing anti-inflammatory pathway involving IL-10 and STAT3. Much work has been expended in understanding these two pathways in macrophages, key cells in the myeloid system. But other cells of the myeloid system also show a response to endotoxin and IL-10. These myeloid cell types have been less well explored. With the aim to understand similarities and differences amongst myeloid cells we performed RNA-seq analysis on 5 cells from the myeloid system: Macrophages, Neutrophils, splenic dendritic cells, mast cells and eosinophils. We treated the cells with IL-10 or LPS (endotoxin), either separately or in combination. Although the 5 cell types show much similarity in the outcome of the pro inflammatory response, the broad outline of their pro and anti-inflammatory response is highly divergent between the 5 myeloid cell types. Overall design: RNA-seq data from 5 myeloid cell types, treated with IL-10, LPS or both in combination. Samples are in biological duplicate.		GSM1335250: Mast cell +IL10 -LPS replicate 1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			TRIzol RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2000	source_name;;Bone marrow-derived mast cell|strain;;C57Bl6cJ|treatment;;IL10	GEO Accession;;GSM1335250		GSM1335250	Mast cell +IL10 -LPS replicate 1	4672570680	25958726	2015-07-22 17:07:11	3149073259	4672570680	25958726	2	25958726	index:0,count:25958726,average:90,stdev:0|index:1,count:25958726,average:90,stdev:0	GSM1335250_r1	GEO			in_mesa	25765318	1.95	2.61	0.12	4370149262	4291500114	4193810523	4140074891	98.2	98.72	25412840	23545498	215.929	635.109	205	490418	79.77	83.21	27326362	20271456	27326362	20271456	79.54	79.93	27326362	20212980	27326362	19472809	679183900	15.54	1.51	0	4.05	0	0.35	0	0.18	0	0.00	0	1.58	0	25412840	0	180	0	178.49	0	1.53	0	0.00	0	1.18	0	0.00	0	150.73	0	0.13	0	392226	0	25958726	0	1050143	0	90221	0	46460	0	0	0	409205	0	7667	0	0	0	64899	0	8746941	0	17953	0	8837460	0	93.85	0	24362697	0	181079	8747169	48.305816798193	25958726.0	25412840.0	392226.0	1050143.0	90221.0	46460.0	0.0	409205.0	24362697.0	97.9	1.5	4.0	0.3	0.2	0.0	1.6	93.9	90	90	90.00	38	2336285340	25.0	24.2	25.8	24.9	0.0	36.5	25.8	bulk
656077	SRR1177059	SRP038980	SRS561951	SRX476248	SRA142452	GEO		Systematic analysis of the pro and anti-inflammatory activation of mouse myeloid cells	Inflammation is a fundamental physiological process and a key line of defense against pathogen invasion. Inflammation is exquisitely controlled: Too high and inflammation can be dangerous to the organism, but too low and the invading pathogen can escape suppression. Multiple opposing molecules initiate either a pro or anti inflammatory program, of particular interest is the pro-inflammatory bacterial endotoxins and an opposing anti-inflammatory pathway involving IL-10 and STAT3. Much work has been expended in understanding these two pathways in macrophages, key cells in the myeloid system. But other cells of the myeloid system also show a response to endotoxin and IL-10. These myeloid cell types have been less well explored. With the aim to understand similarities and differences amongst myeloid cells we performed RNA-seq analysis on 5 cells from the myeloid system: Macrophages, Neutrophils, splenic dendritic cells, mast cells and eosinophils. We treated the cells with IL-10 or LPS (endotoxin), either separately or in combination. Although the 5 cell types show much similarity in the outcome of the pro inflammatory response, the broad outline of their pro and anti-inflammatory response is highly divergent between the 5 myeloid cell types. Overall design: RNA-seq data from 5 myeloid cell types, treated with IL-10, LPS or both in combination. Samples are in biological duplicate.		GSM1335251: Mast cell +IL10 -LPS replicate 2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			TRIzol RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2000	source_name;;Bone marrow-derived mast cell|strain;;C57Bl6cJ|treatment;;IL10	GEO Accession;;GSM1335251		GSM1335251	Mast cell +IL10 -LPS replicate 2	5774024880	32077916	2015-07-22 17:07:11	4109478328	5774024880	32077916	2	32077916	index:0,count:32077916,average:90,stdev:0|index:1,count:32077916,average:90,stdev:0	GSM1335251_r1	GEO			in_mesa	25765318	3.14	2.81	0.13	4865910212	4826019468	4524622453	4515763076	99.18	99.8	31694362	29928145	180.189	457.571	145	333740	82.42	88.74	35541062	26121885	35541062	26121885	84.24	84.81	35541062	26698431	35541062	24966928	515486423	10.59	0.77	0	7.04	0	0.48	0	0.11	0	0.00	0	0.61	0	31694362	0	180	0	178.76	0	1.40	0	0.00	0	1.15	0	0.01	0	315.52	0	0.19	0	245556	0	32077916	0	2257394	0	153190	0	35844	0	0	0	194520	0	7628	0	0	0	84701	0	11864619	0	22372	0	11979320	0	91.77	0	29436968	0	184303	11205904	60.801527918699	32077916.0	31694362.0	245556.0	2257394.0	153190.0	35844.0	0.0	194520.0	29436968.0	98.8	0.8	7.0	0.5	0.1	0.0	0.6	91.8	90	90	90.00	38	2887012440	25.4	24.5	24.5	25.6	0.0	35.8	23.2	bulk
656133	SRR1177060	SRP038980	SRS561952	SRX476249	SRA142452	GEO		Systematic analysis of the pro and anti-inflammatory activation of mouse myeloid cells	Inflammation is a fundamental physiological process and a key line of defense against pathogen invasion. Inflammation is exquisitely controlled: Too high and inflammation can be dangerous to the organism, but too low and the invading pathogen can escape suppression. Multiple opposing molecules initiate either a pro or anti inflammatory program, of particular interest is the pro-inflammatory bacterial endotoxins and an opposing anti-inflammatory pathway involving IL-10 and STAT3. Much work has been expended in understanding these two pathways in macrophages, key cells in the myeloid system. But other cells of the myeloid system also show a response to endotoxin and IL-10. These myeloid cell types have been less well explored. With the aim to understand similarities and differences amongst myeloid cells we performed RNA-seq analysis on 5 cells from the myeloid system: Macrophages, Neutrophils, splenic dendritic cells, mast cells and eosinophils. We treated the cells with IL-10 or LPS (endotoxin), either separately or in combination. Although the 5 cell types show much similarity in the outcome of the pro inflammatory response, the broad outline of their pro and anti-inflammatory response is highly divergent between the 5 myeloid cell types. Overall design: RNA-seq data from 5 myeloid cell types, treated with IL-10, LPS or both in combination. Samples are in biological duplicate.		GSM1335252: Mast cell +IL10 +LPS replicate 1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			TRIzol RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2000	source_name;;Bone marrow-derived mast cell|strain;;C57Bl6cJ|treatment;;IL10, LPS	GEO Accession;;GSM1335252		GSM1335252	Mast cell +IL10 +LPS replicate 1	7960440960	44224672	2015-07-22 17:07:11	5334137691	7960440960	44224672	2	44224672	index:0,count:44224672,average:90,stdev:0|index:1,count:44224672,average:90,stdev:0	GSM1335252_r1	GEO			in_mesa	25765318	4.57	2.38	0.31	7441988890	7239726362	6906615446	6786810537	97.28	98.27	43363882	40678351	206.204	537.920	194	810788	79.74	85.99	48778793	34576483	48778793	34576483	81.76	82.51	48778793	35453342	48778793	33178934	877385378	11.79	1.20	0	7.13	0	0.42	0	0.13	0	0.00	0	1.39	0	43363882	0	180	0	178.62	0	1.59	0	0.00	0	1.18	0	0.00	0	340.92	0	0.10	0	529985	0	44224672	0	3152367	0	185402	0	59411	0	0	0	615977	0	14094	0	0	0	117781	0	14855053	0	25151	0	15012079	0	90.93	0	40211515	0	188858	14930607	79.057318196740	44224672.0	43363882.0	529985.0	3152367.0	185402.0	59411.0	0.0	615977.0	40211515.0	98.1	1.2	7.1	0.4	0.1	0.0	1.4	90.9	90	90	90.00	38	3980220480	25.1	24.1	25.6	25.2	0.0	36.6	26.2	bulk
656142	SRR1177061	SRP038980	SRS561953	SRX476250	SRA142452	GEO		Systematic analysis of the pro and anti-inflammatory activation of mouse myeloid cells	Inflammation is a fundamental physiological process and a key line of defense against pathogen invasion. Inflammation is exquisitely controlled: Too high and inflammation can be dangerous to the organism, but too low and the invading pathogen can escape suppression. Multiple opposing molecules initiate either a pro or anti inflammatory program, of particular interest is the pro-inflammatory bacterial endotoxins and an opposing anti-inflammatory pathway involving IL-10 and STAT3. Much work has been expended in understanding these two pathways in macrophages, key cells in the myeloid system. But other cells of the myeloid system also show a response to endotoxin and IL-10. These myeloid cell types have been less well explored. With the aim to understand similarities and differences amongst myeloid cells we performed RNA-seq analysis on 5 cells from the myeloid system: Macrophages, Neutrophils, splenic dendritic cells, mast cells and eosinophils. We treated the cells with IL-10 or LPS (endotoxin), either separately or in combination. Although the 5 cell types show much similarity in the outcome of the pro inflammatory response, the broad outline of their pro and anti-inflammatory response is highly divergent between the 5 myeloid cell types. Overall design: RNA-seq data from 5 myeloid cell types, treated with IL-10, LPS or both in combination. Samples are in biological duplicate.		GSM1335253: Mast cell +IL10 +LPS replicate 2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			TRIzol RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2000	source_name;;Bone marrow-derived mast cell|strain;;C57Bl6cJ|treatment;;IL10, LPS	GEO Accession;;GSM1335253		GSM1335253	Mast cell +IL10 +LPS replicate 2	6158355480	34213086	2015-07-22 17:07:11	4411937865	6158355480	34213086	2	34213086	index:0,count:34213086,average:90,stdev:0|index:1,count:34213086,average:90,stdev:0	GSM1335253_r1	GEO			in_mesa	25765318	3.0	2.81	0.22	5181583340	5133817444	4809238766	4798789945	99.08	99.78	33825059	31950824	178.870	446.932	145	376820	82.66	89.17	38204744	27960899	38204744	27960899	84.65	85.36	38204744	28631627	38204744	26766134	529814299	10.22	0.77	0	7.21	0	0.51	0	0.10	0	0.00	0	0.52	0	33825059	0	180	0	178.74	0	1.41	0	0.00	0	1.14	0	0.01	0	399.89	0	0.19	0	263328	0	34213086	0	2468142	0	175988	0	32778	0	0	0	179261	0	7872	0	0	0	93366	0	12980565	0	23711	0	13105514	0	91.65	0	31356917	0	182491	12235418	67.046692713613	34213086.0	33825059.0	263328.0	2468142.0	175988.0	32778.0	0.0	179261.0	31356917.0	98.9	0.8	7.2	0.5	0.1	0.0	0.5	91.7	90	90	90.00	38	3079177740	25.4	24.6	24.5	25.5	0.0	35.6	22.9	bulk
656149	SRR1177062	SRP038980	SRS561954	SRX476251	SRA142452	GEO		Systematic analysis of the pro and anti-inflammatory activation of mouse myeloid cells	Inflammation is a fundamental physiological process and a key line of defense against pathogen invasion. Inflammation is exquisitely controlled: Too high and inflammation can be dangerous to the organism, but too low and the invading pathogen can escape suppression. Multiple opposing molecules initiate either a pro or anti inflammatory program, of particular interest is the pro-inflammatory bacterial endotoxins and an opposing anti-inflammatory pathway involving IL-10 and STAT3. Much work has been expended in understanding these two pathways in macrophages, key cells in the myeloid system. But other cells of the myeloid system also show a response to endotoxin and IL-10. These myeloid cell types have been less well explored. With the aim to understand similarities and differences amongst myeloid cells we performed RNA-seq analysis on 5 cells from the myeloid system: Macrophages, Neutrophils, splenic dendritic cells, mast cells and eosinophils. We treated the cells with IL-10 or LPS (endotoxin), either separately or in combination. Although the 5 cell types show much similarity in the outcome of the pro inflammatory response, the broad outline of their pro and anti-inflammatory response is highly divergent between the 5 myeloid cell types. Overall design: RNA-seq data from 5 myeloid cell types, treated with IL-10, LPS or both in combination. Samples are in biological duplicate.		GSM1335254: Neutrophil -IL10 -LPS replicate 1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			TRIzol RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2000	source_name;;Bone marrow neutrophil|strain;;C57Bl6cJ|treatment;;None	GEO Accession;;GSM1335254		GSM1335254	Neutrophil -IL10 -LPS replicate 1	4668852240	25938068	2015-07-22 17:07:11	3007793001	4668852240	25938068	2	25938068	index:0,count:25938068,average:90,stdev:0|index:1,count:25938068,average:90,stdev:0	GSM1335254_r1	GEO			in_mesa	25765318	2.12	2.77	0.1	4574242901	4509140912	4334553327	4294429904	98.58	99.07	25647506	24042155	217.053	520.942	195	789685	83.3	87.9	27946011	21364092	27946011	21364092	84.1	84.49	27946011	21569904	27946011	20535164	487944137	10.67	0.63	0	5.18	0	0.40	0	0.11	0	0.00	0	0.62	0	25647506	0	180	0	178.80	0	1.60	0	0.00	0	1.25	0	0.00	0	253.74	0	0.23	0	164590	0	25938068	0	1342818	0	102999	0	27739	0	0	0	159824	0	15941	0	0	0	50297	0	10594405	0	16664	0	10677307	0	93.70	0	24304688	0	175621	10906167	62.100585920818	25938068.0	25647506.0	164590.0	1342818.0	102999.0	27739.0	0.0	159824.0	24304688.0	98.9	0.6	5.2	0.4	0.1	0.0	0.6	93.7	90	90	90.00	38	2334426120	24.8	24.3	25.8	25.2	0.0	36.9	25.1	bulk
656157	SRR1177063	SRP038980	SRS561955	SRX476252	SRA142452	GEO		Systematic analysis of the pro and anti-inflammatory activation of mouse myeloid cells	Inflammation is a fundamental physiological process and a key line of defense against pathogen invasion. Inflammation is exquisitely controlled: Too high and inflammation can be dangerous to the organism, but too low and the invading pathogen can escape suppression. Multiple opposing molecules initiate either a pro or anti inflammatory program, of particular interest is the pro-inflammatory bacterial endotoxins and an opposing anti-inflammatory pathway involving IL-10 and STAT3. Much work has been expended in understanding these two pathways in macrophages, key cells in the myeloid system. But other cells of the myeloid system also show a response to endotoxin and IL-10. These myeloid cell types have been less well explored. With the aim to understand similarities and differences amongst myeloid cells we performed RNA-seq analysis on 5 cells from the myeloid system: Macrophages, Neutrophils, splenic dendritic cells, mast cells and eosinophils. We treated the cells with IL-10 or LPS (endotoxin), either separately or in combination. Although the 5 cell types show much similarity in the outcome of the pro inflammatory response, the broad outline of their pro and anti-inflammatory response is highly divergent between the 5 myeloid cell types. Overall design: RNA-seq data from 5 myeloid cell types, treated with IL-10, LPS or both in combination. Samples are in biological duplicate.		GSM1335255: Neutrophil -IL10 -LPS replicate 2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			TRIzol RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2000	source_name;;Bone marrow neutrophil|strain;;C57Bl6cJ|treatment;;None	GEO Accession;;GSM1335255		GSM1335255	Neutrophil -IL10 -LPS replicate 2	7192346040	39957478	2015-07-22 17:07:11	4906053847	7192346040	39957478	2	39957478	index:0,count:39957478,average:90,stdev:0|index:1,count:39957478,average:90,stdev:0	GSM1335255_r1	GEO			in_mesa	25765318	2.61	2.9	0.1	6899698824	6832168790	6459059828	6434726724	99.02	99.62	39369828	36553022	222.765	555.851	195	823194	84.86	90.66	43721985	33407797	43721985	33407797	86.7	87.28	43721985	34133516	43721985	32159865	575225748	8.34	1.06	0	6.31	0	0.42	0	0.09	0	0.00	0	0.96	0	39369828	0	180	0	178.68	0	1.59	0	0.00	0	1.22	0	0.00	0	326.92	0	0.11	0	423327	0	39957478	0	2521338	0	167433	0	37674	0	0	0	382543	0	27650	0	0	0	80223	0	16353001	0	22839	0	16483713	0	92.22	0	36848490	0	197755	16691100	84.402922808526	39957478.0	39369828.0	423327.0	2521338.0	167433.0	37674.0	0.0	382543.0	36848490.0	98.5	1.1	6.3	0.4	0.1	0.0	1.0	92.2	90	90	90.00	38	3596173020	24.7	24.6	25.8	24.9	0.0	36.4	25.8	bulk
656165	SRR1177064	SRP038980	SRS561956	SRX476253	SRA142452	GEO		Systematic analysis of the pro and anti-inflammatory activation of mouse myeloid cells	Inflammation is a fundamental physiological process and a key line of defense against pathogen invasion. Inflammation is exquisitely controlled: Too high and inflammation can be dangerous to the organism, but too low and the invading pathogen can escape suppression. Multiple opposing molecules initiate either a pro or anti inflammatory program, of particular interest is the pro-inflammatory bacterial endotoxins and an opposing anti-inflammatory pathway involving IL-10 and STAT3. Much work has been expended in understanding these two pathways in macrophages, key cells in the myeloid system. But other cells of the myeloid system also show a response to endotoxin and IL-10. These myeloid cell types have been less well explored. With the aim to understand similarities and differences amongst myeloid cells we performed RNA-seq analysis on 5 cells from the myeloid system: Macrophages, Neutrophils, splenic dendritic cells, mast cells and eosinophils. We treated the cells with IL-10 or LPS (endotoxin), either separately or in combination. Although the 5 cell types show much similarity in the outcome of the pro inflammatory response, the broad outline of their pro and anti-inflammatory response is highly divergent between the 5 myeloid cell types. Overall design: RNA-seq data from 5 myeloid cell types, treated with IL-10, LPS or both in combination. Samples are in biological duplicate.		GSM1335256: Neutrophil -IL10 +LPS replicate 1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			TRIzol RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2000	source_name;;Bone marrow neutrophil|strain;;C57Bl6cJ|treatment;;LPS	GEO Accession;;GSM1335256		GSM1335256	Neutrophil -IL10 +LPS replicate 1	4946737680	27481876	2015-07-22 17:07:11	3167289920	4946737680	27481876	2	27481876	index:0,count:27481876,average:90,stdev:0|index:1,count:27481876,average:90,stdev:0	GSM1335256_r1	GEO			in_mesa	25765318	2.7	2.4	0.13	4813624491	4694895112	4524671518	4455618541	97.53	98.47	27131644	25933661	205.200	431.854	195	1103010	81.07	86.25	29825119	21996013	29825119	21996013	82.07	82.87	29825119	22266562	29825119	21135096	548804211	11.40	0.66	0	5.93	0	0.45	0	0.15	0	0.00	0	0.68	0	27131644	0	180	0	178.83	0	1.55	0	0.00	0	1.21	0	0.00	0	321.22	0	0.20	0	180051	0	27481876	0	1628915	0	122575	0	41386	0	0	0	186271	0	12393	0	0	0	51163	0	10118427	0	17402	0	10199385	0	92.80	0	25502729	0	156960	10462492	66.657059123344	27481876.0	27131644.0	180051.0	1628915.0	122575.0	41386.0	0.0	186271.0	25502729.0	98.7	0.7	5.9	0.4	0.2	0.0	0.7	92.8	90	90	90.00	38	2473368840	25.4	23.6	24.8	26.2	0.0	37.0	25.1	bulk
656173	SRR1177065	SRP038980	SRS561957	SRX476254	SRA142452	GEO		Systematic analysis of the pro and anti-inflammatory activation of mouse myeloid cells	Inflammation is a fundamental physiological process and a key line of defense against pathogen invasion. Inflammation is exquisitely controlled: Too high and inflammation can be dangerous to the organism, but too low and the invading pathogen can escape suppression. Multiple opposing molecules initiate either a pro or anti inflammatory program, of particular interest is the pro-inflammatory bacterial endotoxins and an opposing anti-inflammatory pathway involving IL-10 and STAT3. Much work has been expended in understanding these two pathways in macrophages, key cells in the myeloid system. But other cells of the myeloid system also show a response to endotoxin and IL-10. These myeloid cell types have been less well explored. With the aim to understand similarities and differences amongst myeloid cells we performed RNA-seq analysis on 5 cells from the myeloid system: Macrophages, Neutrophils, splenic dendritic cells, mast cells and eosinophils. We treated the cells with IL-10 or LPS (endotoxin), either separately or in combination. Although the 5 cell types show much similarity in the outcome of the pro inflammatory response, the broad outline of their pro and anti-inflammatory response is highly divergent between the 5 myeloid cell types. Overall design: RNA-seq data from 5 myeloid cell types, treated with IL-10, LPS or both in combination. Samples are in biological duplicate.		GSM1335257: Neutrophil -IL10 +LPS replicate 2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			TRIzol RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2000	source_name;;Bone marrow neutrophil|strain;;C57Bl6cJ|treatment;;LPS	GEO Accession;;GSM1335257		GSM1335257	Neutrophil -IL10 +LPS replicate 2	7491432420	41619069	2015-07-22 17:07:11	5156625887	7491432420	41619069	2	41619069	index:0,count:41619069,average:90,stdev:0|index:1,count:41619069,average:90,stdev:0	GSM1335257_r1	GEO			in_mesa	25765318	2.49	2.65	0.14	7005668097	6938529819	6550669316	6535380349	99.04	99.77	40728579	38327948	212.372	484.622	195	685054	84.99	90.95	45457478	34615244	45457478	34615244	86.46	87.31	45457478	35213324	45457478	33228351	554998414	7.92	1.13	0	6.41	0	0.55	0	0.11	0	0.00	0	1.49	0	40728579	0	180	0	178.54	0	1.75	0	0.00	0	1.36	0	0.00	0	226.33	0	0.13	0	469972	0	41619069	0	2669549	0	228483	0	43742	0	0	0	618265	0	16945	0	0	0	98757	0	16063779	0	28947	0	16208428	0	91.45	0	38059030	0	194134	16241326	83.660389215696	41619069.0	40728579.0	469972.0	2669549.0	228483.0	43742.0	0.0	618265.0	38059030.0	97.9	1.1	6.4	0.5	0.1	0.0	1.5	91.4	90	90	90.00	38	3745716210	24.4	24.8	26.1	24.5	0.2	36.1	24.3	bulk
656181	SRR1177066	SRP038980	SRS561958	SRX476255	SRA142452	GEO		Systematic analysis of the pro and anti-inflammatory activation of mouse myeloid cells	Inflammation is a fundamental physiological process and a key line of defense against pathogen invasion. Inflammation is exquisitely controlled: Too high and inflammation can be dangerous to the organism, but too low and the invading pathogen can escape suppression. Multiple opposing molecules initiate either a pro or anti inflammatory program, of particular interest is the pro-inflammatory bacterial endotoxins and an opposing anti-inflammatory pathway involving IL-10 and STAT3. Much work has been expended in understanding these two pathways in macrophages, key cells in the myeloid system. But other cells of the myeloid system also show a response to endotoxin and IL-10. These myeloid cell types have been less well explored. With the aim to understand similarities and differences amongst myeloid cells we performed RNA-seq analysis on 5 cells from the myeloid system: Macrophages, Neutrophils, splenic dendritic cells, mast cells and eosinophils. We treated the cells with IL-10 or LPS (endotoxin), either separately or in combination. Although the 5 cell types show much similarity in the outcome of the pro inflammatory response, the broad outline of their pro and anti-inflammatory response is highly divergent between the 5 myeloid cell types. Overall design: RNA-seq data from 5 myeloid cell types, treated with IL-10, LPS or both in combination. Samples are in biological duplicate.		GSM1335258: Neutrophil +IL10 -LPS replicate 1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			TRIzol RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2000	source_name;;Bone marrow neutrophil|strain;;C57Bl6cJ|treatment;;IL10	GEO Accession;;GSM1335258		GSM1335258	Neutrophil +IL10 -LPS replicate 1	4926256740	27368093	2015-07-22 17:07:11	3040808483	4926256740	27368093	2	27368093	index:0,count:27368093,average:90,stdev:0|index:1,count:27368093,average:90,stdev:0	GSM1335258_r1	GEO			in_mesa	25765318	2.2	2.69	0.11	4799502193	4719795157	4548691395	4498692430	98.34	98.9	27047951	25599797	207.554	480.301	195	900666	82.86	87.43	29460210	22411389	29460210	22411389	83.58	84.03	29460210	22606793	29460210	21539340	527523993	10.99	0.61	0	5.17	0	0.39	0	0.12	0	0.00	0	0.66	0	27047951	0	180	0	178.83	0	1.58	0	0.00	0	1.26	0	0.00	0	155.89	0	0.13	0	166995	0	27368093	0	1414636	0	107096	0	31784	0	0	0	181262	0	16929	0	0	0	53671	0	11248005	0	18968	0	11337573	0	93.66	0	25633315	0	176793	11565319	65.417290277330	27368093.0	27047951.0	166995.0	1414636.0	107096.0	31784.0	0.0	181262.0	25633315.0	98.8	0.6	5.2	0.4	0.1	0.0	0.7	93.7	90	90	90.00	38	2463128370	24.7	24.2	25.6	25.5	0.0	37.2	26.0	bulk
656189	SRR1177067	SRP038980	SRS561959	SRX476256	SRA142452	GEO		Systematic analysis of the pro and anti-inflammatory activation of mouse myeloid cells	Inflammation is a fundamental physiological process and a key line of defense against pathogen invasion. Inflammation is exquisitely controlled: Too high and inflammation can be dangerous to the organism, but too low and the invading pathogen can escape suppression. Multiple opposing molecules initiate either a pro or anti inflammatory program, of particular interest is the pro-inflammatory bacterial endotoxins and an opposing anti-inflammatory pathway involving IL-10 and STAT3. Much work has been expended in understanding these two pathways in macrophages, key cells in the myeloid system. But other cells of the myeloid system also show a response to endotoxin and IL-10. These myeloid cell types have been less well explored. With the aim to understand similarities and differences amongst myeloid cells we performed RNA-seq analysis on 5 cells from the myeloid system: Macrophages, Neutrophils, splenic dendritic cells, mast cells and eosinophils. We treated the cells with IL-10 or LPS (endotoxin), either separately or in combination. Although the 5 cell types show much similarity in the outcome of the pro inflammatory response, the broad outline of their pro and anti-inflammatory response is highly divergent between the 5 myeloid cell types. Overall design: RNA-seq data from 5 myeloid cell types, treated with IL-10, LPS or both in combination. Samples are in biological duplicate.		GSM1335259: Neutrophil +IL10 -LPS replicate 2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			TRIzol RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2000	source_name;;Bone marrow neutrophil|strain;;C57Bl6cJ|treatment;;IL10	GEO Accession;;GSM1335259		GSM1335259	Neutrophil +IL10 -LPS replicate 2	8793547200	48853040	2015-07-22 17:07:11	6055258393	8793547200	48853040	2	48853040	index:0,count:48853040,average:90,stdev:0|index:1,count:48853040,average:90,stdev:0	GSM1335259_r1	GEO			in_mesa	25765318	2.36	2.82	0.11	8314338411	8233196544	7801798936	7772079978	99.02	99.62	48013899	44674274	217.757	549.460	195	982574	85.11	90.73	53253805	40862571	53253805	40862571	86.7	87.34	53253805	41627948	53253805	39333346	691920866	8.32	1.05	0	6.10	0	0.47	0	0.09	0	0.00	0	1.16	0	48013899	0	180	0	178.57	0	1.58	0	0.00	0	1.22	0	0.00	0	311.83	0	0.12	0	511880	0	48853040	0	2977707	0	229075	0	44767	0	0	0	565299	0	30321	0	0	0	100444	0	20181108	0	28511	0	20340384	0	92.19	0	45036192	0	209906	20436690	97.361152134765	48853040.0	48013899.0	511880.0	2977707.0	229075.0	44767.0	0.0	565299.0	45036192.0	98.3	1.0	6.1	0.5	0.1	0.0	1.2	92.2	90	90	90.00	38	4396773600	24.5	24.7	26.0	24.7	0.2	36.2	24.3	bulk
656197	SRR1177068	SRP038980	SRS561960	SRX476257	SRA142452	GEO		Systematic analysis of the pro and anti-inflammatory activation of mouse myeloid cells	Inflammation is a fundamental physiological process and a key line of defense against pathogen invasion. Inflammation is exquisitely controlled: Too high and inflammation can be dangerous to the organism, but too low and the invading pathogen can escape suppression. Multiple opposing molecules initiate either a pro or anti inflammatory program, of particular interest is the pro-inflammatory bacterial endotoxins and an opposing anti-inflammatory pathway involving IL-10 and STAT3. Much work has been expended in understanding these two pathways in macrophages, key cells in the myeloid system. But other cells of the myeloid system also show a response to endotoxin and IL-10. These myeloid cell types have been less well explored. With the aim to understand similarities and differences amongst myeloid cells we performed RNA-seq analysis on 5 cells from the myeloid system: Macrophages, Neutrophils, splenic dendritic cells, mast cells and eosinophils. We treated the cells with IL-10 or LPS (endotoxin), either separately or in combination. Although the 5 cell types show much similarity in the outcome of the pro inflammatory response, the broad outline of their pro and anti-inflammatory response is highly divergent between the 5 myeloid cell types. Overall design: RNA-seq data from 5 myeloid cell types, treated with IL-10, LPS or both in combination. Samples are in biological duplicate.		GSM1335260: Neutrophil +IL10 +LPS replicate 1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			TRIzol RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2000	source_name;;Bone marrow neutrophil|strain;;C57Bl6cJ|treatment;;IL10, LPS	GEO Accession;;GSM1335260		GSM1335260	Neutrophil +IL10 +LPS replicate 1	4946737680	27481876	2015-07-22 17:07:11	3191861740	4946737680	27481876	2	27481876	index:0,count:27481876,average:90,stdev:0|index:1,count:27481876,average:90,stdev:0	GSM1335260_r1	GEO			in_mesa	25765318	2.44	2.48	0.14	4802069607	4692615039	4535447594	4467564007	97.72	98.5	27172442	25898206	204.692	437.427	195	1004432	82.52	87.37	29748756	22421829	29748756	22421829	83.52	84.2	29748756	22693337	29748756	21607000	506575521	10.55	0.61	0	5.50	0	0.44	0	0.12	0	0.00	0	0.56	0	27172442	0	180	0	178.83	0	1.58	0	0.00	0	1.21	0	0.00	0	309.17	0	0.20	0	166549	0	27481876	0	1510716	0	121535	0	32652	0	0	0	155247	0	13325	0	0	0	55496	0	10807264	0	18408	0	10894493	0	93.38	0	25661726	0	172553	11117410	64.428958059263	27481876.0	27172442.0	166549.0	1510716.0	121535.0	32652.0	0.0	155247.0	25661726.0	98.9	0.6	5.5	0.4	0.1	0.0	0.6	93.4	90	90	90.00	38	2473368840	24.9	24.1	25.6	25.3	0.0	36.8	25.1	bulk
656205	SRR1177069	SRP038980	SRS561961	SRX476258	SRA142452	GEO		Systematic analysis of the pro and anti-inflammatory activation of mouse myeloid cells	Inflammation is a fundamental physiological process and a key line of defense against pathogen invasion. Inflammation is exquisitely controlled: Too high and inflammation can be dangerous to the organism, but too low and the invading pathogen can escape suppression. Multiple opposing molecules initiate either a pro or anti inflammatory program, of particular interest is the pro-inflammatory bacterial endotoxins and an opposing anti-inflammatory pathway involving IL-10 and STAT3. Much work has been expended in understanding these two pathways in macrophages, key cells in the myeloid system. But other cells of the myeloid system also show a response to endotoxin and IL-10. These myeloid cell types have been less well explored. With the aim to understand similarities and differences amongst myeloid cells we performed RNA-seq analysis on 5 cells from the myeloid system: Macrophages, Neutrophils, splenic dendritic cells, mast cells and eosinophils. We treated the cells with IL-10 or LPS (endotoxin), either separately or in combination. Although the 5 cell types show much similarity in the outcome of the pro inflammatory response, the broad outline of their pro and anti-inflammatory response is highly divergent between the 5 myeloid cell types. Overall design: RNA-seq data from 5 myeloid cell types, treated with IL-10, LPS or both in combination. Samples are in biological duplicate.		GSM1335261: Neutrophil +IL10 +LPS replicate 2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			TRIzol RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2000	source_name;;Bone marrow neutrophil|strain;;C57Bl6cJ|treatment;;IL10, LPS	GEO Accession;;GSM1335261		GSM1335261	Neutrophil +IL10 +LPS replicate 2	8018563320	44547574	2015-07-22 17:07:11	5530962877	8018563320	44547574	2	44547574	index:0,count:44547574,average:90,stdev:0|index:1,count:44547574,average:90,stdev:0	GSM1335261_r1	GEO			in_mesa	25765318	2.73	2.69	0.14	7485691467	7396209746	6979968050	6945109325	98.8	99.5	43621163	40303093	224.932	583.027	198	709312	84.98	91.19	48839392	37067450	48839392	37067450	87.1	87.93	48839392	37995129	48839392	35742713	576531341	7.70	1.21	0	6.67	0	0.51	0	0.10	0	0.00	0	1.47	0	43621163	0	180	0	178.44	0	1.60	0	0.00	0	1.22	0	0.00	0	432.27	0	0.13	0	536949	0	44547574	0	2972586	0	227028	0	44093	0	0	0	655290	0	27850	0	0	0	94832	0	17953187	0	25957	0	18101826	0	91.25	0	40648577	0	199858	18088822	90.508370943370	44547574.0	43621163.0	536949.0	2972586.0	227028.0	44093.0	0.0	655290.0	40648577.0	97.9	1.2	6.7	0.5	0.1	0.0	1.5	91.2	90	90	90.00	38	4009281660	24.6	24.7	25.9	24.7	0.2	36.2	24.2	bulk
656260	SRR1177070	SRP038980	SRS561962	SRX476259	SRA142452	GEO		Systematic analysis of the pro and anti-inflammatory activation of mouse myeloid cells	Inflammation is a fundamental physiological process and a key line of defense against pathogen invasion. Inflammation is exquisitely controlled: Too high and inflammation can be dangerous to the organism, but too low and the invading pathogen can escape suppression. Multiple opposing molecules initiate either a pro or anti inflammatory program, of particular interest is the pro-inflammatory bacterial endotoxins and an opposing anti-inflammatory pathway involving IL-10 and STAT3. Much work has been expended in understanding these two pathways in macrophages, key cells in the myeloid system. But other cells of the myeloid system also show a response to endotoxin and IL-10. These myeloid cell types have been less well explored. With the aim to understand similarities and differences amongst myeloid cells we performed RNA-seq analysis on 5 cells from the myeloid system: Macrophages, Neutrophils, splenic dendritic cells, mast cells and eosinophils. We treated the cells with IL-10 or LPS (endotoxin), either separately or in combination. Although the 5 cell types show much similarity in the outcome of the pro inflammatory response, the broad outline of their pro and anti-inflammatory response is highly divergent between the 5 myeloid cell types. Overall design: RNA-seq data from 5 myeloid cell types, treated with IL-10, LPS or both in combination. Samples are in biological duplicate.		GSM1335262: Splenic dendritic cell -IL10 -LPS replicate 1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			TRIzol RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2000	source_name;;spleen-purified dendritic cells|strain;;C57Bl6cJ|treatment;;None	GEO Accession;;GSM1335262		GSM1335262	Splenic dendritic cell -IL10 -LPS replicate 1	4883906160	27132812	2015-07-22 17:07:11	3358362660	4883906160	27132812	2	27132812	index:0,count:27132812,average:90,stdev:0|index:1,count:27132812,average:90,stdev:0	GSM1335262_r1	GEO			in_mesa	25765318	2.7	3.11	0.13	4106989340	4095741507	3828824583	3836406273	99.73	100.2	26782286	25508277	178.501	433.144	146	326707	84.36	90.6	29779999	22592666	29779999	22592666	86.09	86.53	29779999	23057957	29779999	21577681	351747968	8.56	1.09	0	6.80	0	0.30	0	0.09	0	0.00	0	0.90	0	26782286	0	180	0	178.49	0	1.51	0	0.01	0	1.21	0	0.01	0	309.11	0	0.18	0	295261	0	27132812	0	1845628	0	81057	0	25128	0	0	0	244341	0	5838	0	0	0	65290	0	9519080	0	21868	0	9612076	0	91.91	0	24936658	0	183539	8955070	48.791101618730	27132812.0	26782286.0	295261.0	1845628.0	81057.0	25128.0	0.0	244341.0	24936658.0	98.7	1.1	6.8	0.3	0.1	0.0	0.9	91.9	90	90	90.00	38	2441953080	25.0	24.9	25.0	25.1	0.0	36.0	23.3	bulk
656284	SRR1177073	SRP038980	SRS561965	SRX476262	SRA142452	GEO		Systematic analysis of the pro and anti-inflammatory activation of mouse myeloid cells	Inflammation is a fundamental physiological process and a key line of defense against pathogen invasion. Inflammation is exquisitely controlled: Too high and inflammation can be dangerous to the organism, but too low and the invading pathogen can escape suppression. Multiple opposing molecules initiate either a pro or anti inflammatory program, of particular interest is the pro-inflammatory bacterial endotoxins and an opposing anti-inflammatory pathway involving IL-10 and STAT3. Much work has been expended in understanding these two pathways in macrophages, key cells in the myeloid system. But other cells of the myeloid system also show a response to endotoxin and IL-10. These myeloid cell types have been less well explored. With the aim to understand similarities and differences amongst myeloid cells we performed RNA-seq analysis on 5 cells from the myeloid system: Macrophages, Neutrophils, splenic dendritic cells, mast cells and eosinophils. We treated the cells with IL-10 or LPS (endotoxin), either separately or in combination. Although the 5 cell types show much similarity in the outcome of the pro inflammatory response, the broad outline of their pro and anti-inflammatory response is highly divergent between the 5 myeloid cell types. Overall design: RNA-seq data from 5 myeloid cell types, treated with IL-10, LPS or both in combination. Samples are in biological duplicate.		GSM1335265: Splenic dendritic cell -IL10 +LPS replicate 2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			TRIzol RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2000	source_name;;spleen-purified dendritic cells|strain;;C57Bl6cJ|treatment;;LPS	GEO Accession;;GSM1335265		GSM1335265	Splenic dendritic cell -IL10 +LPS replicate 2	4814626860	26747927	2015-07-22 17:07:14	3382232269	4814626860	26747927	2	26747927	index:0,count:26747927,average:90,stdev:0|index:1,count:26747927,average:90,stdev:0	GSM1335265_r1	GEO			in_mesa	25765318	2.31	2.9	0.1	4069106609	4070660651	3805365385	3827332569	100.04	100.58	26449422	25217307	178.140	418.061	146	327880	85.26	91.27	29245676	22549848	29245676	22549848	86.85	87.36	29245676	22971798	29245676	21582288	333991317	8.21	1.02	0	6.52	0	0.31	0	0.08	0	0.00	0	0.72	0	26449422	0	180	0	178.57	0	1.45	0	0.01	0	1.17	0	0.01	0	413.27	0	0.17	0	273762	0	26747927	0	1743068	0	83796	0	21572	0	0	0	193137	0	5125	0	0	0	61819	0	9053725	0	19612	0	9140281	0	92.37	0	24706354	0	174764	8583559	49.115143851136	26747927.0	26449422.0	273762.0	1743068.0	83796.0	21572.0	0.0	193137.0	24706354.0	98.9	1.0	6.5	0.3	0.1	0.0	0.7	92.4	90	90	90.00	38	2407313430	25.2	24.7	24.8	25.3	0.0	35.7	22.7	bulk
656293	SRR1177074	SRP038980	SRS561966	SRX476263	SRA142452	GEO		Systematic analysis of the pro and anti-inflammatory activation of mouse myeloid cells	Inflammation is a fundamental physiological process and a key line of defense against pathogen invasion. Inflammation is exquisitely controlled: Too high and inflammation can be dangerous to the organism, but too low and the invading pathogen can escape suppression. Multiple opposing molecules initiate either a pro or anti inflammatory program, of particular interest is the pro-inflammatory bacterial endotoxins and an opposing anti-inflammatory pathway involving IL-10 and STAT3. Much work has been expended in understanding these two pathways in macrophages, key cells in the myeloid system. But other cells of the myeloid system also show a response to endotoxin and IL-10. These myeloid cell types have been less well explored. With the aim to understand similarities and differences amongst myeloid cells we performed RNA-seq analysis on 5 cells from the myeloid system: Macrophages, Neutrophils, splenic dendritic cells, mast cells and eosinophils. We treated the cells with IL-10 or LPS (endotoxin), either separately or in combination. Although the 5 cell types show much similarity in the outcome of the pro inflammatory response, the broad outline of their pro and anti-inflammatory response is highly divergent between the 5 myeloid cell types. Overall design: RNA-seq data from 5 myeloid cell types, treated with IL-10, LPS or both in combination. Samples are in biological duplicate.		GSM1335266: Splenic dendritic cell +IL10 -LPS replicate 1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			TRIzol RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2000	source_name;;spleen-purified dendritic cells|strain;;C57Bl6cJ|treatment;;IL10	GEO Accession;;GSM1335266		GSM1335266	Splenic dendritic cell +IL10 -LPS replicate 1	4927055400	27372530	2015-07-22 17:07:14	3460579241	4927055400	27372530	2	27372530	index:0,count:27372530,average:90,stdev:0|index:1,count:27372530,average:90,stdev:0	GSM1335266_r1	GEO			in_mesa	25765318	2.85	3.18	0.14	4161069179	4140871484	3875571718	3876529777	99.51	100.02	27089023	25749277	179.140	434.458	146	329228	84.14	90.45	30149150	22793033	30149150	22793033	86.1	86.55	30149150	23324742	30149150	21811872	358830660	8.62	0.84	0	6.90	0	0.30	0	0.09	0	0.00	0	0.64	0	27089023	0	180	0	178.61	0	1.45	0	0.01	0	1.18	0	0.01	0	363.62	0	0.19	0	229348	0	27372530	0	1888682	0	83252	0	24586	0	0	0	175669	0	5850	0	0	0	66424	0	9822972	0	19861	0	9915107	0	92.06	0	25200341	0	185821	9243080	49.741848337917	27372530.0	27089023.0	229348.0	1888682.0	83252.0	24586.0	0.0	175669.0	25200341.0	99.0	0.8	6.9	0.3	0.1	0.0	0.6	92.1	90	90	90.00	38	2463527700	25.4	24.5	24.6	25.4	0.0	35.8	22.8	bulk
656300	SRR1177075	SRP038980	SRS561968	SRX476264	SRA142452	GEO		Systematic analysis of the pro and anti-inflammatory activation of mouse myeloid cells	Inflammation is a fundamental physiological process and a key line of defense against pathogen invasion. Inflammation is exquisitely controlled: Too high and inflammation can be dangerous to the organism, but too low and the invading pathogen can escape suppression. Multiple opposing molecules initiate either a pro or anti inflammatory program, of particular interest is the pro-inflammatory bacterial endotoxins and an opposing anti-inflammatory pathway involving IL-10 and STAT3. Much work has been expended in understanding these two pathways in macrophages, key cells in the myeloid system. But other cells of the myeloid system also show a response to endotoxin and IL-10. These myeloid cell types have been less well explored. With the aim to understand similarities and differences amongst myeloid cells we performed RNA-seq analysis on 5 cells from the myeloid system: Macrophages, Neutrophils, splenic dendritic cells, mast cells and eosinophils. We treated the cells with IL-10 or LPS (endotoxin), either separately or in combination. Although the 5 cell types show much similarity in the outcome of the pro inflammatory response, the broad outline of their pro and anti-inflammatory response is highly divergent between the 5 myeloid cell types. Overall design: RNA-seq data from 5 myeloid cell types, treated with IL-10, LPS or both in combination. Samples are in biological duplicate.		GSM1335267: Splenic dendritic cell +IL10 -LPS replicate 2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			TRIzol RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2000	source_name;;spleen-purified dendritic cells|strain;;C57Bl6cJ|treatment;;IL10	GEO Accession;;GSM1335267		GSM1335267	Splenic dendritic cell +IL10 -LPS replicate 2	4940506800	27447260	2015-07-22 17:07:14	3472045748	4940506800	27447260	2	27447260	index:0,count:27447260,average:90,stdev:0|index:1,count:27447260,average:90,stdev:0	GSM1335267_r1	GEO			in_mesa	25765318	2.73	3.01	0.12	4164856133	4157250771	3872164376	3885481687	99.82	100.34	27100920	25850709	178.812	423.451	145	332465	85.14	91.69	30238900	23073080	30238900	23073080	86.98	87.52	30238900	23571698	30238900	22025281	314604093	7.55	1.04	0	7.05	0	0.30	0	0.08	0	0.00	0	0.88	0	27100920	0	180	0	178.52	0	1.47	0	0.01	0	1.22	0	0.01	0	297.62	0	0.19	0	286820	0	27447260	0	1936011	0	81883	0	22346	0	0	0	242111	0	5842	0	0	0	63685	0	9534701	0	21478	0	9625706	0	91.68	0	25164909	0	183679	9000167	48.999433794827	27447260.0	27100920.0	286820.0	1936011.0	81883.0	22346.0	0.0	242111.0	25164909.0	98.7	1.0	7.1	0.3	0.1	0.0	0.9	91.7	90	90	90.00	38	2470253400	25.0	24.8	25.0	25.1	0.0	35.7	22.7	bulk
656308	SRR1177076	SRP038980	SRS561967	SRX476265	SRA142452	GEO		Systematic analysis of the pro and anti-inflammatory activation of mouse myeloid cells	Inflammation is a fundamental physiological process and a key line of defense against pathogen invasion. Inflammation is exquisitely controlled: Too high and inflammation can be dangerous to the organism, but too low and the invading pathogen can escape suppression. Multiple opposing molecules initiate either a pro or anti inflammatory program, of particular interest is the pro-inflammatory bacterial endotoxins and an opposing anti-inflammatory pathway involving IL-10 and STAT3. Much work has been expended in understanding these two pathways in macrophages, key cells in the myeloid system. But other cells of the myeloid system also show a response to endotoxin and IL-10. These myeloid cell types have been less well explored. With the aim to understand similarities and differences amongst myeloid cells we performed RNA-seq analysis on 5 cells from the myeloid system: Macrophages, Neutrophils, splenic dendritic cells, mast cells and eosinophils. We treated the cells with IL-10 or LPS (endotoxin), either separately or in combination. Although the 5 cell types show much similarity in the outcome of the pro inflammatory response, the broad outline of their pro and anti-inflammatory response is highly divergent between the 5 myeloid cell types. Overall design: RNA-seq data from 5 myeloid cell types, treated with IL-10, LPS or both in combination. Samples are in biological duplicate.		GSM1335268: Splenic dendritic cell +IL10 +LPS replicate 1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			TRIzol RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2000	source_name;;spleen-purified dendritic cells|strain;;C57Bl6cJ|treatment;;IL10, LPS	GEO Accession;;GSM1335268		GSM1335268	Splenic dendritic cell +IL10 +LPS replicate 1	4682787840	26015488	2015-07-22 17:07:14	3111682395	4682787840	26015488	2	26015488	index:0,count:26015488,average:90,stdev:0|index:1,count:26015488,average:90,stdev:0	GSM1335268_r1	GEO			in_mesa	25765318	2.32	2.95	0.12	3951002859	3947936582	3701766005	3717702716	99.92	100.43	25660954	24440094	178.844	424.988	146	316592	84.54	90.34	28325453	21694633	28325453	21694633	85.87	86.32	28325453	22034948	28325453	20731431	352285833	8.92	1.04	0	6.32	0	0.31	0	0.09	0	0.00	0	0.95	0	25660954	0	180	0	178.54	0	1.50	0	0.01	0	1.22	0	0.01	0	379.17	0	0.15	0	270317	0	26015488	0	1645263	0	81839	0	24419	0	0	0	248276	0	5327	0	0	0	61891	0	9095080	0	19065	0	9181363	0	92.31	0	24015691	0	176460	8595365	48.709990932789	26015488.0	25660954.0	270317.0	1645263.0	81839.0	24419.0	0.0	248276.0	24015691.0	98.6	1.0	6.3	0.3	0.1	0.0	1.0	92.3	90	90	90.00	38	2341393920	25.0	24.9	25.1	25.1	0.0	36.4	24.1	bulk
656316	SRR1177077	SRP038980	SRS561970	SRX476266	SRA142452	GEO		Systematic analysis of the pro and anti-inflammatory activation of mouse myeloid cells	Inflammation is a fundamental physiological process and a key line of defense against pathogen invasion. Inflammation is exquisitely controlled: Too high and inflammation can be dangerous to the organism, but too low and the invading pathogen can escape suppression. Multiple opposing molecules initiate either a pro or anti inflammatory program, of particular interest is the pro-inflammatory bacterial endotoxins and an opposing anti-inflammatory pathway involving IL-10 and STAT3. Much work has been expended in understanding these two pathways in macrophages, key cells in the myeloid system. But other cells of the myeloid system also show a response to endotoxin and IL-10. These myeloid cell types have been less well explored. With the aim to understand similarities and differences amongst myeloid cells we performed RNA-seq analysis on 5 cells from the myeloid system: Macrophages, Neutrophils, splenic dendritic cells, mast cells and eosinophils. We treated the cells with IL-10 or LPS (endotoxin), either separately or in combination. Although the 5 cell types show much similarity in the outcome of the pro inflammatory response, the broad outline of their pro and anti-inflammatory response is highly divergent between the 5 myeloid cell types. Overall design: RNA-seq data from 5 myeloid cell types, treated with IL-10, LPS or both in combination. Samples are in biological duplicate.		GSM1335269: Splenic dendritic cell +IL10 +LPS replicate 2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			TRIzol RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2000	source_name;;spleen-purified dendritic cells|strain;;C57Bl6cJ|treatment;;IL10, LPS	GEO Accession;;GSM1335269		GSM1335269	Splenic dendritic cell +IL10 +LPS replicate 2	4610776680	25615426	2015-07-22 17:07:11	2973708387	4610776680	25615426	2	25615426	index:0,count:25615426,average:90,stdev:0|index:1,count:25615426,average:90,stdev:0	GSM1335269_r1	GEO			in_mesa	25765318	2.14	2.88	0.1	3877607521	3883722933	3632100244	3657271490	100.16	100.69	25289811	24090872	178.014	422.873	146	308215	85.59	91.49	27943713	21645954	27943713	21645954	86.96	87.47	27943713	21991025	27943713	20695953	311380017	8.03	1.18	0	6.36	0	0.33	0	0.08	0	0.00	0	0.86	0	25289811	0	180	0	178.49	0	1.46	0	0.01	0	1.19	0	0.01	0	363.05	0	0.14	0	301988	0	25615426	0	1629440	0	83975	0	21625	0	0	0	220015	0	5370	0	0	0	61719	0	8992675	0	19309	0	9079073	0	92.37	0	23660371	0	175839	8477797	48.213405444753	25615426.0	25289811.0	301988.0	1629440.0	83975.0	21625.0	0.0	220015.0	23660371.0	98.7	1.2	6.4	0.3	0.1	0.0	0.9	92.4	90	90	90.00	38	2305388340	24.8	25.1	25.2	24.9	0.0	36.7	25.0	bulk
670661	SRR1181778	SRP039090	SRS564580	SRX479026	SRA143022	Stanford University	Li Lab	A Quantitative Mammalian Atlas of A-to-I RNA Editing	Human RNA-seq/exome-seq and mouse RNA-seq libraries were generated to identify A-to-I RNA editing events. RNA editing levels at >10,000 exonic sites in >400 human and mouse samples were profiled by mmPCR-seq.		6 Months Old Adult 2 Stomach (Strain 129S1/SvImJ) - RNA-seq	"The Illumina mRNA-seq library preparation workflow was followed with some modifications, as described previously by Tan et al. (2013). The library amplification step was performed with SYBR Green I on a real-time PCR machine to prevent over-amplification. The standard 6bp Illumina barcodes were added to each library in the final PCR step. All libraries were quantified using the Qubit dsDNA High Sensitivity Assay Kit (Invitrogen) and sequenced on HiSeq 2000 (Illumina)."			RNA-Seq	TRANSCRIPTOMIC	cDNA	paired				Illumina HiSeq 2000	age;;6 months|biomaterial_provider;;Laura Attardi (Stanford)|BioSampleModel;;Model organism or animal|genotype;;Wildtype|label;;6 Months Old Adult 2 Stomach (Strain 129S1/SvImJ)|sex;;male|strain;;129S1/SvImJ|tissue;;Stomach		202	6 Months Old Adult 2 Stomach (Strain 129S1/SvImJ)		3076235174	15228887	2017-01-20 00:00:00	1969693215	3076235174	15228887	2	15228887	index:0,count:15228887,average:101,stdev:0|index:1,count:15228887,average:101,stdev:0	6 Months Old Adult 2 Stomach (Strain 129S1/SvImJ) - RNA-seq	Stanford University			in_mesa	29022589	0.13	2.07	0.01	2816784325	2878452359	2577631420	2641284132	102.19	102.47	14213320	10922581	334.261	1107.095	234	91791	89.42	97.66	16374922	12709530	16374922	12709530	92.98	93.09	16374922	13214844	16374922	12114301	60042745	2.13	0.42	0	7.88	0	0.59	0	0.03	0	0.00	0	6.05	0	14213320	0	202	0	198.18	0	2.29	0	0.01	0	2.72	0	0.01	0	172.95	0	1.16	0	63737	0	15228887	0	1199511	0	89300	0	4808	0	0	0	921459	0	2516	0	0	0	33439	0	7832720	0	10587	0	7879262	0	85.45	0	13013809	0	139344	8717969	62.564365885865	15228887.0	14213320.0	63737.0	1199511.0	89300.0	4808.0	0.0	921459.0	13013809.0	93.3	0.4	7.9	0.6	0.0	0.0	6.1	85.5	101	101	101.00	38	1538117587	23.2	25.6	25.9	25.3	0.0	32.0	13.3	bulk
1520763	SRR1258347	SRP041343	SRS595523	SRX523362	SRA159047	GEO		A high resolution sequencing and modeling identifies distinct dynamic RNA regulatory strategies	To monitor the relative regulatory contributions of RNA production, processing and degradation, we sampled RNA from mouse DCs every 15 minutes, for the first 3 hours of their response to LPS (13 samples in total), following a short (10 minute) metabolic labeling pulse with 4sU preceding the sampled time point. We isolated RNA from each of these samples in two ways. First, to comprehensively measure total RNA regardless of its transcription time, we isolated RNA depleted of rRNA. Second, to measure only newly made RNA, we isolated 4sU-labeled RNA, which could only have been transcribed during the 10 minute labeling pulse and is thus enriched for short-lived transcripts, including mRNA precursors and processing intermediates. We deeply sequenced each isolated RNA population to provide the necessary depth to study exons, introns, and splicing junctions across the transcriptome. We showed our approach general utility by also applying it to lincRNAs and early zebrafish development data Overall design: Time-course mRNA profiles of mouse DCs that were stimulated with LPS, and labeled with a short (10 minute) 4sU pulse (0-3 hours, 15 min. intervals, 13 time points).		GSM1372454: LPS_0min_RNA_total; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted with the miRNeasy kit's procedure (Qiagen). For preparation of RNA-Sequencing samples, we used 10 μg total RNA and removed rRNA with the RiboZero kit (Epicenter). After taking an aliquot of 100 ng ribosomal depleted total RNA, we followed with 4sU purification for the remainder of the sample as desceibed in Rabani et. al., Nat. Biotech., 2011 We prepared the RNA-Seq libraries using the dUTP second strand (strand specific) protocol as described in Levin et. al, Nat. Methods, 2010.	Illumina HiSeq 2000	cell type;;dendritic cell|source_name;;Mouse dendritic cells|stimulation;;LPS|strain;;C57BL/6|time post stimulation;;0 min|treatment;;ribosomal delpetion	GEO Accession;;GSM1372454		GSM1372454	LPS_0min_RNA_total	9508169088	47070144	2014-12-16 07:10:52	6121893709	9508169088	47070144	2	47070144	index:0,count:47070144,average:101,stdev:0|index:1,count:47070144,average:101,stdev:0	GSM1372454_r1	GEO					13.18	2.05	0.08	7571801420	7250456981	6613463281	6314027062	95.76	95.47	38824461	34875436	305.944	938.095	282	335641	58.85	67.29	44610801	22850075	44610801	22850075	66.8	64.61	44610801	25935918	44610801	21939395	1918337941	25.34	0.47	0	10.34	0	0.11	0	0.10	0	0.00	0	17.31	0	38824461	0	202	0	198.74	0	4.13	0	0.05	0	3.40	0	0.06	0	165.16	0	0.52	0	222798	0	47070144	0	4866997	0	51110	0	49084	0	0	0	8145489	0	5438	0	0	0	48230	0	7704200	0	19377	0	7777245	0	72.14	0	33957464	0	181089	8039958	44.397826483111	47070144.0	38824461.0	222798.0	4866997.0	51110.0	49084.0	0.0	8145489.0	33957464.0	82.5	0.5	10.3	0.1	0.1	0.0	17.3	72.1	101	101	101.00	38	4754084544	23.3	26.0	25.1	25.6	0.0	35.3	17.6	bulk
1520780	SRR1258348	SRP041343	SRS595539	SRX523363	SRA159047	GEO		A high resolution sequencing and modeling identifies distinct dynamic RNA regulatory strategies	To monitor the relative regulatory contributions of RNA production, processing and degradation, we sampled RNA from mouse DCs every 15 minutes, for the first 3 hours of their response to LPS (13 samples in total), following a short (10 minute) metabolic labeling pulse with 4sU preceding the sampled time point. We isolated RNA from each of these samples in two ways. First, to comprehensively measure total RNA regardless of its transcription time, we isolated RNA depleted of rRNA. Second, to measure only newly made RNA, we isolated 4sU-labeled RNA, which could only have been transcribed during the 10 minute labeling pulse and is thus enriched for short-lived transcripts, including mRNA precursors and processing intermediates. We deeply sequenced each isolated RNA population to provide the necessary depth to study exons, introns, and splicing junctions across the transcriptome. We showed our approach general utility by also applying it to lincRNAs and early zebrafish development data Overall design: Time-course mRNA profiles of mouse DCs that were stimulated with LPS, and labeled with a short (10 minute) 4sU pulse (0-3 hours, 15 min. intervals, 13 time points).		GSM1372455: LPS_15min_RNA_total; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted with the miRNeasy kit's procedure (Qiagen). For preparation of RNA-Sequencing samples, we used 10 μg total RNA and removed rRNA with the RiboZero kit (Epicenter). After taking an aliquot of 100 ng ribosomal depleted total RNA, we followed with 4sU purification for the remainder of the sample as desceibed in Rabani et. al., Nat. Biotech., 2011 We prepared the RNA-Seq libraries using the dUTP second strand (strand specific) protocol as described in Levin et. al, Nat. Methods, 2010.	Illumina HiSeq 2000	cell type;;dendritic cell|source_name;;Mouse dendritic cells|stimulation;;LPS|strain;;C57BL/6|time post stimulation;;15 min|treatment;;ribosomal delpetion	GEO Accession;;GSM1372455		GSM1372455	LPS_15min_RNA_total	10468538294	51824447	2014-12-16 07:10:52	6760048472	10468538294	51824447	2	51824447	index:0,count:51824447,average:101,stdev:0|index:1,count:51824447,average:101,stdev:0	GSM1372455_r1	GEO					12.26	1.65	0.07	7651792932	7407848988	6779152463	6558146483	96.81	96.74	39506489	36607757	306.333	770.562	270	356255	55.07	62.1	44803851	21755207	44803851	21755207	58.19	55.62	44803851	22990003	44803851	19484330	2193075516	28.66	0.98	0	8.63	0	0.10	0	0.10	0	0.00	0	23.58	0	39506489	0	202	0	197.57	0	4.62	0	0.08	0	3.20	0	0.07	0	164.81	0	0.65	0	506459	0	51824447	0	4474481	0	50155	0	49905	0	0	0	12217898	0	3705	0	0	0	35871	0	5682309	0	24743	0	5746628	0	67.60	0	35032008	0	172279	5924070	34.386489357380	51824447.0	39506489.0	506459.0	4474481.0	50155.0	49905.0	0.0	12217898.0	35032008.0	76.2	1.0	8.6	0.1	0.1	0.0	23.6	67.6	101	101	101.00	38	5234269147	22.5	27.4	25.7	24.5	0.0	35.2	17.7	bulk
1520796	SRR1258349	SRP041343	SRS595540	SRX523364	SRA159047	GEO		A high resolution sequencing and modeling identifies distinct dynamic RNA regulatory strategies	To monitor the relative regulatory contributions of RNA production, processing and degradation, we sampled RNA from mouse DCs every 15 minutes, for the first 3 hours of their response to LPS (13 samples in total), following a short (10 minute) metabolic labeling pulse with 4sU preceding the sampled time point. We isolated RNA from each of these samples in two ways. First, to comprehensively measure total RNA regardless of its transcription time, we isolated RNA depleted of rRNA. Second, to measure only newly made RNA, we isolated 4sU-labeled RNA, which could only have been transcribed during the 10 minute labeling pulse and is thus enriched for short-lived transcripts, including mRNA precursors and processing intermediates. We deeply sequenced each isolated RNA population to provide the necessary depth to study exons, introns, and splicing junctions across the transcriptome. We showed our approach general utility by also applying it to lincRNAs and early zebrafish development data Overall design: Time-course mRNA profiles of mouse DCs that were stimulated with LPS, and labeled with a short (10 minute) 4sU pulse (0-3 hours, 15 min. intervals, 13 time points).		GSM1372456: LPS_30min_RNA_total; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted with the miRNeasy kit's procedure (Qiagen). For preparation of RNA-Sequencing samples, we used 10 μg total RNA and removed rRNA with the RiboZero kit (Epicenter). After taking an aliquot of 100 ng ribosomal depleted total RNA, we followed with 4sU purification for the remainder of the sample as desceibed in Rabani et. al., Nat. Biotech., 2011 We prepared the RNA-Seq libraries using the dUTP second strand (strand specific) protocol as described in Levin et. al, Nat. Methods, 2010.	Illumina HiSeq 2000	cell type;;dendritic cell|source_name;;Mouse dendritic cells|stimulation;;LPS|strain;;C57BL/6|time post stimulation;;30 min|treatment;;ribosomal delpetion	GEO Accession;;GSM1372456		GSM1372456	LPS_30min_RNA_total	8694457336	43041868	2014-12-16 07:10:52	5582420467	8694457336	43041868	2	43041868	index:0,count:43041868,average:101,stdev:0|index:1,count:43041868,average:101,stdev:0	GSM1372456_r1	GEO					14.08	1.7	0.08	6572875372	6215673208	5748989940	5414098842	94.57	94.17	33885252	30997939	306.615	838.427	286	307806	56.38	64.37	38846622	19103428	38846622	19103428	63.18	60.74	38846622	21409244	38846622	18026252	1720319774	26.17	0.72	0	9.78	0	0.11	0	0.09	0	0.00	0	21.07	0	33885252	0	202	0	197.86	0	4.46	0	0.07	0	3.40	0	0.08	0	181.23	0	0.61	0	310096	0	43041868	0	4209223	0	46415	0	40727	0	0	0	9069474	0	3615	0	0	0	34234	0	5594564	0	21966	0	5654379	0	68.95	0	29676029	0	169980	5830880	34.303329803506	43041868.0	33885252.0	310096.0	4209223.0	46415.0	40727.0	0.0	9069474.0	29676029.0	78.7	0.7	9.8	0.1	0.1	0.0	21.1	68.9	101	101	101.00	38	4347228668	23.2	26.5	25.0	25.3	0.0	35.1	17.2	bulk
1520908	SRR1258350	SRP041343	SRS595524	SRX523365	SRA159047	GEO		A high resolution sequencing and modeling identifies distinct dynamic RNA regulatory strategies	To monitor the relative regulatory contributions of RNA production, processing and degradation, we sampled RNA from mouse DCs every 15 minutes, for the first 3 hours of their response to LPS (13 samples in total), following a short (10 minute) metabolic labeling pulse with 4sU preceding the sampled time point. We isolated RNA from each of these samples in two ways. First, to comprehensively measure total RNA regardless of its transcription time, we isolated RNA depleted of rRNA. Second, to measure only newly made RNA, we isolated 4sU-labeled RNA, which could only have been transcribed during the 10 minute labeling pulse and is thus enriched for short-lived transcripts, including mRNA precursors and processing intermediates. We deeply sequenced each isolated RNA population to provide the necessary depth to study exons, introns, and splicing junctions across the transcriptome. We showed our approach general utility by also applying it to lincRNAs and early zebrafish development data Overall design: Time-course mRNA profiles of mouse DCs that were stimulated with LPS, and labeled with a short (10 minute) 4sU pulse (0-3 hours, 15 min. intervals, 13 time points).		GSM1372457: LPS_45min_RNA_total; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted with the miRNeasy kit's procedure (Qiagen). For preparation of RNA-Sequencing samples, we used 10 μg total RNA and removed rRNA with the RiboZero kit (Epicenter). After taking an aliquot of 100 ng ribosomal depleted total RNA, we followed with 4sU purification for the remainder of the sample as desceibed in Rabani et. al., Nat. Biotech., 2011 We prepared the RNA-Seq libraries using the dUTP second strand (strand specific) protocol as described in Levin et. al, Nat. Methods, 2010.	Illumina HiSeq 2000	cell type;;dendritic cell|source_name;;Mouse dendritic cells|stimulation;;LPS|strain;;C57BL/6|time post stimulation;;45 min|treatment;;ribosomal delpetion	GEO Accession;;GSM1372457		GSM1372457	LPS_45min_RNA_total	10608057876	52515138	2014-12-16 07:10:52	6858493448	10608057876	52515138	2	52515138	index:0,count:52515138,average:101,stdev:0|index:1,count:52515138,average:101,stdev:0	GSM1372457_r1	GEO					12.79	1.59	0.1	7977850336	7586476231	7076141891	6715454120	95.09	94.9	41447753	38814009	293.092	692.998	270	370305	53.21	59.91	46986611	22054365	46986611	22054365	56.77	54.25	46986611	23530719	46986611	19968826	2328182596	29.18	0.89	0	8.83	0	0.11	0	0.10	0	0.00	0	20.87	0	41447753	0	202	0	197.42	0	4.58	0	0.08	0	3.44	0	0.09	0	156.89	0	0.69	0	468535	0	52515138	0	4635595	0	56801	0	53132	0	0	0	10957452	0	3516	0	0	0	34624	0	5572166	0	29568	0	5639874	0	70.10	0	36812158	0	176867	5788696	32.729090220335	52515138.0	41447753.0	468535.0	4635595.0	56801.0	53132.0	0.0	10957452.0	36812158.0	78.9	0.9	8.8	0.1	0.1	0.0	20.9	70.1	101	101	101.00	38	5304028938	22.6	27.1	25.4	24.9	0.0	35.2	17.8	bulk
1520924	SRR1258351	SRP041343	SRS596838	SRX523366	SRA159047	GEO		A high resolution sequencing and modeling identifies distinct dynamic RNA regulatory strategies	To monitor the relative regulatory contributions of RNA production, processing and degradation, we sampled RNA from mouse DCs every 15 minutes, for the first 3 hours of their response to LPS (13 samples in total), following a short (10 minute) metabolic labeling pulse with 4sU preceding the sampled time point. We isolated RNA from each of these samples in two ways. First, to comprehensively measure total RNA regardless of its transcription time, we isolated RNA depleted of rRNA. Second, to measure only newly made RNA, we isolated 4sU-labeled RNA, which could only have been transcribed during the 10 minute labeling pulse and is thus enriched for short-lived transcripts, including mRNA precursors and processing intermediates. We deeply sequenced each isolated RNA population to provide the necessary depth to study exons, introns, and splicing junctions across the transcriptome. We showed our approach general utility by also applying it to lincRNAs and early zebrafish development data Overall design: Time-course mRNA profiles of mouse DCs that were stimulated with LPS, and labeled with a short (10 minute) 4sU pulse (0-3 hours, 15 min. intervals, 13 time points).		GSM1372458: LPS_60min_RNA_total; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted with the miRNeasy kit's procedure (Qiagen). For preparation of RNA-Sequencing samples, we used 10 μg total RNA and removed rRNA with the RiboZero kit (Epicenter). After taking an aliquot of 100 ng ribosomal depleted total RNA, we followed with 4sU purification for the remainder of the sample as desceibed in Rabani et. al., Nat. Biotech., 2011 We prepared the RNA-Seq libraries using the dUTP second strand (strand specific) protocol as described in Levin et. al, Nat. Methods, 2010.	Illumina HiSeq 2000	cell type;;dendritic cell|source_name;;Mouse dendritic cells|stimulation;;LPS|strain;;C57BL/6|time post stimulation;;60 min|treatment;;ribosomal delpetion	GEO Accession;;GSM1372458		GSM1372458	LPS_60min_RNA_total	9788382882	48457341	2014-12-16 07:10:52	6360023245	9788382882	48457341	2	48457341	index:0,count:48457341,average:101,stdev:0|index:1,count:48457341,average:101,stdev:0	GSM1372458_r1	GEO					9.7	1.5	0.1	7062286431	7000841690	6341764272	6304410542	99.13	99.41	36618779	34274689	312.551	722.695	270	355919	53.35	59.39	41019974	19537856	41019974	19537856	51.65	48.92	41019974	18914745	41019974	16094862	2146902915	30.40	1.18	0	7.68	0	0.09	0	0.09	0	0.00	0	24.25	0	36618779	0	202	0	196.83	0	4.73	0	0.09	0	3.23	0	0.09	0	175.15	0	0.73	0	573357	0	48457341	0	3720611	0	42667	0	44503	0	0	0	11751392	0	2495	0	0	0	26634	0	4426352	0	29323	0	4484804	0	67.89	0	32898168	0	165611	4604032	27.800278966977	48457341.0	36618779.0	573357.0	3720611.0	42667.0	44503.0	0.0	11751392.0	32898168.0	75.6	1.2	7.7	0.1	0.1	0.0	24.3	67.9	101	101	101.00	38	4894191441	21.9	28.2	26.1	23.8	0.0	35.2	18.2	bulk
1520940	SRR1258352	SRP041343	SRS595541	SRX523367	SRA159047	GEO		A high resolution sequencing and modeling identifies distinct dynamic RNA regulatory strategies	To monitor the relative regulatory contributions of RNA production, processing and degradation, we sampled RNA from mouse DCs every 15 minutes, for the first 3 hours of their response to LPS (13 samples in total), following a short (10 minute) metabolic labeling pulse with 4sU preceding the sampled time point. We isolated RNA from each of these samples in two ways. First, to comprehensively measure total RNA regardless of its transcription time, we isolated RNA depleted of rRNA. Second, to measure only newly made RNA, we isolated 4sU-labeled RNA, which could only have been transcribed during the 10 minute labeling pulse and is thus enriched for short-lived transcripts, including mRNA precursors and processing intermediates. We deeply sequenced each isolated RNA population to provide the necessary depth to study exons, introns, and splicing junctions across the transcriptome. We showed our approach general utility by also applying it to lincRNAs and early zebrafish development data Overall design: Time-course mRNA profiles of mouse DCs that were stimulated with LPS, and labeled with a short (10 minute) 4sU pulse (0-3 hours, 15 min. intervals, 13 time points).		GSM1372459: LPS_75min_RNA_total; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted with the miRNeasy kit's procedure (Qiagen). For preparation of RNA-Sequencing samples, we used 10 μg total RNA and removed rRNA with the RiboZero kit (Epicenter). After taking an aliquot of 100 ng ribosomal depleted total RNA, we followed with 4sU purification for the remainder of the sample as desceibed in Rabani et. al., Nat. Biotech., 2011 We prepared the RNA-Seq libraries using the dUTP second strand (strand specific) protocol as described in Levin et. al, Nat. Methods, 2010.	Illumina HiSeq 2000	cell type;;dendritic cell|source_name;;Mouse dendritic cells|stimulation;;LPS|strain;;C57BL/6|time post stimulation;;75 min|treatment;;ribosomal delpetion	GEO Accession;;GSM1372459		GSM1372459	LPS_75min_RNA_total	9676676478	47904339	2014-12-16 07:10:52	6291734166	9676676478	47904339	2	47904339	index:0,count:47904339,average:101,stdev:0|index:1,count:47904339,average:101,stdev:0	GSM1372459_r1	GEO					7.1	1.28	0.1	6622440272	6668362263	5891562621	5960152432	100.69	101.16	34561482	32513334	300.958	663.281	270	316320	54.39	61.12	39062203	18799358	39062203	18799358	50.13	47.38	39062203	17325982	39062203	14572765	1827635451	27.60	1.36	0	7.93	0	0.07	0	0.06	0	0.00	0	27.72	0	34561482	0	202	0	196.28	0	4.87	0	0.11	0	3.24	0	0.11	0	146.90	0	0.82	0	651631	0	47904339	0	3801042	0	35231	0	30339	0	0	0	13277287	0	2330	0	0	0	24560	0	4206498	0	34728	0	4268116	0	64.21	0	30760440	0	157566	4361113	27.678007945877	47904339.0	34561482.0	651631.0	3801042.0	35231.0	30339.0	0.0	13277287.0	30760440.0	72.1	1.4	7.9	0.1	0.1	0.0	27.7	64.2	101	101	101.00	38	4838338239	21.0	29.4	26.7	22.8	0.0	35.0	18.1	bulk
1520956	SRR1258353	SRP041343	SRS596837	SRX523368	SRA159047	GEO		A high resolution sequencing and modeling identifies distinct dynamic RNA regulatory strategies	To monitor the relative regulatory contributions of RNA production, processing and degradation, we sampled RNA from mouse DCs every 15 minutes, for the first 3 hours of their response to LPS (13 samples in total), following a short (10 minute) metabolic labeling pulse with 4sU preceding the sampled time point. We isolated RNA from each of these samples in two ways. First, to comprehensively measure total RNA regardless of its transcription time, we isolated RNA depleted of rRNA. Second, to measure only newly made RNA, we isolated 4sU-labeled RNA, which could only have been transcribed during the 10 minute labeling pulse and is thus enriched for short-lived transcripts, including mRNA precursors and processing intermediates. We deeply sequenced each isolated RNA population to provide the necessary depth to study exons, introns, and splicing junctions across the transcriptome. We showed our approach general utility by also applying it to lincRNAs and early zebrafish development data Overall design: Time-course mRNA profiles of mouse DCs that were stimulated with LPS, and labeled with a short (10 minute) 4sU pulse (0-3 hours, 15 min. intervals, 13 time points).		GSM1372460: LPS_90min_RNA_total; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted with the miRNeasy kit's procedure (Qiagen). For preparation of RNA-Sequencing samples, we used 10 μg total RNA and removed rRNA with the RiboZero kit (Epicenter). After taking an aliquot of 100 ng ribosomal depleted total RNA, we followed with 4sU purification for the remainder of the sample as desceibed in Rabani et. al., Nat. Biotech., 2011 We prepared the RNA-Seq libraries using the dUTP second strand (strand specific) protocol as described in Levin et. al, Nat. Methods, 2010.	Illumina HiSeq 2000	cell type;;dendritic cell|source_name;;Mouse dendritic cells|stimulation;;LPS|strain;;C57BL/6|time post stimulation;;90 min|treatment;;ribosomal delpetion	GEO Accession;;GSM1372460		GSM1372460	LPS_90min_RNA_total	8997571870	44542435	2014-12-16 07:10:52	5814917001	8997571870	44542435	2	44542435	index:0,count:44542435,average:101,stdev:0|index:1,count:44542435,average:101,stdev:0	GSM1372460_r1	GEO					9.78	1.44	0.09	6238173066	6168588262	5505395459	5455448946	98.88	99.09	32415939	30024984	305.448	752.526	270	308254	56.21	63.63	36873883	18220122	36873883	18220122	55.85	53.25	36873883	18105794	36873883	15247046	1609398467	25.80	1.14	0	8.49	0	0.09	0	0.06	0	0.00	0	27.07	0	32415939	0	202	0	196.65	0	4.62	0	0.09	0	3.17	0	0.09	0	139.07	0	0.76	0	506335	0	44542435	0	3781006	0	39433	0	28638	0	0	0	12058425	0	2570	0	0	0	27745	0	4680485	0	26387	0	4737187	0	64.29	0	28634933	0	158983	4866448	30.609863947718	44542435.0	32415939.0	506335.0	3781006.0	39433.0	28638.0	0.0	12058425.0	28634933.0	72.8	1.1	8.5	0.1	0.1	0.0	27.1	64.3	101	101	101.00	38	4498785935	21.7	28.4	26.2	23.7	0.0	35.0	17.7	bulk
1520971	SRR1258354	SRP041343	SRS596839	SRX523369	SRA159047	GEO		A high resolution sequencing and modeling identifies distinct dynamic RNA regulatory strategies	To monitor the relative regulatory contributions of RNA production, processing and degradation, we sampled RNA from mouse DCs every 15 minutes, for the first 3 hours of their response to LPS (13 samples in total), following a short (10 minute) metabolic labeling pulse with 4sU preceding the sampled time point. We isolated RNA from each of these samples in two ways. First, to comprehensively measure total RNA regardless of its transcription time, we isolated RNA depleted of rRNA. Second, to measure only newly made RNA, we isolated 4sU-labeled RNA, which could only have been transcribed during the 10 minute labeling pulse and is thus enriched for short-lived transcripts, including mRNA precursors and processing intermediates. We deeply sequenced each isolated RNA population to provide the necessary depth to study exons, introns, and splicing junctions across the transcriptome. We showed our approach general utility by also applying it to lincRNAs and early zebrafish development data Overall design: Time-course mRNA profiles of mouse DCs that were stimulated with LPS, and labeled with a short (10 minute) 4sU pulse (0-3 hours, 15 min. intervals, 13 time points).		GSM1372461: LPS_105min_RNA_total; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted with the miRNeasy kit's procedure (Qiagen). For preparation of RNA-Sequencing samples, we used 10 μg total RNA and removed rRNA with the RiboZero kit (Epicenter). After taking an aliquot of 100 ng ribosomal depleted total RNA, we followed with 4sU purification for the remainder of the sample as desceibed in Rabani et. al., Nat. Biotech., 2011 We prepared the RNA-Seq libraries using the dUTP second strand (strand specific) protocol as described in Levin et. al, Nat. Methods, 2010.	Illumina HiSeq 2000	cell type;;dendritic cell|source_name;;Mouse dendritic cells|stimulation;;LPS|strain;;C57BL/6|time post stimulation;;105 min|treatment;;ribosomal delpetion	GEO Accession;;GSM1372461		GSM1372461	LPS_105min_RNA_total	11243121636	55659018	2014-12-16 07:10:52	7310995586	11243121636	55659018	2	55659018	index:0,count:55659018,average:101,stdev:0|index:1,count:55659018,average:101,stdev:0	GSM1372461_r1	GEO					10.14	1.3	0.09	8492292097	8425810009	7588269096	7551103231	99.22	99.51	44062102	41265240	307.902	699.523	270	467311	55.37	61.87	49539098	24395027	49539098	24395027	52.61	50.1	49539098	23181880	49539098	19755579	2147709105	25.29	1.26	0	8.32	0	0.08	0	0.07	0	0.00	0	20.69	0	44062102	0	202	0	196.38	0	4.74	0	0.11	0	3.34	0	0.10	0	178.74	0	0.82	0	699300	0	55659018	0	4632992	0	42678	0	37952	0	0	0	11516286	0	3036	0	0	0	32537	0	5391063	0	38405	0	5465041	0	70.84	0	39429110	0	170848	5625678	32.927971061997	55659018.0	44062102.0	699300.0	4632992.0	42678.0	37952.0	0.0	11516286.0	39429110.0	79.2	1.3	8.3	0.1	0.1	0.0	20.7	70.8	101	101	101.00	38	5621560818	21.9	27.9	25.6	24.7	0.0	35.4	18.7	bulk
1520986	SRR1258355	SRP041343	SRS596840	SRX523370	SRA159047	GEO		A high resolution sequencing and modeling identifies distinct dynamic RNA regulatory strategies	To monitor the relative regulatory contributions of RNA production, processing and degradation, we sampled RNA from mouse DCs every 15 minutes, for the first 3 hours of their response to LPS (13 samples in total), following a short (10 minute) metabolic labeling pulse with 4sU preceding the sampled time point. We isolated RNA from each of these samples in two ways. First, to comprehensively measure total RNA regardless of its transcription time, we isolated RNA depleted of rRNA. Second, to measure only newly made RNA, we isolated 4sU-labeled RNA, which could only have been transcribed during the 10 minute labeling pulse and is thus enriched for short-lived transcripts, including mRNA precursors and processing intermediates. We deeply sequenced each isolated RNA population to provide the necessary depth to study exons, introns, and splicing junctions across the transcriptome. We showed our approach general utility by also applying it to lincRNAs and early zebrafish development data Overall design: Time-course mRNA profiles of mouse DCs that were stimulated with LPS, and labeled with a short (10 minute) 4sU pulse (0-3 hours, 15 min. intervals, 13 time points).		GSM1372462: LPS_120min_RNA_total; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted with the miRNeasy kit's procedure (Qiagen). For preparation of RNA-Sequencing samples, we used 10 μg total RNA and removed rRNA with the RiboZero kit (Epicenter). After taking an aliquot of 100 ng ribosomal depleted total RNA, we followed with 4sU purification for the remainder of the sample as desceibed in Rabani et. al., Nat. Biotech., 2011 We prepared the RNA-Seq libraries using the dUTP second strand (strand specific) protocol as described in Levin et. al, Nat. Methods, 2010.	Illumina HiSeq 2000	cell type;;dendritic cell|source_name;;Mouse dendritic cells|stimulation;;LPS|strain;;C57BL/6|time post stimulation;;120 min|treatment;;ribosomal delpetion	GEO Accession;;GSM1372462		GSM1372462	LPS_120min_RNA_total	10321013856	51094128	2014-12-16 07:10:52	6669596409	10321013856	51094128	2	51094128	index:0,count:51094128,average:101,stdev:0|index:1,count:51094128,average:101,stdev:0	GSM1372462_r1	GEO					10.76	1.49	0.09	7779624324	7515164541	6779266415	6540041800	96.6	96.47	40207739	37168596	306.818	766.005	270	434018	54.34	62.24	46137857	21847916	46137857	21847916	57.74	54.7	46137857	23217494	46137857	19201072	2039137074	26.21	0.98	0	9.99	0	0.09	0	0.08	0	0.00	0	21.14	0	40207739	0	202	0	196.92	0	4.54	0	0.08	0	3.36	0	0.08	0	165.26	0	0.73	0	502492	0	51094128	0	5103001	0	46560	0	40662	0	0	0	10799167	0	3322	0	0	0	35667	0	5903010	0	29126	0	5971125	0	68.71	0	35104738	0	173390	6157378	35.511725012977	51094128.0	40207739.0	502492.0	5103001.0	46560.0	40662.0	0.0	10799167.0	35104738.0	78.7	1.0	10.0	0.1	0.1	0.0	21.1	68.7	101	101	101.00	38	5160506928	22.2	27.4	25.5	25.0	0.0	35.4	18.6	bulk
1521002	SRR1258356	SRP041343	SRS595525	SRX523371	SRA159047	GEO		A high resolution sequencing and modeling identifies distinct dynamic RNA regulatory strategies	To monitor the relative regulatory contributions of RNA production, processing and degradation, we sampled RNA from mouse DCs every 15 minutes, for the first 3 hours of their response to LPS (13 samples in total), following a short (10 minute) metabolic labeling pulse with 4sU preceding the sampled time point. We isolated RNA from each of these samples in two ways. First, to comprehensively measure total RNA regardless of its transcription time, we isolated RNA depleted of rRNA. Second, to measure only newly made RNA, we isolated 4sU-labeled RNA, which could only have been transcribed during the 10 minute labeling pulse and is thus enriched for short-lived transcripts, including mRNA precursors and processing intermediates. We deeply sequenced each isolated RNA population to provide the necessary depth to study exons, introns, and splicing junctions across the transcriptome. We showed our approach general utility by also applying it to lincRNAs and early zebrafish development data Overall design: Time-course mRNA profiles of mouse DCs that were stimulated with LPS, and labeled with a short (10 minute) 4sU pulse (0-3 hours, 15 min. intervals, 13 time points).		GSM1372463: LPS_135min_RNA_total; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted with the miRNeasy kit's procedure (Qiagen). For preparation of RNA-Sequencing samples, we used 10 μg total RNA and removed rRNA with the RiboZero kit (Epicenter). After taking an aliquot of 100 ng ribosomal depleted total RNA, we followed with 4sU purification for the remainder of the sample as desceibed in Rabani et. al., Nat. Biotech., 2011 We prepared the RNA-Seq libraries using the dUTP second strand (strand specific) protocol as described in Levin et. al, Nat. Methods, 2010.	Illumina HiSeq 2000	cell type;;dendritic cell|source_name;;Mouse dendritic cells|stimulation;;LPS|strain;;C57BL/6|time post stimulation;;135 min|treatment;;ribosomal delpetion	GEO Accession;;GSM1372463		GSM1372463	LPS_135min_RNA_total	8353248228	41352714	2014-12-16 07:10:52	5421466387	8353248228	41352714	2	41352714	index:0,count:41352714,average:101,stdev:0|index:1,count:41352714,average:101,stdev:0	GSM1372463_r1	GEO					11.24	1.8	0.08	6196249528	5857207165	5435837612	5117614712	94.53	94.15	31962421	28786964	310.300	927.814	270	333093	56.91	64.77	36557507	18190089	36557507	18190089	63.49	61.25	36557507	20291450	36557507	17202098	1600651975	25.83	0.75	0	9.38	0	0.09	0	0.08	0	0.00	0	22.53	0	31962421	0	202	0	197.57	0	4.33	0	0.06	0	3.32	0	0.07	0	156.21	0	0.65	0	311957	0	41352714	0	3879040	0	38919	0	33987	0	0	0	9317387	0	3424	0	0	0	36886	0	5995326	0	19222	0	6054858	0	67.91	0	28083381	0	165160	6249292	37.837805764108	41352714.0	31962421.0	311957.0	3879040.0	38919.0	33987.0	0.0	9317387.0	28083381.0	77.3	0.8	9.4	0.1	0.1	0.0	22.5	67.9	101	101	101.00	38	4176624114	22.0	27.3	26.0	24.7	0.0	35.4	18.5	bulk
1521018	SRR1258357	SRP041343	SRS595526	SRX523372	SRA159047	GEO		A high resolution sequencing and modeling identifies distinct dynamic RNA regulatory strategies	To monitor the relative regulatory contributions of RNA production, processing and degradation, we sampled RNA from mouse DCs every 15 minutes, for the first 3 hours of their response to LPS (13 samples in total), following a short (10 minute) metabolic labeling pulse with 4sU preceding the sampled time point. We isolated RNA from each of these samples in two ways. First, to comprehensively measure total RNA regardless of its transcription time, we isolated RNA depleted of rRNA. Second, to measure only newly made RNA, we isolated 4sU-labeled RNA, which could only have been transcribed during the 10 minute labeling pulse and is thus enriched for short-lived transcripts, including mRNA precursors and processing intermediates. We deeply sequenced each isolated RNA population to provide the necessary depth to study exons, introns, and splicing junctions across the transcriptome. We showed our approach general utility by also applying it to lincRNAs and early zebrafish development data Overall design: Time-course mRNA profiles of mouse DCs that were stimulated with LPS, and labeled with a short (10 minute) 4sU pulse (0-3 hours, 15 min. intervals, 13 time points).		GSM1372464: LPS_150min_RNA_total; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted with the miRNeasy kit's procedure (Qiagen). For preparation of RNA-Sequencing samples, we used 10 μg total RNA and removed rRNA with the RiboZero kit (Epicenter). After taking an aliquot of 100 ng ribosomal depleted total RNA, we followed with 4sU purification for the remainder of the sample as desceibed in Rabani et. al., Nat. Biotech., 2011 We prepared the RNA-Seq libraries using the dUTP second strand (strand specific) protocol as described in Levin et. al, Nat. Methods, 2010.	Illumina HiSeq 2000	cell type;;dendritic cell|source_name;;Mouse dendritic cells|stimulation;;LPS|strain;;C57BL/6|time post stimulation;;150 min|treatment;;ribosomal delpetion	GEO Accession;;GSM1372464		GSM1372464	LPS_150min_RNA_total	9571925944	47385772	2014-12-16 07:10:52	6154086596	9571925944	47385772	2	47385772	index:0,count:47385772,average:101,stdev:0|index:1,count:47385772,average:101,stdev:0	GSM1372464_r1	GEO					12.55	1.87	0.08	7411169274	7090797625	6322883268	6025062162	95.68	95.29	37995014	34000281	308.127	950.026	287	370665	59.1	69.15	44407480	22456381	44407480	22456381	68.84	66.45	44407480	26154474	44407480	21579062	1702159832	22.97	0.46	0	11.65	0	0.11	0	0.09	0	0.00	0	19.62	0	37995014	0	202	0	198.55	0	3.90	0	0.04	0	3.33	0	0.06	0	185.02	0	0.54	0	219522	0	47385772	0	5520061	0	50515	0	42291	0	0	0	9297952	0	4362	0	0	0	47498	0	7676958	0	18641	0	7747459	0	68.53	0	32474953	0	176981	8012659	45.274119820772	47385772.0	37995014.0	219522.0	5520061.0	50515.0	42291.0	0.0	9297952.0	32474953.0	80.2	0.5	11.6	0.1	0.1	0.0	19.6	68.5	101	101	101.00	38	4785962972	22.8	26.2	25.4	25.5	0.0	35.3	17.8	bulk
1521033	SRR1258358	SRP041343	SRS595527	SRX523373	SRA159047	GEO		A high resolution sequencing and modeling identifies distinct dynamic RNA regulatory strategies	To monitor the relative regulatory contributions of RNA production, processing and degradation, we sampled RNA from mouse DCs every 15 minutes, for the first 3 hours of their response to LPS (13 samples in total), following a short (10 minute) metabolic labeling pulse with 4sU preceding the sampled time point. We isolated RNA from each of these samples in two ways. First, to comprehensively measure total RNA regardless of its transcription time, we isolated RNA depleted of rRNA. Second, to measure only newly made RNA, we isolated 4sU-labeled RNA, which could only have been transcribed during the 10 minute labeling pulse and is thus enriched for short-lived transcripts, including mRNA precursors and processing intermediates. We deeply sequenced each isolated RNA population to provide the necessary depth to study exons, introns, and splicing junctions across the transcriptome. We showed our approach general utility by also applying it to lincRNAs and early zebrafish development data Overall design: Time-course mRNA profiles of mouse DCs that were stimulated with LPS, and labeled with a short (10 minute) 4sU pulse (0-3 hours, 15 min. intervals, 13 time points).		GSM1372465: LPS_165min_RNA_total; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted with the miRNeasy kit's procedure (Qiagen). For preparation of RNA-Sequencing samples, we used 10 μg total RNA and removed rRNA with the RiboZero kit (Epicenter). After taking an aliquot of 100 ng ribosomal depleted total RNA, we followed with 4sU purification for the remainder of the sample as desceibed in Rabani et. al., Nat. Biotech., 2011 We prepared the RNA-Seq libraries using the dUTP second strand (strand specific) protocol as described in Levin et. al, Nat. Methods, 2010.	Illumina HiSeq 2000	cell type;;dendritic cell|source_name;;Mouse dendritic cells|stimulation;;LPS|strain;;C57BL/6|time post stimulation;;165 min|treatment;;ribosomal delpetion	GEO Accession;;GSM1372465		GSM1372465	LPS_165min_RNA_total	9353033492	46302146	2014-12-16 07:10:52	6056671726	9353033492	46302146	2	46302146	index:0,count:46302146,average:101,stdev:0|index:1,count:46302146,average:101,stdev:0	GSM1372465_r1	GEO					11.62	1.81	0.08	7071221179	6727310997	6017486944	5695748490	95.14	94.65	36329636	32521413	305.716	952.894	287	338656	57.92	67.92	42539419	21040480	42539419	21040480	67.63	65.08	42539419	24571322	42539419	20160533	1651511666	23.36	0.48	0	11.56	0	0.10	0	0.09	0	0.00	0	21.35	0	36329636	0	202	0	198.25	0	4.01	0	0.05	0	3.56	0	0.06	0	144.32	0	0.57	0	221789	0	46302146	0	5350531	0	47660	0	41306	0	0	0	9883544	0	4210	0	0	0	45209	0	7321506	0	17364	0	7388289	0	66.91	0	30979105	0	176350	7643588	43.343283243550	46302146.0	36329636.0	221789.0	5350531.0	47660.0	41306.0	0.0	9883544.0	30979105.0	78.5	0.5	11.6	0.1	0.1	0.0	21.3	66.9	101	101	101.00	38	4676516746	22.1	27.1	26.0	24.8	0.0	35.3	18.2	bulk
1521049	SRR1258359	SRP041343	SRS595528	SRX523374	SRA159047	GEO		A high resolution sequencing and modeling identifies distinct dynamic RNA regulatory strategies	To monitor the relative regulatory contributions of RNA production, processing and degradation, we sampled RNA from mouse DCs every 15 minutes, for the first 3 hours of their response to LPS (13 samples in total), following a short (10 minute) metabolic labeling pulse with 4sU preceding the sampled time point. We isolated RNA from each of these samples in two ways. First, to comprehensively measure total RNA regardless of its transcription time, we isolated RNA depleted of rRNA. Second, to measure only newly made RNA, we isolated 4sU-labeled RNA, which could only have been transcribed during the 10 minute labeling pulse and is thus enriched for short-lived transcripts, including mRNA precursors and processing intermediates. We deeply sequenced each isolated RNA population to provide the necessary depth to study exons, introns, and splicing junctions across the transcriptome. We showed our approach general utility by also applying it to lincRNAs and early zebrafish development data Overall design: Time-course mRNA profiles of mouse DCs that were stimulated with LPS, and labeled with a short (10 minute) 4sU pulse (0-3 hours, 15 min. intervals, 13 time points).		GSM1372466: LPS_180min_RNA_total; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted with the miRNeasy kit's procedure (Qiagen). For preparation of RNA-Sequencing samples, we used 10 μg total RNA and removed rRNA with the RiboZero kit (Epicenter). After taking an aliquot of 100 ng ribosomal depleted total RNA, we followed with 4sU purification for the remainder of the sample as desceibed in Rabani et. al., Nat. Biotech., 2011 We prepared the RNA-Seq libraries using the dUTP second strand (strand specific) protocol as described in Levin et. al, Nat. Methods, 2010.	Illumina HiSeq 2000	cell type;;dendritic cell|source_name;;Mouse dendritic cells|stimulation;;LPS|strain;;C57BL/6|time post stimulation;;180 min|treatment;;ribosomal delpetion	GEO Accession;;GSM1372466		GSM1372466	LPS_180min_RNA_total	10161614444	50305022	2014-12-16 07:10:52	6561928499	10161614444	50305022	2	50305022	index:0,count:50305022,average:101,stdev:0|index:1,count:50305022,average:101,stdev:0	GSM1372466_r1	GEO					11.54	1.81	0.07	7823955712	7422035486	6679923679	6306363220	94.86	94.41	40711630	36899755	291.157	866.777	281	325657	56.98	66.59	47616177	23196030	47616177	23196030	66.04	63.85	47616177	26885105	47616177	22239672	1905836184	24.36	0.51	0	11.69	0	0.11	0	0.10	0	0.00	0	18.86	0	40711630	0	202	0	198.35	0	4.08	0	0.05	0	3.62	0	0.07	0	175.65	0	0.57	0	257098	0	50305022	0	5878952	0	56636	0	50335	0	0	0	9486421	0	4555	0	0	0	50014	0	7928180	0	21617	0	8004366	0	69.24	0	34832678	0	178099	8225775	46.186531086643	50305022.0	40711630.0	257098.0	5878952.0	56636.0	50335.0	0.0	9486421.0	34832678.0	80.9	0.5	11.7	0.1	0.1	0.0	18.9	69.2	101	101	101.00	38	5080807222	22.4	26.7	25.8	25.1	0.0	35.5	18.5	bulk
461091	SRR1291248	SRP042078	SRS613250	SRX546213	SRA165378	GEO		Transcriptome of Smooth Muscle Cells, Interstitial Cells of Cajal and PDGFRa+ Cells	Genome scale expression data on absolute numbers of gene isoforms offer essential clues for cellular functions and biological processes. Gastrointestinal (GI) motility is regulated by smooth muscle cells (SMC) closely contacted with interstitial cells of Cajal (ICC) and fibroblast-like PDGFRa+ cells (PaC), forming an electrical syncytium. To uncover genetic identifies and cellular functions of the cells, we isolated these three cell populations from mouse small intestine and colon, obtained the transcriptome for each type of cells, and built each cell type transcriptome browser. To our knowledge, this is the first genetic resource providing a comprehensive reference for all mRNA transcripts expressed in these unique GI cell populations. Integration of these data with the UCSC genome browser revealed novel cell-specific markers, ion channel and transporter isoforms, and unique cellular and biological functions of these cells in GI physiology. Our transcriptome browsers bring new insight into the alternative expression of genes in different types of the cells and provides references for future functional studies. Overall design: mRNA profiles of SMC, ICC and PDGFRa cells isolated from mouse jejunum and colon were generated by deep sequencing using Illumina Hiseq2000..		GSM1388406: SMC Jejunum; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			mirVana miRNA Isolation Kit TruSeq RNA Sample Preparation	Illumina HiSeq 2000	age;;4 weeks|background strain;;C57BL/6|cell population;;Sorted primary cells|cell type;;SMC|source_name;;SMC in jejunum|strain;;smMHCCre-eGFP/+|tissue;;Jejunum	GEO Accession;;GSM1388406		GSM1388406	SMC Jejunum	15070238800	75351194	2015-07-31 20:26:22	9646329703	15070238800	75351194	2	75351194	index:0,count:75351194,average:100,stdev:0|index:1,count:75351194,average:100,stdev:0	GSM1388406_r1	GEO			in_mesa	26241044	8.04	3.81	0.05	11995402975	12042734834	11076075619	11180998986	100.39	100.95	72637219	68052359	192.195	536.219	146	707004	86.22	93.46	80374864	62625064	80374864	62625064	89.54	89.6	80374864	65039412	80374864	60033513	675505891	5.63	1.13	0	7.48	0	0.25	0	0.05	0	0.00	0	3.30	0	72637219	0	200	0	198.19	0	1.76	0	0.01	0	1.48	0	0.01	0	221.26	0	0.21	0	854127	0	75351194	0	5632824	0	191842	0	38846	0	0	0	2483287	0	16460	0	0	0	181539	0	34324374	0	51843	0	34574216	0	88.92	0	67004395	0	221518	31237711	141.016581045333	75351194.0	72637219.0	854127.0	5632824.0	191842.0	38846.0	0.0	2483287.0	67004395.0	96.4	1.1	7.5	0.3	0.1	0.0	3.3	88.9	100	100	100.00	38	7535119400	25.0	25.1	24.8	25.1	0.0	36.3	21.1	bulk
461095	SRR1291249	SRP042078	SRS613251	SRX546214	SRA165378	GEO		Transcriptome of Smooth Muscle Cells, Interstitial Cells of Cajal and PDGFRa+ Cells	Genome scale expression data on absolute numbers of gene isoforms offer essential clues for cellular functions and biological processes. Gastrointestinal (GI) motility is regulated by smooth muscle cells (SMC) closely contacted with interstitial cells of Cajal (ICC) and fibroblast-like PDGFRa+ cells (PaC), forming an electrical syncytium. To uncover genetic identifies and cellular functions of the cells, we isolated these three cell populations from mouse small intestine and colon, obtained the transcriptome for each type of cells, and built each cell type transcriptome browser. To our knowledge, this is the first genetic resource providing a comprehensive reference for all mRNA transcripts expressed in these unique GI cell populations. Integration of these data with the UCSC genome browser revealed novel cell-specific markers, ion channel and transporter isoforms, and unique cellular and biological functions of these cells in GI physiology. Our transcriptome browsers bring new insight into the alternative expression of genes in different types of the cells and provides references for future functional studies. Overall design: mRNA profiles of SMC, ICC and PDGFRa cells isolated from mouse jejunum and colon were generated by deep sequencing using Illumina Hiseq2000..		GSM1388407: SMC Colon; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			mirVana miRNA Isolation Kit TruSeq RNA Sample Preparation	Illumina HiSeq 2000	age;;4 weeks|background strain;;C57BL/6|cell population;;Sorted primary cells|cell type;;SMC|source_name;;SMC in colon|strain;;smMHCCre-eGFP/+|tissue;;Colon	GEO Accession;;GSM1388407		GSM1388407	SMC Colon	15144592600	75722963	2015-07-31 20:26:22	9728489419	15144592600	75722963	2	75722963	index:0,count:75722963,average:100,stdev:0|index:1,count:75722963,average:100,stdev:0	GSM1388407_r1	GEO			in_mesa	26241044	6.12	3.73	0.05	11861301320	11975396276	11128291828	11292069245	100.96	101.47	72928407	68054676	190.180	542.591	146	720567	87.37	93.21	79374592	63720059	79374592	63720059	88.64	88.8	79374592	64645841	79374592	60701173	701339597	5.91	1.10	0	6.03	0	0.23	0	0.05	0	0.00	0	3.41	0	72928407	0	200	0	198.12	0	1.68	0	0.01	0	1.57	0	0.01	0	284.26	0	0.21	0	834361	0	75722963	0	4568982	0	177738	0	35652	0	0	0	2581166	0	15351	0	0	0	166420	0	36713268	0	46649	0	36941688	0	90.28	0	68359425	0	235562	32788441	139.192403698389	75722963.0	72928407.0	834361.0	4568982.0	177738.0	35652.0	0.0	2581166.0	68359425.0	96.3	1.1	6.0	0.2	0.0	0.0	3.4	90.3	100	100	100.00	38	7572296300	24.7	25.5	25.1	24.7	0.0	36.2	20.9	bulk
461123	SRR1291250	SRP042078	SRS613252	SRX546215	SRA165378	GEO		Transcriptome of Smooth Muscle Cells, Interstitial Cells of Cajal and PDGFRa+ Cells	Genome scale expression data on absolute numbers of gene isoforms offer essential clues for cellular functions and biological processes. Gastrointestinal (GI) motility is regulated by smooth muscle cells (SMC) closely contacted with interstitial cells of Cajal (ICC) and fibroblast-like PDGFRa+ cells (PaC), forming an electrical syncytium. To uncover genetic identifies and cellular functions of the cells, we isolated these three cell populations from mouse small intestine and colon, obtained the transcriptome for each type of cells, and built each cell type transcriptome browser. To our knowledge, this is the first genetic resource providing a comprehensive reference for all mRNA transcripts expressed in these unique GI cell populations. Integration of these data with the UCSC genome browser revealed novel cell-specific markers, ion channel and transporter isoforms, and unique cellular and biological functions of these cells in GI physiology. Our transcriptome browsers bring new insight into the alternative expression of genes in different types of the cells and provides references for future functional studies. Overall design: mRNA profiles of SMC, ICC and PDGFRa cells isolated from mouse jejunum and colon were generated by deep sequencing using Illumina Hiseq2000..		GSM1388408: ICC Jejunum; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			mirVana miRNA Isolation Kit TruSeq RNA Sample Preparation	Illumina HiSeq 2000	age;;4 weeks|background strain;;C57BL/6|cell population;;Sorted primary cells|cell type;;ICC|source_name;;ICC in jejunum|strain;;KitcopGFP/+|tissue;;Jejunum	GEO Accession;;GSM1388408		GSM1388408	ICC Jejunum	20877832008	103355604	2015-07-31 20:26:22	14397995701	20877832008	103355604	2	103355604	index:0,count:103355604,average:101,stdev:0|index:1,count:103355604,average:101,stdev:0	GSM1388408_r1	GEO			in_mesa	26241044	12.06	2.69	0.13	15791620723	14918123538	14296670148	13566581826	94.47	94.89	98691117	94073252	186.682	524.906	134	904877	72.28	79.98	111009438	71338062	111009438	71338062	77.8	76.85	111009438	76781784	111009438	68549914	2257841614	14.30	1.42	0	9.19	0	0.27	0	0.20	0	0.00	0	4.03	0	98691117	0	202	0	200.11	0	1.93	0	0.01	0	1.53	0	0.01	0	258.03	0	0.29	0	1470029	0	103355604	0	9497173	0	283580	0	211731	0	0	0	4169176	0	18114	0	0	0	205676	0	29306946	0	82840	0	29613576	0	86.30	0	89193944	0	287201	25492764	88.762796786919	103355604.0	98691117.0	1470029.0	9497173.0	283580.0	211731.0	0.0	4169176.0	89193944.0	95.5	1.4	9.2	0.3	0.2	0.0	4.0	86.3	101	101	101.00	38	10438916004	26.0	23.9	24.1	26.0	0.0	34.9	18.0	bulk
461127	SRR1291251	SRP042078	SRS613253	SRX546216	SRA165378	GEO		Transcriptome of Smooth Muscle Cells, Interstitial Cells of Cajal and PDGFRa+ Cells	Genome scale expression data on absolute numbers of gene isoforms offer essential clues for cellular functions and biological processes. Gastrointestinal (GI) motility is regulated by smooth muscle cells (SMC) closely contacted with interstitial cells of Cajal (ICC) and fibroblast-like PDGFRa+ cells (PaC), forming an electrical syncytium. To uncover genetic identifies and cellular functions of the cells, we isolated these three cell populations from mouse small intestine and colon, obtained the transcriptome for each type of cells, and built each cell type transcriptome browser. To our knowledge, this is the first genetic resource providing a comprehensive reference for all mRNA transcripts expressed in these unique GI cell populations. Integration of these data with the UCSC genome browser revealed novel cell-specific markers, ion channel and transporter isoforms, and unique cellular and biological functions of these cells in GI physiology. Our transcriptome browsers bring new insight into the alternative expression of genes in different types of the cells and provides references for future functional studies. Overall design: mRNA profiles of SMC, ICC and PDGFRa cells isolated from mouse jejunum and colon were generated by deep sequencing using Illumina Hiseq2000..		GSM1388409: ICC Colon; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			mirVana miRNA Isolation Kit TruSeq RNA Sample Preparation	Illumina HiSeq 2000	age;;4 weeks|background strain;;C57BL/6|cell population;;Sorted primary cells|cell type;;ICC|source_name;;ICC in colon|strain;;KitcopGFP/+|tissue;;Colon	GEO Accession;;GSM1388409		GSM1388409	ICC Colon	19508745092	96577946	2015-07-31 20:26:22	13483461201	19508745092	96577946	2	96577946	index:0,count:96577946,average:101,stdev:0|index:1,count:96577946,average:101,stdev:0	GSM1388409_r1	GEO			in_mesa	26241044	4.28	3.13	0.1	14776563829	14468759516	14013098396	13786724824	97.92	98.38	93057787	87629280	184.611	579.040	136	867827	80.1	84.55	100329058	74543509	100329058	74543509	81.24	81.27	100329058	75602754	100329058	71650112	1987891649	13.45	1.34	0	5.07	0	0.25	0	0.16	0	0.00	0	3.23	0	93057787	0	202	0	200.15	0	1.90	0	0.01	0	1.41	0	0.01	0	239.28	0	0.27	0	1290781	0	96577946	0	4892622	0	244870	0	152076	0	0	0	3123213	0	20355	0	0	0	233137	0	35489959	0	77133	0	35820584	0	91.29	0	88165165	0	282172	30632405	108.559336149583	96577946.0	93057787.0	1290781.0	4892622.0	244870.0	152076.0	0.0	3123213.0	88165165.0	96.4	1.3	5.1	0.3	0.2	0.0	3.2	91.3	101	101	101.00	38	9754372546	25.6	24.4	24.5	25.5	0.0	34.9	18.1	bulk
922262	SRR1291252	SRP042078	SRS613254	SRX546217	SRA165378	GEO		Transcriptome of Smooth Muscle Cells, Interstitial Cells of Cajal and PDGFRa+ Cells	Genome scale expression data on absolute numbers of gene isoforms offer essential clues for cellular functions and biological processes. Gastrointestinal (GI) motility is regulated by smooth muscle cells (SMC) closely contacted with interstitial cells of Cajal (ICC) and fibroblast-like PDGFRa+ cells (PaC), forming an electrical syncytium. To uncover genetic identifies and cellular functions of the cells, we isolated these three cell populations from mouse small intestine and colon, obtained the transcriptome for each type of cells, and built each cell type transcriptome browser. To our knowledge, this is the first genetic resource providing a comprehensive reference for all mRNA transcripts expressed in these unique GI cell populations. Integration of these data with the UCSC genome browser revealed novel cell-specific markers, ion channel and transporter isoforms, and unique cellular and biological functions of these cells in GI physiology. Our transcriptome browsers bring new insight into the alternative expression of genes in different types of the cells and provides references for future functional studies. Overall design: mRNA profiles of SMC, ICC and PDGFRa cells isolated from mouse jejunum and colon were generated by deep sequencing using Illumina Hiseq2000..		GSM1388410: PDGFRαC Jejunum; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			mirVana miRNA Isolation Kit TruSeq RNA Sample Preparation	Illumina HiSeq 2000	age;;4 weeks|background strain;;C57BL/6|cell population;;Sorted primary cells|cell type;;PDGFRalpha|source_name;;PDGFRa cells in jejunum|strain;;PdgfraeGFP/+|tissue;;Jejunum	GEO Accession;;GSM1388410		GSM1388410	PDGFRaC Jejunum	14941935200	74709676	2015-07-31 20:26:22	9573373980	14941935200	74709676	2	74709676	index:0,count:74709676,average:100,stdev:0|index:1,count:74709676,average:100,stdev:0	GSM1388410_r1	GEO			in_mesa	26241044	17.03	2.4	0.03	11591079236	11473603134	9950450322	9939482170	98.99	99.89	71488011	68101969	184.238	442.709	146	802721	80.23	93.67	84254447	57353881	84254447	57353881	89.41	89.32	84254447	63917248	84254447	54695113	445679553	3.85	1.21	0	13.73	0	0.25	0	0.03	0	0.00	0	4.04	0	71488011	0	200	0	197.84	0	2.13	0	0.01	0	2.09	0	0.02	0	268.95	0	0.27	0	901384	0	74709676	0	10255753	0	187346	0	18850	0	0	0	3015469	0	13265	0	0	0	147935	0	25434086	0	43897	0	25639183	0	81.96	0	61232258	0	219593	23229313	105.783485812389	74709676.0	71488011.0	901384.0	10255753.0	187346.0	18850.0	0.0	3015469.0	61232258.0	95.7	1.2	13.7	0.3	0.0	0.0	4.0	82.0	100	100	100.00	38	7470967600	25.4	24.7	24.5	25.5	0.0	36.3	20.7	bulk
922271	SRR1291253	SRP042078	SRS613255	SRX546218	SRA165378	GEO		Transcriptome of Smooth Muscle Cells, Interstitial Cells of Cajal and PDGFRa+ Cells	Genome scale expression data on absolute numbers of gene isoforms offer essential clues for cellular functions and biological processes. Gastrointestinal (GI) motility is regulated by smooth muscle cells (SMC) closely contacted with interstitial cells of Cajal (ICC) and fibroblast-like PDGFRa+ cells (PaC), forming an electrical syncytium. To uncover genetic identifies and cellular functions of the cells, we isolated these three cell populations from mouse small intestine and colon, obtained the transcriptome for each type of cells, and built each cell type transcriptome browser. To our knowledge, this is the first genetic resource providing a comprehensive reference for all mRNA transcripts expressed in these unique GI cell populations. Integration of these data with the UCSC genome browser revealed novel cell-specific markers, ion channel and transporter isoforms, and unique cellular and biological functions of these cells in GI physiology. Our transcriptome browsers bring new insight into the alternative expression of genes in different types of the cells and provides references for future functional studies. Overall design: mRNA profiles of SMC, ICC and PDGFRa cells isolated from mouse jejunum and colon were generated by deep sequencing using Illumina Hiseq2000..		GSM1388411: PDGFRαC Colon; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			mirVana miRNA Isolation Kit TruSeq RNA Sample Preparation	Illumina HiSeq 2000	age;;4 weeks|background strain;;C57BL/6|cell population;;Sorted primary cells|cell type;;PDGFRalpha|source_name;;PDGFRa cell in colon|strain;;PdgfraeGFP/+|tissue;;Colon	GEO Accession;;GSM1388411		GSM1388411	PDGFRaC Colon	13656309000	68281545	2015-07-31 20:26:22	8847055941	13656309000	68281545	2	68281545	index:0,count:68281545,average:100,stdev:0|index:1,count:68281545,average:100,stdev:0	GSM1388411_r1	GEO			in_mesa	26241044	4.08	2.7	0.07	10442688935	10373795400	9871312711	9854102617	99.34	99.83	65119615	60866359	190.113	556.068	146	596733	84.83	89.85	70604305	55238717	70604305	55238717	86.02	86.34	70604305	56015525	70604305	53079583	935389582	8.96	1.38	0	5.33	0	0.19	0	0.06	0	0.00	0	4.38	0	65119615	0	200	0	197.88	0	1.80	0	0.01	0	1.59	0	0.01	0	238.89	0	0.25	0	942341	0	68281545	0	3640361	0	129173	0	42876	0	0	0	2989881	0	15309	0	0	0	153843	0	29753086	0	46451	0	29968689	0	90.04	0	61479254	0	224450	26356325	117.426264201381	68281545.0	65119615.0	942341.0	3640361.0	129173.0	42876.0	0.0	2989881.0	61479254.0	95.4	1.4	5.3	0.2	0.1	0.0	4.4	90.0	100	100	100.00	38	6828154500	24.7	25.5	25.2	24.6	0.0	36.0	19.9	bulk
922278	SRR1291254	SRP042078	SRS613256	SRX546219	SRA165378	GEO		Transcriptome of Smooth Muscle Cells, Interstitial Cells of Cajal and PDGFRa+ Cells	Genome scale expression data on absolute numbers of gene isoforms offer essential clues for cellular functions and biological processes. Gastrointestinal (GI) motility is regulated by smooth muscle cells (SMC) closely contacted with interstitial cells of Cajal (ICC) and fibroblast-like PDGFRa+ cells (PaC), forming an electrical syncytium. To uncover genetic identifies and cellular functions of the cells, we isolated these three cell populations from mouse small intestine and colon, obtained the transcriptome for each type of cells, and built each cell type transcriptome browser. To our knowledge, this is the first genetic resource providing a comprehensive reference for all mRNA transcripts expressed in these unique GI cell populations. Integration of these data with the UCSC genome browser revealed novel cell-specific markers, ion channel and transporter isoforms, and unique cellular and biological functions of these cells in GI physiology. Our transcriptome browsers bring new insight into the alternative expression of genes in different types of the cells and provides references for future functional studies. Overall design: mRNA profiles of SMC, ICC and PDGFRa cells isolated from mouse jejunum and colon were generated by deep sequencing using Illumina Hiseq2000..		GSM1388412: SM Jejunum; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			mirVana miRNA Isolation Kit TruSeq RNA Sample Preparation	Illumina HiSeq 2000	age;;4 weeks|background strain;;C57BL/6|cell population;;Unsorted mixed cells|cell type;;SM|source_name;;Jejunum SM|strain;;KitcopGFP/+|tissue;;Jejunum	GEO Accession;;GSM1388412		GSM1388412	SM Jejunum	24062944980	119123490	2015-07-31 20:26:22	17351090389	24062944980	119123490	2	119123490	index:0,count:119123490,average:101,stdev:0|index:1,count:119123490,average:101,stdev:0	GSM1388412_r1	GEO			in_mesa	26241044	8.03	3.78	0.04	17574093885	17598243856	16329181836	16452376110	100.14	100.75	110391488	101755031	187.883	688.518	136	951305	88.63	95.51	121389062	97837423	121389062	97837423	91.71	92.02	121389062	101242873	121389062	94256685	643743730	3.66	1.25	0	6.68	0	0.29	0	0.04	0	0.00	0	7.01	0	110391488	0	202	0	198.82	0	1.84	0	0.01	0	1.37	0	0.01	0	199.00	0	0.55	0	1488544	0	119123490	0	7958410	0	342257	0	44153	0	0	0	8345592	0	25263	0	0	0	308752	0	51856354	0	76430	0	52266799	0	85.99	0	102433078	0	287601	45362502	157.727205399147	119123490.0	110391488.0	1488544.0	7958410.0	342257.0	44153.0	0.0	8345592.0	102433078.0	92.7	1.2	6.7	0.3	0.0	0.0	7.0	86.0	101	101	101.00	38	12031472490	25.4	24.7	24.6	25.3	0.0	33.9	17.2	bulk
922285	SRR1291255	SRP042078	SRS613257	SRX546220	SRA165378	GEO		Transcriptome of Smooth Muscle Cells, Interstitial Cells of Cajal and PDGFRa+ Cells	Genome scale expression data on absolute numbers of gene isoforms offer essential clues for cellular functions and biological processes. Gastrointestinal (GI) motility is regulated by smooth muscle cells (SMC) closely contacted with interstitial cells of Cajal (ICC) and fibroblast-like PDGFRa+ cells (PaC), forming an electrical syncytium. To uncover genetic identifies and cellular functions of the cells, we isolated these three cell populations from mouse small intestine and colon, obtained the transcriptome for each type of cells, and built each cell type transcriptome browser. To our knowledge, this is the first genetic resource providing a comprehensive reference for all mRNA transcripts expressed in these unique GI cell populations. Integration of these data with the UCSC genome browser revealed novel cell-specific markers, ion channel and transporter isoforms, and unique cellular and biological functions of these cells in GI physiology. Our transcriptome browsers bring new insight into the alternative expression of genes in different types of the cells and provides references for future functional studies. Overall design: mRNA profiles of SMC, ICC and PDGFRa cells isolated from mouse jejunum and colon were generated by deep sequencing using Illumina Hiseq2000..		GSM1388413: SM Colon; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			mirVana miRNA Isolation Kit TruSeq RNA Sample Preparation	Illumina HiSeq 2000	age;;4 weeks|background strain;;C57BL/6|cell population;;Unsorted mixed cells|cell type;;SM|source_name;;Colon SM|strain;;KitcopGFP/+|tissue;;Colon	GEO Accession;;GSM1388413		GSM1388413	SM Colon	21487145616	106372008	2015-07-31 20:26:22	15521089638	21487145616	106372008	2	106372008	index:0,count:106372008,average:101,stdev:0|index:1,count:106372008,average:101,stdev:0	GSM1388413_r1	GEO			in_mesa	26241044	6.39	3.67	0.04	15767535496	15814774705	14773904448	14903061692	100.3	100.87	98569943	90963008	188.933	678.117	137	835273	87.79	93.8	107604292	86530777	107604292	86530777	89.88	90.11	107604292	88592344	107604292	83128793	850664128	5.40	1.27	0	5.94	0	0.27	0	0.05	0	0.00	0	7.01	0	98569943	0	202	0	198.84	0	1.86	0	0.01	0	1.36	0	0.01	0	231.94	0	0.55	0	1354514	0	106372008	0	6316185	0	286125	0	56911	0	0	0	7459029	0	22846	0	0	0	264572	0	46431042	0	72489	0	46790949	0	86.73	0	92253758	0	290428	40842986	140.630331786191	106372008.0	98569943.0	1354514.0	6316185.0	286125.0	56911.0	0.0	7459029.0	92253758.0	92.7	1.3	5.9	0.3	0.1	0.0	7.0	86.7	101	101	101.00	38	10743572808	25.3	24.8	24.7	25.2	0.0	33.8	17.0	bulk
922292	SRR1291256	SRP042078	SRS613258	SRX546221	SRA165378	GEO		Transcriptome of Smooth Muscle Cells, Interstitial Cells of Cajal and PDGFRa+ Cells	Genome scale expression data on absolute numbers of gene isoforms offer essential clues for cellular functions and biological processes. Gastrointestinal (GI) motility is regulated by smooth muscle cells (SMC) closely contacted with interstitial cells of Cajal (ICC) and fibroblast-like PDGFRa+ cells (PaC), forming an electrical syncytium. To uncover genetic identifies and cellular functions of the cells, we isolated these three cell populations from mouse small intestine and colon, obtained the transcriptome for each type of cells, and built each cell type transcriptome browser. To our knowledge, this is the first genetic resource providing a comprehensive reference for all mRNA transcripts expressed in these unique GI cell populations. Integration of these data with the UCSC genome browser revealed novel cell-specific markers, ion channel and transporter isoforms, and unique cellular and biological functions of these cells in GI physiology. Our transcriptome browsers bring new insight into the alternative expression of genes in different types of the cells and provides references for future functional studies. Overall design: mRNA profiles of SMC, ICC and PDGFRa cells isolated from mouse jejunum and colon were generated by deep sequencing using Illumina Hiseq2000..		GSM1388414: Mu Colon; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			mirVana miRNA Isolation Kit TruSeq RNA Sample Preparation	Illumina HiSeq 2000	age;;4 weeks|background strain;;C57BL/6|cell population;;Unsorted mixed cells|cell type;;mucosal|source_name;;Colon mucosa|strain;;PdgfraeGFP/+|tissue;;Colon mucosa	GEO Accession;;GSM1388414		GSM1388414	Mu Colon	16883523600	84417618	2015-07-31 20:26:22	10955988923	16883523600	84417618	2	84417618	index:0,count:84417618,average:100,stdev:0|index:1,count:84417618,average:100,stdev:0	GSM1388414_r1	GEO			in_mesa	26241044	6.74	2.32	0.1	13185308818	13069734809	11953529823	11930659983	99.12	99.81	80180620	74877487	191.220	628.462	146	787243	82.96	91.6	91254684	66515386	91254684	66515386	88.38	88.54	91254684	70867598	91254684	64291353	974471208	7.39	1.04	0	8.96	0	0.28	0	0.08	0	0.00	0	4.66	0	80180620	0	200	0	198.20	0	1.55	0	0.00	0	1.27	0	0.00	0	242.35	0	0.23	0	878002	0	84417618	0	7566047	0	235916	0	71295	0	0	0	3929787	0	20035	0	0	0	242493	0	37339280	0	102215	0	37704023	0	86.02	0	72614573	0	285925	35008939	122.440986272624	84417618.0	80180620.0	878002.0	7566047.0	235916.0	71295.0	0.0	3929787.0	72614573.0	95.0	1.0	9.0	0.3	0.1	0.0	4.7	86.0	100	100	100.00	38	8441761800	25.2	24.8	24.6	25.4	0.0	36.2	20.9	bulk
922300	SRR1291257	SRP042078	SRS613259	SRX546222	SRA165378	GEO		Transcriptome of Smooth Muscle Cells, Interstitial Cells of Cajal and PDGFRa+ Cells	Genome scale expression data on absolute numbers of gene isoforms offer essential clues for cellular functions and biological processes. Gastrointestinal (GI) motility is regulated by smooth muscle cells (SMC) closely contacted with interstitial cells of Cajal (ICC) and fibroblast-like PDGFRa+ cells (PaC), forming an electrical syncytium. To uncover genetic identifies and cellular functions of the cells, we isolated these three cell populations from mouse small intestine and colon, obtained the transcriptome for each type of cells, and built each cell type transcriptome browser. To our knowledge, this is the first genetic resource providing a comprehensive reference for all mRNA transcripts expressed in these unique GI cell populations. Integration of these data with the UCSC genome browser revealed novel cell-specific markers, ion channel and transporter isoforms, and unique cellular and biological functions of these cells in GI physiology. Our transcriptome browsers bring new insight into the alternative expression of genes in different types of the cells and provides references for future functional studies. Overall design: mRNA profiles of SMC, ICC and PDGFRa cells isolated from mouse jejunum and colon were generated by deep sequencing using Illumina Hiseq2000..		GSM1388415: PDGFRαC Mu Colon; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			mirVana miRNA Isolation Kit TruSeq RNA Sample Preparation	Illumina HiSeq 2000	age;;4 weeks|background strain;;C57BL/6|cell population;;Sorted primary cells|cell type;;PDGFRalpha|source_name;;PDGFRa cells in colon mucosa|strain;;PdgfraeGFP/+|tissue;;Colon mucosa	GEO Accession;;GSM1388415		GSM1388415	PDGFRaC Mu Colon	15415150800	77075754	2015-07-31 20:26:22	9978650913	15415150800	77075754	2	77075754	index:0,count:77075754,average:100,stdev:0|index:1,count:77075754,average:100,stdev:0	GSM1388415_r1	GEO			in_mesa	26241044	2.64	2.82	0.06	11985573127	11903819133	11344174764	11315423811	99.32	99.75	74352724	69410587	190.230	566.617	146	719380	84.05	88.9	80948659	62491566	80948659	62491566	85.37	85.62	80948659	63474866	80948659	60183551	1208958388	10.09	1.26	0	5.26	0	0.21	0	0.07	0	0.00	0	3.25	0	74352724	0	200	0	198.03	0	1.68	0	0.01	0	1.54	0	0.01	0	209.89	0	0.23	0	974085	0	77075754	0	4057457	0	163388	0	56349	0	0	0	2503293	0	15851	0	0	0	218286	0	35746535	0	61453	0	36042125	0	91.20	0	70295267	0	260335	32158754	123.528353851768	77075754.0	74352724.0	974085.0	4057457.0	163388.0	56349.0	0.0	2503293.0	70295267.0	96.5	1.3	5.3	0.2	0.1	0.0	3.2	91.2	100	100	100.00	38	7707575400	24.7	25.4	25.2	24.8	0.0	36.1	20.7	bulk
1509257	SRR1382078	SRP043153	SRS634994	SRX591752	SRA170153	GEO		Musashi proteins are post-transcriptional regulators of the epithelial-luminal cell state	mRNA-seq and ribosome profiling of neural stem cells overexpressing or knocked out for Musashi RNA-binding proteins Overall design: Study of the global effects of Musashi (Msi) proteins on the transcriptome of embryonic neural stem cells. Neural stem cells were derived from brains of E12.5 or E13.5 embryos engineered to have inducible Msi1 or Msi2 genes, or from embryos with double floxed alleles of Msi1 and Msi2 carrying a Tamoxifen-induclble Cre (CreER). The overexpression mice were made using the Flp-in system (OpenBioSystems), where a cDNA of interest (in this case Msi1 or Msi2) is knocked into the Collagen (Col1A1) locus. The expression of the cDNA of interest is driven by m2rTTA that is knocked into the Rosa26 locus (R26). KH2 describes a strain containing the R26-m2rTTA but lacking Msi1 or Msi2 cDNA. MSI1 describes a strain containing R26-m2rTTA and Msi1 cDNA in Col1A1. MSI2 describes a strain containing R26-m2rTTA and Msi2 cDNA in Col1A1. C1 describes a strain lacking the CreER allele but containing double floxed alleles of Msi1/Msi2 (used as Tamoxifen control). C4 describes a strain carrying the CreER allele and double floxed alleles of Msi1/Msi2.		GSM1410654: KH2 control, No Dox (E13.5); Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Poly(A)+ RNA was selected by oligo-dT magnetic beads, and prepared for paired end RNA sequencing using Illumina paired end sequencing primers.	Illumina HiSeq 2000	developmental stage;;E13.5|source_name;;NSCs|time point;;72 hours|treatment;;No Dox	GEO Accession;;GSM1410654		GSM1410654	KH2 control, No Dox (E13.5)	4379737200	54746715	2015-07-22 17:06:27	3002728111	4379737200	54746715	2	54746715	index:0,count:54746715,average:40,stdev:0|index:1,count:54746715,average:40,stdev:0	GSM1410654_r1	GEO					2.14	3.41	0.06	4129321159	4117962888	3767548257	3785386334	99.72	100.47	52097840	43654809	210.187	1228.370	160	1204379	80.45	88.12	60798875	41911292	60798875	41911292	84.65	84.92	60798875	44099824	60798875	40387617	441839654	10.70	1.17	0	8.29	0	0.62	0	0.20	0	0.00	0	4.02	0	52097840	0	80	0	79.23	0	1.52	0	0.00	0	1.15	0	0.00	0	507.96	0	0.20	0	639762	0	54746715	0	4538373	0	339322	0	108115	0	0	0	2201438	0	4754	0	0	0	36245	0	5117474	0	9407	0	5167880	0	86.87	0	47559467	0	159478	5256623	32.961430416735	54746715.0	52097840.0	639762.0	4538373.0	339322.0	108115.0	0.0	2201438.0	47559467.0	95.2	1.2	8.3	0.6	0.2	0.0	4.0	86.9	40	40	40.00	36	2189868600	23.3	26.7	24.1	25.9	0.0	36.9	24.7	bulk
1509274	SRR1382079	SRP043153	SRS634995	SRX591753	SRA170153	GEO		Musashi proteins are post-transcriptional regulators of the epithelial-luminal cell state	mRNA-seq and ribosome profiling of neural stem cells overexpressing or knocked out for Musashi RNA-binding proteins Overall design: Study of the global effects of Musashi (Msi) proteins on the transcriptome of embryonic neural stem cells. Neural stem cells were derived from brains of E12.5 or E13.5 embryos engineered to have inducible Msi1 or Msi2 genes, or from embryos with double floxed alleles of Msi1 and Msi2 carrying a Tamoxifen-induclble Cre (CreER). The overexpression mice were made using the Flp-in system (OpenBioSystems), where a cDNA of interest (in this case Msi1 or Msi2) is knocked into the Collagen (Col1A1) locus. The expression of the cDNA of interest is driven by m2rTTA that is knocked into the Rosa26 locus (R26). KH2 describes a strain containing the R26-m2rTTA but lacking Msi1 or Msi2 cDNA. MSI1 describes a strain containing R26-m2rTTA and Msi1 cDNA in Col1A1. MSI2 describes a strain containing R26-m2rTTA and Msi2 cDNA in Col1A1. C1 describes a strain lacking the CreER allele but containing double floxed alleles of Msi1/Msi2 (used as Tamoxifen control). C4 describes a strain carrying the CreER allele and double floxed alleles of Msi1/Msi2.		GSM1410655: MSI1, No Dox (E13.5); Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Poly(A)+ RNA was selected by oligo-dT magnetic beads, and prepared for paired end RNA sequencing using Illumina paired end sequencing primers.	Illumina HiSeq 2000	developmental stage;;E13.5|source_name;;NSCs|time point;;72 hours|treatment;;No Dox	GEO Accession;;GSM1410655		GSM1410655	MSI1, No Dox (E13.5)	3302467920	41280849	2015-07-22 17:06:27	2266734358	3302467920	41280849	2	41280849	index:0,count:41280849,average:40,stdev:0|index:1,count:41280849,average:40,stdev:0	GSM1410655_r1	GEO					2.86	3.48	0.09	3116624343	3093402927	2861741952	2860727999	99.25	99.96	39294813	33367735	206.070	1159.811	173	691894	76.44	83.21	45283350	30037039	45283350	30037039	80.46	80.39	45283350	31617786	45283350	29017699	478639617	15.36	1.02	0	7.75	0	0.58	0	0.26	0	0.00	0	3.97	0	39294813	0	80	0	79.30	0	1.43	0	0.00	0	1.15	0	0.00	0	493.72	0	0.19	0	419196	0	41280849	0	3198118	0	239405	0	108358	0	0	0	1638273	0	3131	0	0	0	24058	0	3470670	0	6185	0	3504044	0	87.44	0	36096695	0	149133	3566562	23.915310494659	41280849.0	39294813.0	419196.0	3198118.0	239405.0	108358.0	0.0	1638273.0	36096695.0	95.2	1.0	7.7	0.6	0.3	0.0	4.0	87.4	40	40	40.00	36	1651233960	24.1	25.8	23.4	26.7	0.0	36.9	24.9	bulk
1509389	SRR1382080	SRP043153	SRS634996	SRX591754	SRA170153	GEO		Musashi proteins are post-transcriptional regulators of the epithelial-luminal cell state	mRNA-seq and ribosome profiling of neural stem cells overexpressing or knocked out for Musashi RNA-binding proteins Overall design: Study of the global effects of Musashi (Msi) proteins on the transcriptome of embryonic neural stem cells. Neural stem cells were derived from brains of E12.5 or E13.5 embryos engineered to have inducible Msi1 or Msi2 genes, or from embryos with double floxed alleles of Msi1 and Msi2 carrying a Tamoxifen-induclble Cre (CreER). The overexpression mice were made using the Flp-in system (OpenBioSystems), where a cDNA of interest (in this case Msi1 or Msi2) is knocked into the Collagen (Col1A1) locus. The expression of the cDNA of interest is driven by m2rTTA that is knocked into the Rosa26 locus (R26). KH2 describes a strain containing the R26-m2rTTA but lacking Msi1 or Msi2 cDNA. MSI1 describes a strain containing R26-m2rTTA and Msi1 cDNA in Col1A1. MSI2 describes a strain containing R26-m2rTTA and Msi2 cDNA in Col1A1. C1 describes a strain lacking the CreER allele but containing double floxed alleles of Msi1/Msi2 (used as Tamoxifen control). C4 describes a strain carrying the CreER allele and double floxed alleles of Msi1/Msi2.		GSM1410656: MSI1, No Dox, technical replicate (E13.5); Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Poly(A)+ RNA was selected by oligo-dT magnetic beads, and prepared for paired end RNA sequencing using Illumina paired end sequencing primers.	Illumina HiSeq 2000	developmental stage;;E13.5|source_name;;NSCs|time point;;72 hours|treatment;;No Dox	GEO Accession;;GSM1410656		GSM1410656	MSI1, No Dox, technical replicate (E13.5)	7273375760	99166757	2014-06-15 12:59:04	4823423729	7273375760	99166757	2	99166757	index:0,count:99166757,average:40,stdev:0|index:1,count:82667637,average:40,stdev:0	GSM1410656_r1	GEO					2.85	3.51	0.09	6909245148	6849467826	6310886428	6306878199	99.13	99.94	79100560	67125241	206.860	1162.434	172	1423311	90.72	98.76	112039897	71759567	112039897	71759567	96.11	95.3	112039897	76025288	112039897	69241390	1065009515	15.41	1.02	0.51	7.79	12.92	0.58	1.20	0.27	0.66	0.00	0.00	3.46	1.14	79100560	16004178	80	40	79.30	39.68	1.43	1.37	0.00	0.00	1.16	1.13	0.00	0.00	528.60	771.39	0.16	0.19	843772	83990	82667637	16499120	6442135	2131836	482888	198019	221868	109190	0	0	2862321	187733	6463	608	0	0	49413	4571	6999124	656696	12272	1056	7067272	662931	87.89	84.08	72658425	13872342	175660	7917172	45.071000796994	99166757.0	95104738.0	927762.0	8573971.0	680907.0	331058.0	0.0	3050054.0	86530767.0	95.9	0.9	8.6	0.7	0.3	0.0	3.1	87.3	40	40	40.00	38	659964800	24.2	25.7	23.3	26.8	0.0	36.8	24.8	bulk
1509405	SRR1382081	SRP043153	SRS634997	SRX591755	SRA170153	GEO		Musashi proteins are post-transcriptional regulators of the epithelial-luminal cell state	mRNA-seq and ribosome profiling of neural stem cells overexpressing or knocked out for Musashi RNA-binding proteins Overall design: Study of the global effects of Musashi (Msi) proteins on the transcriptome of embryonic neural stem cells. Neural stem cells were derived from brains of E12.5 or E13.5 embryos engineered to have inducible Msi1 or Msi2 genes, or from embryos with double floxed alleles of Msi1 and Msi2 carrying a Tamoxifen-induclble Cre (CreER). The overexpression mice were made using the Flp-in system (OpenBioSystems), where a cDNA of interest (in this case Msi1 or Msi2) is knocked into the Collagen (Col1A1) locus. The expression of the cDNA of interest is driven by m2rTTA that is knocked into the Rosa26 locus (R26). KH2 describes a strain containing the R26-m2rTTA but lacking Msi1 or Msi2 cDNA. MSI1 describes a strain containing R26-m2rTTA and Msi1 cDNA in Col1A1. MSI2 describes a strain containing R26-m2rTTA and Msi2 cDNA in Col1A1. C1 describes a strain lacking the CreER allele but containing double floxed alleles of Msi1/Msi2 (used as Tamoxifen control). C4 describes a strain carrying the CreER allele and double floxed alleles of Msi1/Msi2.		GSM1410657: MSI1, DOX (E13.5); Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Poly(A)+ RNA was selected by oligo-dT magnetic beads, and prepared for paired end RNA sequencing using Illumina paired end sequencing primers.	Illumina HiSeq 2000	developmental stage;;E13.5|source_name;;NSCs|time point;;72 hours|treatment;;DOX 1ug/ml	GEO Accession;;GSM1410657		GSM1410657	MSI1, DOX (E13.5)	1358203400	19024314	2014-07-20 17:48:08	886830388	1358203400	19024314	2	19024314	index:0,count:19024314,average:40,stdev:0|index:1,count:14930771,average:40,stdev:0	GSM1410657_r1	GEO					2.64	3.25	0.08	1291095459	1280597154	1182270487	1181508276	99.19	99.94	14293259	12091708	209.688	1175.239	170	353004	98.44	106.73	21490715	14070915	21490715	14070915	103.82	102.86	21490715	14839557	21490715	13560884	178759517	13.85	1.00	0.22	7.43	12.53	0.65	1.14	0.24	0.57	0.00	0.00	3.37	1.21	14293259	3974191	80	40	79.29	39.65	1.46	1.37	0.00	0.00	1.13	1.12	0.00	0.00	484.24	491.23	0.13	0.28	149693	8935	14930771	4093543	1109687	512811	97529	46496	36262	23365	0	0	503721	49491	1287	147	0	0	9378	1200	1327785	165741	2338	267	1340788	167355	88.30	84.56	13183572	3461380	126858	1539892	12.138706270003	19024314.0	18267450.0	158628.0	1622498.0	144025.0	59627.0	0.0	553212.0	16644952.0	96.0	0.8	8.5	0.8	0.3	0.0	2.9	87.5	40	40	40.00	38	163741720	23.4	26.2	24.1	26.3	0.0	36.4	23.6	bulk
1509422	SRR1382082	SRP043153	SRS634998	SRX591756	SRA170153	GEO		Musashi proteins are post-transcriptional regulators of the epithelial-luminal cell state	mRNA-seq and ribosome profiling of neural stem cells overexpressing or knocked out for Musashi RNA-binding proteins Overall design: Study of the global effects of Musashi (Msi) proteins on the transcriptome of embryonic neural stem cells. Neural stem cells were derived from brains of E12.5 or E13.5 embryos engineered to have inducible Msi1 or Msi2 genes, or from embryos with double floxed alleles of Msi1 and Msi2 carrying a Tamoxifen-induclble Cre (CreER). The overexpression mice were made using the Flp-in system (OpenBioSystems), where a cDNA of interest (in this case Msi1 or Msi2) is knocked into the Collagen (Col1A1) locus. The expression of the cDNA of interest is driven by m2rTTA that is knocked into the Rosa26 locus (R26). KH2 describes a strain containing the R26-m2rTTA but lacking Msi1 or Msi2 cDNA. MSI1 describes a strain containing R26-m2rTTA and Msi1 cDNA in Col1A1. MSI2 describes a strain containing R26-m2rTTA and Msi2 cDNA in Col1A1. C1 describes a strain lacking the CreER allele but containing double floxed alleles of Msi1/Msi2 (used as Tamoxifen control). C4 describes a strain carrying the CreER allele and double floxed alleles of Msi1/Msi2.		GSM1410658: KH2 control, No Dox (E12.5); Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Poly(A)+ RNA was selected by oligo-dT magnetic beads, and prepared for paired end RNA sequencing using Illumina paired end sequencing primers.	Illumina HiSeq 2000	developmental stage;;E12.5|source_name;;NSCs|time point;;72 hours|treatment;;No Dox	GEO Accession;;GSM1410658		GSM1410658	KH2 control, No Dox (E12.5)	6260562600	52171355	2015-07-22 17:06:27	4398486372	6260562600	52171355	2	52171355	index:0,count:52171355,average:60,stdev:0|index:1,count:52171355,average:60,stdev:0	GSM1410658_r1	GEO					3.45	4.03	0.03	6027353090	6023071766	5439834646	5475426750	99.93	100.65	50803418	43802863	221.423	1065.175	184	1446500	84.56	93.66	58999102	42959768	58999102	42959768	90.44	90.82	58999102	45947501	58999102	41656324	352144885	5.84	0.94	0	9.46	0	0.67	0	0.07	0	0.00	0	1.89	0	50803418	0	120	0	118.77	0	1.67	0	0.01	0	1.36	0	0.00	0	278.25	0	0.37	0	490937	0	52171355	0	4934950	0	347240	0	35219	0	0	0	985478	0	8261	0	0	0	67999	0	10353310	0	22159	0	10451729	0	87.92	0	45868468	0	195445	10771328	55.111811507074	52171355.0	50803418.0	490937.0	4934950.0	347240.0	35219.0	0.0	985478.0	45868468.0	97.4	0.9	9.5	0.7	0.1	0.0	1.9	87.9	60	60	60.00	38	3130281300	25.4	24.6	24.4	25.6	0.0	36.1	21.0	bulk
1509439	SRR1382083	SRP043153	SRS634999	SRX591757	SRA170153	GEO		Musashi proteins are post-transcriptional regulators of the epithelial-luminal cell state	mRNA-seq and ribosome profiling of neural stem cells overexpressing or knocked out for Musashi RNA-binding proteins Overall design: Study of the global effects of Musashi (Msi) proteins on the transcriptome of embryonic neural stem cells. Neural stem cells were derived from brains of E12.5 or E13.5 embryos engineered to have inducible Msi1 or Msi2 genes, or from embryos with double floxed alleles of Msi1 and Msi2 carrying a Tamoxifen-induclble Cre (CreER). The overexpression mice were made using the Flp-in system (OpenBioSystems), where a cDNA of interest (in this case Msi1 or Msi2) is knocked into the Collagen (Col1A1) locus. The expression of the cDNA of interest is driven by m2rTTA that is knocked into the Rosa26 locus (R26). KH2 describes a strain containing the R26-m2rTTA but lacking Msi1 or Msi2 cDNA. MSI1 describes a strain containing R26-m2rTTA and Msi1 cDNA in Col1A1. MSI2 describes a strain containing R26-m2rTTA and Msi2 cDNA in Col1A1. C1 describes a strain lacking the CreER allele but containing double floxed alleles of Msi1/Msi2 (used as Tamoxifen control). C4 describes a strain carrying the CreER allele and double floxed alleles of Msi1/Msi2.		GSM1410659: KH2 control, Dox (E12.5); Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Poly(A)+ RNA was selected by oligo-dT magnetic beads, and prepared for paired end RNA sequencing using Illumina paired end sequencing primers.	Illumina HiSeq 2000	developmental stage;;E12.5|source_name;;NSCs|time point;;72 hours|treatment;;DOX 1ug/ml	GEO Accession;;GSM1410659		GSM1410659	KH2 control, Dox (E12.5)	11164592880	93038274	2015-07-22 17:06:27	7807642423	11164592880	93038274	2	93038274	index:0,count:93038274,average:60,stdev:0|index:1,count:93038274,average:60,stdev:0	GSM1410659_r1	GEO					4.4	3.99	0.03	10610925872	10582621196	9545979827	9593249287	99.73	100.5	89432160	78517707	208.289	954.445	175	2942655	83.63	92.92	103798903	74789711	103798903	74789711	89.82	90.1	103798903	80329567	103798903	72522724	677382377	6.38	0.89	0	9.61	0	0.62	0	0.07	0	0.00	0	3.18	0	89432160	0	120	0	118.74	0	1.66	0	0.01	0	1.36	0	0.00	0	326.45	0	0.40	0	825178	0	93038274	0	8942557	0	576495	0	67040	0	0	0	2962579	0	13863	0	0	0	118194	0	17573978	0	38309	0	17744344	0	86.51	0	80489603	0	221556	18253949	82.389775045587	93038274.0	89432160.0	825178.0	8942557.0	576495.0	67040.0	0.0	2962579.0	80489603.0	96.1	0.9	9.6	0.6	0.1	0.0	3.2	86.5	60	60	60.00	38	5582296440	25.6	24.3	24.1	25.9	0.0	36.1	21.3	bulk
1509471	SRR1382085	SRP043153	SRS635001	SRX591759	SRA170153	GEO		Musashi proteins are post-transcriptional regulators of the epithelial-luminal cell state	mRNA-seq and ribosome profiling of neural stem cells overexpressing or knocked out for Musashi RNA-binding proteins Overall design: Study of the global effects of Musashi (Msi) proteins on the transcriptome of embryonic neural stem cells. Neural stem cells were derived from brains of E12.5 or E13.5 embryos engineered to have inducible Msi1 or Msi2 genes, or from embryos with double floxed alleles of Msi1 and Msi2 carrying a Tamoxifen-induclble Cre (CreER). The overexpression mice were made using the Flp-in system (OpenBioSystems), where a cDNA of interest (in this case Msi1 or Msi2) is knocked into the Collagen (Col1A1) locus. The expression of the cDNA of interest is driven by m2rTTA that is knocked into the Rosa26 locus (R26). KH2 describes a strain containing the R26-m2rTTA but lacking Msi1 or Msi2 cDNA. MSI1 describes a strain containing R26-m2rTTA and Msi1 cDNA in Col1A1. MSI2 describes a strain containing R26-m2rTTA and Msi2 cDNA in Col1A1. C1 describes a strain lacking the CreER allele but containing double floxed alleles of Msi1/Msi2 (used as Tamoxifen control). C4 describes a strain carrying the CreER allele and double floxed alleles of Msi1/Msi2.		GSM1410661: MSI1, DOX (E12.5); Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Poly(A)+ RNA was selected by oligo-dT magnetic beads, and prepared for paired end RNA sequencing using Illumina paired end sequencing primers.	Illumina HiSeq 2000	developmental stage;;E12.5|source_name;;NSCs|time point;;72 hours|treatment;;DOX 1ug/ml	GEO Accession;;GSM1410661		GSM1410661	MSI1, DOX (E12.5)	4041860160	33682168	2015-07-22 17:06:27	2819844121	4041860160	33682168	2	33682168	index:0,count:33682168,average:60,stdev:0|index:1,count:33682168,average:60,stdev:0	GSM1410661_r1	GEO					4.46	3.61	0.07	3850739398	3825259795	3483620148	3485407447	99.34	100.05	32439200	28240989	216.475	1004.338	182	1059634	82.83	91.52	37350095	26868931	37350095	26868931	88.64	88.81	37350095	28753740	37350095	26073068	287105116	7.46	0.78	0	9.15	0	0.57	0	0.10	0	0.00	0	3.03	0	32439200	0	120	0	118.79	0	1.70	0	0.01	0	1.41	0	0.01	0	341.57	0	0.40	0	261653	0	33682168	0	3081412	0	190829	0	32507	0	0	0	1019632	0	4881	0	0	0	41891	0	6196746	0	13790	0	6257308	0	87.16	0	29357788	0	180359	6431776	35.660965075211	33682168.0	32439200.0	261653.0	3081412.0	190829.0	32507.0	0.0	1019632.0	29357788.0	96.3	0.8	9.1	0.6	0.1	0.0	3.0	87.2	60	60	60.00	38	2020930080	25.7	24.2	24.0	26.1	0.0	36.2	21.4	bulk
1509487	SRR1382086	SRP043153	SRS635002	SRX591760	SRA170153	GEO		Musashi proteins are post-transcriptional regulators of the epithelial-luminal cell state	mRNA-seq and ribosome profiling of neural stem cells overexpressing or knocked out for Musashi RNA-binding proteins Overall design: Study of the global effects of Musashi (Msi) proteins on the transcriptome of embryonic neural stem cells. Neural stem cells were derived from brains of E12.5 or E13.5 embryos engineered to have inducible Msi1 or Msi2 genes, or from embryos with double floxed alleles of Msi1 and Msi2 carrying a Tamoxifen-induclble Cre (CreER). The overexpression mice were made using the Flp-in system (OpenBioSystems), where a cDNA of interest (in this case Msi1 or Msi2) is knocked into the Collagen (Col1A1) locus. The expression of the cDNA of interest is driven by m2rTTA that is knocked into the Rosa26 locus (R26). KH2 describes a strain containing the R26-m2rTTA but lacking Msi1 or Msi2 cDNA. MSI1 describes a strain containing R26-m2rTTA and Msi1 cDNA in Col1A1. MSI2 describes a strain containing R26-m2rTTA and Msi2 cDNA in Col1A1. C1 describes a strain lacking the CreER allele but containing double floxed alleles of Msi1/Msi2 (used as Tamoxifen control). C4 describes a strain carrying the CreER allele and double floxed alleles of Msi1/Msi2.		GSM1410662: MSI2, No Dox (E12.5); Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Poly(A)+ RNA was selected by oligo-dT magnetic beads, and prepared for paired end RNA sequencing using Illumina paired end sequencing primers.	Illumina HiSeq 2000	developmental stage;;E12.5|source_name;;NSCs|time point;;72 hours|treatment;;No Dox	GEO Accession;;GSM1410662		GSM1410662	MSI2, No Dox (E12.5)	6772374480	56436454	2015-07-22 17:06:27	4729401363	6772374480	56436454	2	56436454	index:0,count:56436454,average:60,stdev:0|index:1,count:56436454,average:60,stdev:0	GSM1410662_r1	GEO					3.69	3.8	0.07	6537192854	6513872576	5880536475	5904162309	99.64	100.4	55042062	47723347	218.060	1018.527	182	1753553	83.29	92.55	64213050	45842693	64213050	45842693	89.52	89.82	64213050	49273887	64213050	44487907	445068363	6.81	0.79	0	9.76	0	0.74	0	0.09	0	0.00	0	1.64	0	55042062	0	120	0	118.85	0	1.58	0	0.01	0	1.31	0	0.00	0	366.74	0	0.34	0	443580	0	56436454	0	5509621	0	417817	0	50887	0	0	0	925688	0	8629	0	0	0	75000	0	11019873	0	23240	0	11126742	0	87.77	0	49532441	0	196589	11471234	58.351352313710	56436454.0	55042062.0	443580.0	5509621.0	417817.0	50887.0	0.0	925688.0	49532441.0	97.5	0.8	9.8	0.7	0.1	0.0	1.6	87.8	60	60	60.00	38	3386187240	25.6	24.3	24.2	25.9	0.0	36.1	21.2	bulk
1509502	SRR1382087	SRP043153	SRS635003	SRX591761	SRA170153	GEO		Musashi proteins are post-transcriptional regulators of the epithelial-luminal cell state	mRNA-seq and ribosome profiling of neural stem cells overexpressing or knocked out for Musashi RNA-binding proteins Overall design: Study of the global effects of Musashi (Msi) proteins on the transcriptome of embryonic neural stem cells. Neural stem cells were derived from brains of E12.5 or E13.5 embryos engineered to have inducible Msi1 or Msi2 genes, or from embryos with double floxed alleles of Msi1 and Msi2 carrying a Tamoxifen-induclble Cre (CreER). The overexpression mice were made using the Flp-in system (OpenBioSystems), where a cDNA of interest (in this case Msi1 or Msi2) is knocked into the Collagen (Col1A1) locus. The expression of the cDNA of interest is driven by m2rTTA that is knocked into the Rosa26 locus (R26). KH2 describes a strain containing the R26-m2rTTA but lacking Msi1 or Msi2 cDNA. MSI1 describes a strain containing R26-m2rTTA and Msi1 cDNA in Col1A1. MSI2 describes a strain containing R26-m2rTTA and Msi2 cDNA in Col1A1. C1 describes a strain lacking the CreER allele but containing double floxed alleles of Msi1/Msi2 (used as Tamoxifen control). C4 describes a strain carrying the CreER allele and double floxed alleles of Msi1/Msi2.		GSM1410663: MSI2, DOX (E12.5); Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Poly(A)+ RNA was selected by oligo-dT magnetic beads, and prepared for paired end RNA sequencing using Illumina paired end sequencing primers.	Illumina HiSeq 2000	developmental stage;;E12.5|source_name;;NSCs|time point;;72 hours|treatment;;DOX 1ug/ml	GEO Accession;;GSM1410663		GSM1410663	MSI2, DOX (E12.5)	8152982280	67941519	2015-07-22 17:06:27	5714896514	8152982280	67941519	2	67941519	index:0,count:67941519,average:60,stdev:0|index:1,count:67941519,average:60,stdev:0	GSM1410663_r1	GEO					4.44	3.63	0.06	7877604474	7848384788	7041275974	7070826349	99.63	100.42	66317653	59366207	192.510	817.221	163	1933705	83.01	92.83	77848467	55052050	77848467	55052050	89.68	89.95	77848467	59471369	77848467	53343856	504167027	6.40	0.73	0	10.33	0	0.70	0	0.09	0	0.00	0	1.60	0	66317653	0	120	0	118.85	0	1.61	0	0.01	0	1.33	0	0.00	0	375.71	0	0.34	0	499068	0	67941519	0	7015477	0	478227	0	59731	0	0	0	1085908	0	10165	0	0	0	93267	0	13376329	0	27377	0	13507138	0	87.28	0	59302176	0	206788	13903989	67.237890980134	67941519.0	66317653.0	499068.0	7015477.0	478227.0	59731.0	0.0	1085908.0	59302176.0	97.6	0.7	10.3	0.7	0.1	0.0	1.6	87.3	60	60	60.00	38	4076491140	25.5	24.4	24.2	25.9	0.0	36.1	21.1	bulk
1509518	SRR1382088	SRP043153	SRS635004	SRX591762	SRA170153	GEO		Musashi proteins are post-transcriptional regulators of the epithelial-luminal cell state	mRNA-seq and ribosome profiling of neural stem cells overexpressing or knocked out for Musashi RNA-binding proteins Overall design: Study of the global effects of Musashi (Msi) proteins on the transcriptome of embryonic neural stem cells. Neural stem cells were derived from brains of E12.5 or E13.5 embryos engineered to have inducible Msi1 or Msi2 genes, or from embryos with double floxed alleles of Msi1 and Msi2 carrying a Tamoxifen-induclble Cre (CreER). The overexpression mice were made using the Flp-in system (OpenBioSystems), where a cDNA of interest (in this case Msi1 or Msi2) is knocked into the Collagen (Col1A1) locus. The expression of the cDNA of interest is driven by m2rTTA that is knocked into the Rosa26 locus (R26). KH2 describes a strain containing the R26-m2rTTA but lacking Msi1 or Msi2 cDNA. MSI1 describes a strain containing R26-m2rTTA and Msi1 cDNA in Col1A1. MSI2 describes a strain containing R26-m2rTTA and Msi2 cDNA in Col1A1. C1 describes a strain lacking the CreER allele but containing double floxed alleles of Msi1/Msi2 (used as Tamoxifen control). C4 describes a strain carrying the CreER allele and double floxed alleles of Msi1/Msi2.		GSM1410664: Cre-less Msi1/Msi2 floxed control line C1, No Tam (E12.5); Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Poly(A)+ RNA was selected by oligo-dT magnetic beads, and prepared for paired end RNA sequencing using Illumina paired end sequencing primers.	Illumina HiSeq 2000	developmental stage;;E12.5|source_name;;NSCs|time point;;48 hours|treatment;;No 4-OHT	GEO Accession;;GSM1410664		GSM1410664	Cre-less Msi1/Msi2 floxed control line C1, No Tam (E12.5)	12919499040	107662492	2015-07-22 17:06:27	9117771894	12919499040	107662492	2	107662492	index:0,count:107662492,average:60,stdev:0|index:1,count:107662492,average:60,stdev:0	GSM1410664_r1	GEO					4.77	3.49	0.05	12543176436	12563938806	11443919300	11532304321	100.17	100.77	105395092	93194643	197.927	884.878	163	3523300	86.75	95.04	119501355	91425720	119501355	91425720	91.65	92.08	119501355	96594275	119501355	88585995	565817122	4.51	0.13	0	8.54	0	0.29	0	0.08	0	0.00	0	1.74	0	105395092	0	120	0	118.97	0	1.58	0	0.01	0	1.31	0	0.00	0	329.58	0	0.41	0	134601	0	107662492	0	9193277	0	313424	0	81040	0	0	0	1872936	0	17868	0	0	0	145418	0	22232083	0	40199	0	22435568	0	89.35	0	96201815	0	238295	22963454	96.365656014604	107662492.0	105395092.0	134601.0	9193277.0	313424.0	81040.0	0.0	1872936.0	96201815.0	97.9	0.1	8.5	0.3	0.1	0.0	1.7	89.4	60	60	60.00	38	6459749520	25.0	24.1	24.0	26.9	0.0	35.9	20.9	bulk
1509533	SRR1382089	SRP043153	SRS635005	SRX591763	SRA170153	GEO		Musashi proteins are post-transcriptional regulators of the epithelial-luminal cell state	mRNA-seq and ribosome profiling of neural stem cells overexpressing or knocked out for Musashi RNA-binding proteins Overall design: Study of the global effects of Musashi (Msi) proteins on the transcriptome of embryonic neural stem cells. Neural stem cells were derived from brains of E12.5 or E13.5 embryos engineered to have inducible Msi1 or Msi2 genes, or from embryos with double floxed alleles of Msi1 and Msi2 carrying a Tamoxifen-induclble Cre (CreER). The overexpression mice were made using the Flp-in system (OpenBioSystems), where a cDNA of interest (in this case Msi1 or Msi2) is knocked into the Collagen (Col1A1) locus. The expression of the cDNA of interest is driven by m2rTTA that is knocked into the Rosa26 locus (R26). KH2 describes a strain containing the R26-m2rTTA but lacking Msi1 or Msi2 cDNA. MSI1 describes a strain containing R26-m2rTTA and Msi1 cDNA in Col1A1. MSI2 describes a strain containing R26-m2rTTA and Msi2 cDNA in Col1A1. C1 describes a strain lacking the CreER allele but containing double floxed alleles of Msi1/Msi2 (used as Tamoxifen control). C4 describes a strain carrying the CreER allele and double floxed alleles of Msi1/Msi2.		GSM1410665: Cre-less Msi1/Msi2 floxed control line C1, TAM (E12.5); Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Poly(A)+ RNA was selected by oligo-dT magnetic beads, and prepared for paired end RNA sequencing using Illumina paired end sequencing primers.	Illumina HiSeq 2000	developmental stage;;E12.5|source_name;;NSCs|time point;;48 hours|treatment;;4-OHT	GEO Accession;;GSM1410665		GSM1410665	Cre-less Msi1/Msi2 floxed control line C1, TAM (E12.5)	11463141960	95526183	2015-07-22 17:06:27	8108899501	11463141960	95526183	2	95526183	index:0,count:95526183,average:60,stdev:0|index:1,count:95526183,average:60,stdev:0	GSM1410665_r1	GEO					4.66	3.53	0.06	11113335260	11125253529	10145442879	10218973537	100.11	100.72	93397742	83260986	191.494	838.858	160	3127428	86.42	94.63	105943581	80718363	105943581	80718363	91.25	91.67	105943581	85230029	105943581	78193601	543785765	4.89	0.14	0	8.48	0	0.30	0	0.07	0	0.00	0	1.85	0	93397742	0	120	0	118.95	0	1.56	0	0.01	0	1.31	0	0.00	0	338.81	0	0.42	0	134685	0	95526183	0	8096552	0	286450	0	71139	0	0	0	1770852	0	15707	0	0	0	129039	0	19674555	0	37070	0	19856371	0	89.30	0	85301190	0	232100	20329027	87.587363205515	95526183.0	93397742.0	134685.0	8096552.0	286450.0	71139.0	0.0	1770852.0	85301190.0	97.8	0.1	8.5	0.3	0.1	0.0	1.9	89.3	60	60	60.00	38	5731570980	24.9	24.1	24.1	26.9	0.0	35.9	20.8	bulk
1509644	SRR1382090	SRP043153	SRS635006	SRX591764	SRA170153	GEO		Musashi proteins are post-transcriptional regulators of the epithelial-luminal cell state	mRNA-seq and ribosome profiling of neural stem cells overexpressing or knocked out for Musashi RNA-binding proteins Overall design: Study of the global effects of Musashi (Msi) proteins on the transcriptome of embryonic neural stem cells. Neural stem cells were derived from brains of E12.5 or E13.5 embryos engineered to have inducible Msi1 or Msi2 genes, or from embryos with double floxed alleles of Msi1 and Msi2 carrying a Tamoxifen-induclble Cre (CreER). The overexpression mice were made using the Flp-in system (OpenBioSystems), where a cDNA of interest (in this case Msi1 or Msi2) is knocked into the Collagen (Col1A1) locus. The expression of the cDNA of interest is driven by m2rTTA that is knocked into the Rosa26 locus (R26). KH2 describes a strain containing the R26-m2rTTA but lacking Msi1 or Msi2 cDNA. MSI1 describes a strain containing R26-m2rTTA and Msi1 cDNA in Col1A1. MSI2 describes a strain containing R26-m2rTTA and Msi2 cDNA in Col1A1. C1 describes a strain lacking the CreER allele but containing double floxed alleles of Msi1/Msi2 (used as Tamoxifen control). C4 describes a strain carrying the CreER allele and double floxed alleles of Msi1/Msi2.		GSM1410666: Cre-carrying Msi1/Msi2 floxed line C4, No Tam (E12.5); Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Poly(A)+ RNA was selected by oligo-dT magnetic beads, and prepared for paired end RNA sequencing using Illumina paired end sequencing primers.	Illumina HiSeq 2000	developmental stage;;E12.5|source_name;;NSCs|time point;;48 hours|treatment;;No 4-OHT	GEO Accession;;GSM1410666		GSM1410666	Cre-carrying Msi1/Msi2 floxed line C4, No Tam (E12.5)	10527444600	87728705	2015-07-22 17:06:27	7411350377	10527444600	87728705	2	87728705	index:0,count:87728705,average:60,stdev:0|index:1,count:87728705,average:60,stdev:0	GSM1410666_r1	GEO					4.8	3.58	0.05	10257389970	10266838068	9356453505	9422850943	100.09	100.71	86267029	78060914	180.898	743.906	152	2666942	86.11	94.37	98031381	74287379	98031381	74287379	90.98	91.39	98031381	78489705	98031381	71949104	527112525	5.14	0.12	0	8.60	0	0.30	0	0.07	0	0.00	0	1.29	0	86267029	0	120	0	118.86	0	1.56	0	0.01	0	1.31	0	0.00	0	327.96	0	0.38	0	105372	0	87728705	0	7543745	0	265441	0	65749	0	0	0	1130486	0	13892	0	0	0	118076	0	17986012	0	33661	0	18151641	0	89.73	0	78723284	0	226403	18574533	82.041903154994	87728705.0	86267029.0	105372.0	7543745.0	265441.0	65749.0	0.0	1130486.0	78723284.0	98.3	0.1	8.6	0.3	0.1	0.0	1.3	89.7	60	60	60.00	38	5263722300	25.1	23.9	23.7	27.0	0.2	35.9	20.7	bulk
1509662	SRR1382091	SRP043153	SRS635007	SRX591765	SRA170153	GEO		Musashi proteins are post-transcriptional regulators of the epithelial-luminal cell state	mRNA-seq and ribosome profiling of neural stem cells overexpressing or knocked out for Musashi RNA-binding proteins Overall design: Study of the global effects of Musashi (Msi) proteins on the transcriptome of embryonic neural stem cells. Neural stem cells were derived from brains of E12.5 or E13.5 embryos engineered to have inducible Msi1 or Msi2 genes, or from embryos with double floxed alleles of Msi1 and Msi2 carrying a Tamoxifen-induclble Cre (CreER). The overexpression mice were made using the Flp-in system (OpenBioSystems), where a cDNA of interest (in this case Msi1 or Msi2) is knocked into the Collagen (Col1A1) locus. The expression of the cDNA of interest is driven by m2rTTA that is knocked into the Rosa26 locus (R26). KH2 describes a strain containing the R26-m2rTTA but lacking Msi1 or Msi2 cDNA. MSI1 describes a strain containing R26-m2rTTA and Msi1 cDNA in Col1A1. MSI2 describes a strain containing R26-m2rTTA and Msi2 cDNA in Col1A1. C1 describes a strain lacking the CreER allele but containing double floxed alleles of Msi1/Msi2 (used as Tamoxifen control). C4 describes a strain carrying the CreER allele and double floxed alleles of Msi1/Msi2.		GSM1410667: Cre-carrying Msi1/Msi2 floxed line C4, TAM (E12.5); Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Poly(A)+ RNA was selected by oligo-dT magnetic beads, and prepared for paired end RNA sequencing using Illumina paired end sequencing primers.	Illumina HiSeq 2000	developmental stage;;E12.5|source_name;;NSCs|time point;;48 hours|treatment;;4-OHT	GEO Accession;;GSM1410667		GSM1410667	Cre-carrying Msi1/Msi2 floxed line C4, TAM (E12.5)	12793216560	106610138	2015-07-22 17:06:27	9005458277	12793216560	106610138	2	106610138	index:0,count:106610138,average:60,stdev:0|index:1,count:106610138,average:60,stdev:0	GSM1410667_r1	GEO					5.0	3.57	0.06	12415044541	12438813891	11282299214	11376904926	100.19	100.84	104431171	93705110	183.652	797.693	154	4087491	86.62	95.27	119466961	90456836	119466961	90456836	91.81	92.24	119466961	95873283	119466961	87579239	534426177	4.30	0.12	0	8.90	0	0.34	0	0.07	0	0.00	0	1.63	0	104431171	0	120	0	118.83	0	1.58	0	0.01	0	1.31	0	0.00	0	329.16	0	0.38	0	130455	0	106610138	0	9484202	0	366710	0	72806	0	0	0	1739451	0	17907	0	0	0	151785	0	22950317	0	40391	0	23160400	0	89.06	0	94946969	0	228238	23713391	103.897646316564	106610138.0	104431171.0	130455.0	9484202.0	366710.0	72806.0	0.0	1739451.0	94946969.0	98.0	0.1	8.9	0.3	0.1	0.0	1.6	89.1	60	60	60.00	38	6396608280	24.5	24.1	24.3	26.8	0.2	35.9	20.6	bulk
3018896	SRR1382084	SRP043153	SRS635000	SRX591758	SRA170153	GEO		Musashi proteins are post-transcriptional regulators of the epithelial-luminal cell state	mRNA-seq and ribosome profiling of neural stem cells overexpressing or knocked out for Musashi RNA-binding proteins Overall design: Study of the global effects of Musashi (Msi) proteins on the transcriptome of embryonic neural stem cells. Neural stem cells were derived from brains of E12.5 or E13.5 embryos engineered to have inducible Msi1 or Msi2 genes, or from embryos with double floxed alleles of Msi1 and Msi2 carrying a Tamoxifen-induclble Cre (CreER). The overexpression mice were made using the Flp-in system (OpenBioSystems), where a cDNA of interest (in this case Msi1 or Msi2) is knocked into the Collagen (Col1A1) locus. The expression of the cDNA of interest is driven by m2rTTA that is knocked into the Rosa26 locus (R26). KH2 describes a strain containing the R26-m2rTTA but lacking Msi1 or Msi2 cDNA. MSI1 describes a strain containing R26-m2rTTA and Msi1 cDNA in Col1A1. MSI2 describes a strain containing R26-m2rTTA and Msi2 cDNA in Col1A1. C1 describes a strain lacking the CreER allele but containing double floxed alleles of Msi1/Msi2 (used as Tamoxifen control). C4 describes a strain carrying the CreER allele and double floxed alleles of Msi1/Msi2.		GSM1410660: MSI1, No Dox (E12.5); Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Poly(A)+ RNA was selected by oligo-dT magnetic beads, and prepared for paired end RNA sequencing using Illumina paired end sequencing primers.	Illumina HiSeq 2000	developmental stage;;E12.5|source_name;;NSCs|time point;;72 hours|treatment;;No Dox	GEO Accession;;GSM1410660		GSM1410660	MSI1, No Dox (E12.5)	10483283760	87360698	2015-07-22 17:06:27	7328975616	10483283760	87360698	2	87360698	index:0,count:87360698,average:60,stdev:0|index:1,count:87360698,average:60,stdev:0	GSM1410660_r1	GEO					3.5	3.79	0.07	9967571404	9937833507	9039956175	9075767128	99.7	100.4	84014344	73218966	214.563	1011.889	179	1884941	83.56	92.1	96960716	70201395	96960716	70201395	89.07	89.33	96960716	74831924	96960716	68088521	720269194	7.23	0.81	0	8.92	0	0.60	0	0.08	0	0.00	0	3.15	0	84014344	0	120	0	118.75	0	1.69	0	0.01	0	1.40	0	0.00	0	294.47	0	0.41	0	703267	0	87360698	0	7790664	0	523868	0	72244	0	0	0	2750242	0	12668	0	0	0	109564	0	16352364	0	35970	0	16510566	0	87.25	0	76223680	0	222747	16994854	76.296668417532	87360698.0	84014344.0	703267.0	7790664.0	523868.0	72244.0	0.0	2750242.0	76223680.0	96.2	0.8	8.9	0.6	0.1	0.0	3.1	87.3	60	60	60.00	38	5241641880	25.5	24.4	24.2	25.8	0.0	36.1	21.2	bulk
1913498	SRR1574329	SRP047079	SRS700492	SRX700307	SRA184282	GEO		MEF2D drives photoreceptor development through a genome-wide competition for tissue-specific enhancers (RNA-Seq)	Organismal development requires the precise coordination of genetic programs to regulate cell fate and function. MEF2 transcription factors play essential roles in this process but how these broadly expressed factors contribute to the generation of specific cell types during development is poorly understood.  Here we show that despite being expressed in virtually all mammalian tissues, in the retina MEF2D binds to retina-specific enhancers and controls photoreceptor cell development. MEF2D achieves specificity by cooperating with a retina-specific factor CRX, which recruits MEF2D away from canonical MEF2 binding sites, and redirects it to retina-specific enhancers that lack the consensus MEF2 sequence.  Once bound to retina-specific enhancers, MEF2D and CRX co-activate the expression of photoreceptor-specific genes that are critical for retinal function. These findings demonstrate that broadly expressed TFs acquire specific functions through competitive recruitment to enhancers by tissue-specific TFs, and through cooperative activation of these enhancers to regulate tissue-specific genes. Overall design: Total RNA-seq data from WT, Mef2d KO and Crx KO P11 mouse retinae		GSM1503669: P11_WT_Retina_1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Retinae were dissected from p11 knockout or wild-type littermate controls. Both retinae from each animal were pooled for each sample.  RNA was extracted using trizol and Qiagen Rneasy purification with on-column DNase digestion. Illumina library construction and sequencing was carried out as follows: total RNA was depleted of ribosomal RNA using the Ribozero rRNA removal kit (Epicentre), heat-fragmented to 200-700 bp in length and cloned using Uricil-N-Glycosylase-based strand-specific cloning. cDNA fragments were sequenced using an Illumina HiSeq 2000 Strand-specific, rRNA depleted total RNA, Paired (WT vs. Mef2d KO) or single-end (WT vs. Crx KO) 49 bp sequencing	Illumina HiSeq 2000	age;;postnatal day 11|gender;;male|genotype;;wild type|source_name;;Retina, postnatal day 11, male|tissue;;retina	GEO Accession;;GSM1503669		GSM1503669	P11_WT_Retina_1	19460430000	108113500	2015-07-22 17:06:50	13328237530	19460430000	108113500	2	108113500	index:0,count:108113500,average:90,stdev:0|index:1,count:108113500,average:90,stdev:0	GSM1503669_r1	GEO					1.04	2.6	0.07	14126775077	13810195869	12657745022	12392071876	97.76	97.9	102091087	97672186	152.855	482.607	119	1399092	61.92	69.05	120030668	63210953	120030668	63210953	66.36	65.45	120030668	67749906	120030668	59916488	3711814761	26.28	0.99	0	9.76	0	3.59	0	0.27	0	0.00	0	1.72	0	102091087	0	180	0	178.87	0	1.74	0	0.01	0	1.29	0	0.00	0	149.47	0	0.19	0	1067537	0	108113500	0	10550810	0	3876483	0	287344	0	0	0	1858586	0	20259	0	0	0	206366	0	24903993	0	76588	0	25207206	0	84.67	0	91540277	0	279089	20960200	75.102207539530	108113500.0	102091087.0	1067537.0	10550810.0	3876483.0	287344.0	0.0	1858586.0	91540277.0	94.4	1.0	9.8	3.6	0.3	0.0	1.7	84.7	90	90	90.00	38	9730215000	24.3	24.1	23.7	27.9	0.0	36.0	22.6	bulk
1913612	SRR1574330	SRP047079	SRS700494	SRX700308	SRA184282	GEO		MEF2D drives photoreceptor development through a genome-wide competition for tissue-specific enhancers (RNA-Seq)	Organismal development requires the precise coordination of genetic programs to regulate cell fate and function. MEF2 transcription factors play essential roles in this process but how these broadly expressed factors contribute to the generation of specific cell types during development is poorly understood.  Here we show that despite being expressed in virtually all mammalian tissues, in the retina MEF2D binds to retina-specific enhancers and controls photoreceptor cell development. MEF2D achieves specificity by cooperating with a retina-specific factor CRX, which recruits MEF2D away from canonical MEF2 binding sites, and redirects it to retina-specific enhancers that lack the consensus MEF2 sequence.  Once bound to retina-specific enhancers, MEF2D and CRX co-activate the expression of photoreceptor-specific genes that are critical for retinal function. These findings demonstrate that broadly expressed TFs acquire specific functions through competitive recruitment to enhancers by tissue-specific TFs, and through cooperative activation of these enhancers to regulate tissue-specific genes. Overall design: Total RNA-seq data from WT, Mef2d KO and Crx KO P11 mouse retinae		GSM1503670: P11_WT_Retina_2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Retinae were dissected from p11 knockout or wild-type littermate controls. Both retinae from each animal were pooled for each sample.  RNA was extracted using trizol and Qiagen Rneasy purification with on-column DNase digestion. Illumina library construction and sequencing was carried out as follows: total RNA was depleted of ribosomal RNA using the Ribozero rRNA removal kit (Epicentre), heat-fragmented to 200-700 bp in length and cloned using Uricil-N-Glycosylase-based strand-specific cloning. cDNA fragments were sequenced using an Illumina HiSeq 2000 Strand-specific, rRNA depleted total RNA, Paired (WT vs. Mef2d KO) or single-end (WT vs. Crx KO) 49 bp sequencing	Illumina HiSeq 2000	age;;postnatal day 11|gender;;female|genotype;;wild type|source_name;;Retina, postnatal day 11, female|tissue;;retina	GEO Accession;;GSM1503670		GSM1503670	P11_WT_Retina_2	19080685620	106003809	2015-07-22 17:06:50	12862013484	19080685620	106003809	2	106003809	index:0,count:106003809,average:90,stdev:0|index:1,count:106003809,average:90,stdev:0	GSM1503670_r1	GEO					0.91	2.57	0.03	14027229596	13712337198	12400089246	12131545503	97.76	97.83	99155103	95177701	155.512	464.665	127	1289506	59.73	67.49	118582608	59228416	118582608	59228416	65.37	63.94	118582608	64821291	118582608	56109564	3838242843	27.36	0.82	0	10.75	0	4.60	0	0.30	0	0.00	0	1.56	0	99155103	0	180	0	178.93	0	1.58	0	0.01	0	1.26	0	0.00	0	317.22	0	0.15	0	865612	0	106003809	0	11399864	0	4880539	0	313532	0	0	0	1654635	0	19314	0	0	0	194442	0	23226454	0	71552	0	23511762	0	82.78	0	87755239	0	277434	20020106	72.161688906190	106003809.0	99155103.0	865612.0	11399864.0	4880539.0	313532.0	0.0	1654635.0	87755239.0	93.5	0.8	10.8	4.6	0.3	0.0	1.6	82.8	90	90	90.00	38	9540342810	24.3	24.2	24.0	27.5	0.0	36.2	23.2	bulk
1913661	SRR1574333	SRP047079	SRS700496	SRX700311	SRA184282	GEO		MEF2D drives photoreceptor development through a genome-wide competition for tissue-specific enhancers (RNA-Seq)	Organismal development requires the precise coordination of genetic programs to regulate cell fate and function. MEF2 transcription factors play essential roles in this process but how these broadly expressed factors contribute to the generation of specific cell types during development is poorly understood.  Here we show that despite being expressed in virtually all mammalian tissues, in the retina MEF2D binds to retina-specific enhancers and controls photoreceptor cell development. MEF2D achieves specificity by cooperating with a retina-specific factor CRX, which recruits MEF2D away from canonical MEF2 binding sites, and redirects it to retina-specific enhancers that lack the consensus MEF2 sequence.  Once bound to retina-specific enhancers, MEF2D and CRX co-activate the expression of photoreceptor-specific genes that are critical for retinal function. These findings demonstrate that broadly expressed TFs acquire specific functions through competitive recruitment to enhancers by tissue-specific TFs, and through cooperative activation of these enhancers to regulate tissue-specific genes. Overall design: Total RNA-seq data from WT, Mef2d KO and Crx KO P11 mouse retinae		GSM1503673: P11_WT_Retina_3; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Retinae were dissected from p11 knockout or wild-type littermate controls. Both retinae from each animal were pooled for each sample.  RNA was extracted using trizol and Qiagen Rneasy purification with on-column DNase digestion. Illumina library construction and sequencing was carried out as follows: total RNA was depleted of ribosomal RNA using the Ribozero rRNA removal kit (Epicentre), heat-fragmented to 200-700 bp in length and cloned using Uricil-N-Glycosylase-based strand-specific cloning. cDNA fragments were sequenced using an Illumina HiSeq 2000 Strand-specific, rRNA depleted total RNA, Paired (WT vs. Mef2d KO) or single-end (WT vs. Crx KO) 49 bp sequencing	Illumina HiSeq 2000	age;;postnatal day 11|gender;;male|genotype;;wild type|source_name;;Retina, postnatal day 11, male|tissue;;retina	GEO Accession;;GSM1503673		GSM1503673	P11_WT_Retina_3	8631943880	176162120	2015-07-22 17:06:50	8666179162	8631943880	176162120	1	176162120	index:0,count:176162120,average:49,stdev:0	GSM1503673_r1	GEO					7.9	3.3	0.09	8288093233	8024755369	7424644765	7240471640	96.82	97.52	0	0	0	0	0	0	59.62	66.53	209329647	102377839	209329647	102377839	63.37	64.26	209329647	108831875	209329647	98877204	2329918609	28.11	0.41	0	10.14	0	0.63	0	0.47	0	0.00	0	1.42	0	171730206	0	49	0	48.25	0	1.41	0	0.01	0	1.28	0	0.00	0	561.22	0	0.71	0	728186	0	176162120	0	17858407	0	1104703	0	828799	0	0	0	2498412	0	3782	0	0	0	43366	0	5654046	0	31157	0	5732351	0	87.35	0	153871799	0	191348	6093797	31.846672032109	176162120.0	171730206.0	728186.0	17858407.0	1104703.0	828799.0	0.0	2498412.0	153871799.0	97.5	0.4	10.1	0.6	0.5	0.0	1.4	87.3	49	49	49.00	36	8631943880	23.8	23.2	25.4	27.6	0.0	36.1	23.5	bulk
1913677	SRR1574334	SRP047079	SRS700497	SRX700312	SRA184282	GEO		MEF2D drives photoreceptor development through a genome-wide competition for tissue-specific enhancers (RNA-Seq)	Organismal development requires the precise coordination of genetic programs to regulate cell fate and function. MEF2 transcription factors play essential roles in this process but how these broadly expressed factors contribute to the generation of specific cell types during development is poorly understood.  Here we show that despite being expressed in virtually all mammalian tissues, in the retina MEF2D binds to retina-specific enhancers and controls photoreceptor cell development. MEF2D achieves specificity by cooperating with a retina-specific factor CRX, which recruits MEF2D away from canonical MEF2 binding sites, and redirects it to retina-specific enhancers that lack the consensus MEF2 sequence.  Once bound to retina-specific enhancers, MEF2D and CRX co-activate the expression of photoreceptor-specific genes that are critical for retinal function. These findings demonstrate that broadly expressed TFs acquire specific functions through competitive recruitment to enhancers by tissue-specific TFs, and through cooperative activation of these enhancers to regulate tissue-specific genes. Overall design: Total RNA-seq data from WT, Mef2d KO and Crx KO P11 mouse retinae		GSM1503674: P11_WT_Retina_4; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Retinae were dissected from p11 knockout or wild-type littermate controls. Both retinae from each animal were pooled for each sample.  RNA was extracted using trizol and Qiagen Rneasy purification with on-column DNase digestion. Illumina library construction and sequencing was carried out as follows: total RNA was depleted of ribosomal RNA using the Ribozero rRNA removal kit (Epicentre), heat-fragmented to 200-700 bp in length and cloned using Uricil-N-Glycosylase-based strand-specific cloning. cDNA fragments were sequenced using an Illumina HiSeq 2000 Strand-specific, rRNA depleted total RNA, Paired (WT vs. Mef2d KO) or single-end (WT vs. Crx KO) 49 bp sequencing	Illumina HiSeq 2000	age;;postnatal day 11|gender;;female|genotype;;wild type|source_name;;Retina, postnatal day 11, female|tissue;;retina	GEO Accession;;GSM1503674		GSM1503674	P11_WT_Retina_4	8634123890	176206610	2015-07-22 17:06:50	8628949011	8634123890	176206610	1	176206610	index:0,count:176206610,average:49,stdev:0	GSM1503674_r1	GEO					7.33	3.47	0.05	8286843488	8034596601	7390176144	7214908126	96.96	97.63	0	0	0	0	0	0	60.99	68.37	210970183	104837440	210970183	104837440	64.84	65.93	210970183	111461736	210970183	101093250	2185895363	26.38	0.43	0	10.53	0	0.59	0	0.42	0	0.00	0	1.44	0	171892454	0	49	0	48.20	0	1.38	0	0.01	0	1.26	0	0.00	0	593.40	0	0.74	0	751777	0	176206610	0	18554409	0	1045888	0	738026	0	0	0	2530242	0	3868	0	0	0	43440	0	5836204	0	31399	0	5914911	0	87.02	0	153338045	0	190514	6206621	32.578293458748	176206610.0	171892454.0	751777.0	18554409.0	1045888.0	738026.0	0.0	2530242.0	153338045.0	97.6	0.4	10.5	0.6	0.4	0.0	1.4	87.0	49	49	49.00	36	8634123890	23.6	23.4	25.6	27.4	0.0	36.2	23.8	bulk
862983	SRR1706560	SRP051076	SRS788248	SRX806615	SRA214041	GEO		Transcriptional profiling of cutaneous Mrgprd free nerve endings and C-LTMRs	Cutaneous C-unmyelinated free nerve endings and hair follicles-innervating C-LTMRs convey two opposite aspects of touch sensation: a sensation of pain and a sensation of pleasant touch. The molecular mechanisms underlying these diametrically opposite functions are unknown. Here we used a mouse model that genetically marks C-LTMRs and the free nerve endings MRGPRD+ neurons in combination with fluorescent cell surface labeling, flow cytometry and RNA deep-sequencing technology. Cluster analysis of the RNA-Seq profiles of the purified neuronal subsets revealed 156 and 184 genes differentially expressed in MRGPRD-expressing neurons and C-LTMRs, respectively. 48 MRGPD- and 67 C-LTMRs-enriched genes were validated using a triple staining experiment approach and the Cav3.3 channel, found to be exclusively expressed in C-LTMRs, was validated using electrophysiology. Furthermore, our study greatly expands the molecular characterization of C-LTMRs and suggests that this particular population of neurons shares common transcriptional signatures with A and A low threshold mechanoreceptors. Overall design: RNA profiles of FACS-sorted subsets of sensory neurons, namely Mrgprd+ neurons (DP, double-positive=IB4+GINIP+), C-LTMRs (IB4-GINIP+) and remaining cells (DN, double-negative=IB4-GINIP-) were generated by deep sequencing in duplicate using Illumina HiSeq 2000.		GSM1564174: DP-1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Neurons were sorted directly in RLT-lysis buffer from RNeasy Micro Kit (Qiagen), snap-frozen at -80°C and processed for RNA extraction following manufacturer's recommendations. 50 nanograms of high-quality total RNAs were amplified with the Amino Allyl Message Amp II Amplification kit (Life Technologies, Carlsbad, CA). RNA-Seq libraries were constructed with the TruSeq RNA sample preparation (Low-throughput protocol) kit from Illumina.	Illumina HiSeq 2000	genotype/variation;;GINIP+/mcherry|sensory neuron subset;;Mrgprd+ (DP, double-positive=IB4+GINIP+)|source_name;;Mrgprd+ sensory neurons|tissue;;dorsal root ganglia (DRG)	GEO Accession;;GSM1564174		GSM1564174	DP-1	11172041200	55860206	2015-02-02 16:00:02	7728756873	11172041200	55860206	2	55860206	index:0,count:55860206,average:100,stdev:0|index:1,count:55860206,average:100,stdev:0	GSM1564174_r1	GEO					2.88	3.32	0.07	8638924765	8602793448	7903206840	7936333392	99.58	100.42	52253397	49492728	191.311	557.023	147	479059	87.64	95.97	59483294	45796207	59483294	45796207	91.04	91.99	59483294	47569188	59483294	43897329	231255172	2.68	1.14	0	8.11	0	0.40	0	0.06	0	0.00	0	6.00	0	52253397	0	200	0	197.86	0	1.56	0	0.01	0	1.43	0	0.01	0	278.53	0	0.41	0	638094	0	55860206	0	4532539	0	221583	0	32039	0	0	0	3353187	0	12274	0	0	0	101302	0	17211505	0	74252	0	17399333	0	85.43	0	47720858	0	184300	16311129	88.503141616929	55860206.0	52253397.0	638094.0	4532539.0	221583.0	32039.0	0.0	3353187.0	47720858.0	93.5	1.1	8.1	0.4	0.1	0.0	6.0	85.4	100	100	100.00	38	5586020600	26.0	24.0	23.9	26.1	0.0	33.2	14.2	bulk
862991	SRR1706561	SRP051076	SRS788250	SRX806616	SRA214041	GEO		Transcriptional profiling of cutaneous Mrgprd free nerve endings and C-LTMRs	Cutaneous C-unmyelinated free nerve endings and hair follicles-innervating C-LTMRs convey two opposite aspects of touch sensation: a sensation of pain and a sensation of pleasant touch. The molecular mechanisms underlying these diametrically opposite functions are unknown. Here we used a mouse model that genetically marks C-LTMRs and the free nerve endings MRGPRD+ neurons in combination with fluorescent cell surface labeling, flow cytometry and RNA deep-sequencing technology. Cluster analysis of the RNA-Seq profiles of the purified neuronal subsets revealed 156 and 184 genes differentially expressed in MRGPRD-expressing neurons and C-LTMRs, respectively. 48 MRGPD- and 67 C-LTMRs-enriched genes were validated using a triple staining experiment approach and the Cav3.3 channel, found to be exclusively expressed in C-LTMRs, was validated using electrophysiology. Furthermore, our study greatly expands the molecular characterization of C-LTMRs and suggests that this particular population of neurons shares common transcriptional signatures with A and A low threshold mechanoreceptors. Overall design: RNA profiles of FACS-sorted subsets of sensory neurons, namely Mrgprd+ neurons (DP, double-positive=IB4+GINIP+), C-LTMRs (IB4-GINIP+) and remaining cells (DN, double-negative=IB4-GINIP-) were generated by deep sequencing in duplicate using Illumina HiSeq 2000.		GSM1564175: DP-2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Neurons were sorted directly in RLT-lysis buffer from RNeasy Micro Kit (Qiagen), snap-frozen at -80°C and processed for RNA extraction following manufacturer's recommendations. 50 nanograms of high-quality total RNAs were amplified with the Amino Allyl Message Amp II Amplification kit (Life Technologies, Carlsbad, CA). RNA-Seq libraries were constructed with the TruSeq RNA sample preparation (Low-throughput protocol) kit from Illumina.	Illumina HiSeq 2000	genotype/variation;;GINIP+/mcherry|sensory neuron subset;;Mrgprd+ (DP, double-positive=IB4+GINIP+)|source_name;;Mrgprd+ sensory neurons|tissue;;dorsal root ganglia (DRG)	GEO Accession;;GSM1564175		GSM1564175	DP-2	10052702000	50263510	2015-02-02 16:00:02	6969297939	10052702000	50263510	2	50263510	index:0,count:50263510,average:100,stdev:0|index:1,count:50263510,average:100,stdev:0	GSM1564175_r1	GEO					2.88	3.32	0.05	7821239705	7801311574	7155182618	7195504898	99.75	100.56	47542160	45171095	188.410	518.418	147	454047	88.34	96.71	54081079	41998952	54081079	41998952	91.72	92.7	54081079	43606810	54081079	40255983	162522118	2.08	1.00	0	8.19	0	0.38	0	0.06	0	0.00	0	4.98	0	47542160	0	200	0	197.95	0	1.59	0	0.01	0	1.43	0	0.01	0	265.71	0	0.40	0	502461	0	50263510	0	4116671	0	192730	0	27755	0	0	0	2500865	0	11652	0	0	0	92843	0	15752013	0	93051	0	15949559	0	86.40	0	43425489	0	180956	14887288	82.270209332655	50263510.0	47542160.0	502461.0	4116671.0	192730.0	27755.0	0.0	2500865.0	43425489.0	94.6	1.0	8.2	0.4	0.1	0.0	5.0	86.4	100	100	100.00	38	5026351000	26.0	24.0	23.9	26.1	0.0	33.4	14.5	bulk
862999	SRR1706562	SRP051076	SRS788249	SRX806617	SRA214041	GEO		Transcriptional profiling of cutaneous Mrgprd free nerve endings and C-LTMRs	Cutaneous C-unmyelinated free nerve endings and hair follicles-innervating C-LTMRs convey two opposite aspects of touch sensation: a sensation of pain and a sensation of pleasant touch. The molecular mechanisms underlying these diametrically opposite functions are unknown. Here we used a mouse model that genetically marks C-LTMRs and the free nerve endings MRGPRD+ neurons in combination with fluorescent cell surface labeling, flow cytometry and RNA deep-sequencing technology. Cluster analysis of the RNA-Seq profiles of the purified neuronal subsets revealed 156 and 184 genes differentially expressed in MRGPRD-expressing neurons and C-LTMRs, respectively. 48 MRGPD- and 67 C-LTMRs-enriched genes were validated using a triple staining experiment approach and the Cav3.3 channel, found to be exclusively expressed in C-LTMRs, was validated using electrophysiology. Furthermore, our study greatly expands the molecular characterization of C-LTMRs and suggests that this particular population of neurons shares common transcriptional signatures with A and A low threshold mechanoreceptors. Overall design: RNA profiles of FACS-sorted subsets of sensory neurons, namely Mrgprd+ neurons (DP, double-positive=IB4+GINIP+), C-LTMRs (IB4-GINIP+) and remaining cells (DN, double-negative=IB4-GINIP-) were generated by deep sequencing in duplicate using Illumina HiSeq 2000.		GSM1564176: C-LTMRs-1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Neurons were sorted directly in RLT-lysis buffer from RNeasy Micro Kit (Qiagen), snap-frozen at -80°C and processed for RNA extraction following manufacturer's recommendations. 50 nanograms of high-quality total RNAs were amplified with the Amino Allyl Message Amp II Amplification kit (Life Technologies, Carlsbad, CA). RNA-Seq libraries were constructed with the TruSeq RNA sample preparation (Low-throughput protocol) kit from Illumina.	Illumina HiSeq 2000	genotype/variation;;GINIP+/mcherry|sensory neuron subset;;C-LTMR (IB4-GINIP+)|source_name;;C-LTMR sensory neurons|tissue;;dorsal root ganglia (DRG)	GEO Accession;;GSM1564176		GSM1564176	C-LTMRs-1	9124042800	45620214	2015-02-02 16:00:02	6315467489	9124042800	45620214	2	45620214	index:0,count:45620214,average:100,stdev:0|index:1,count:45620214,average:100,stdev:0	GSM1564176_r1	GEO					3.94	3.15	0.06	7066951328	7034722722	6423289478	6446331551	99.54	100.36	42812455	40634672	190.230	540.041	148	401519	87.03	95.91	49045789	37259674	49045789	37259674	91.28	92.09	49045789	39077946	49045789	35774471	194812361	2.76	1.22	0	8.69	0	0.39	0	0.06	0	0.00	0	5.71	0	42812455	0	200	0	197.86	0	1.58	0	0.01	0	1.43	0	0.01	0	212.74	0	0.40	0	556245	0	45620214	0	3963944	0	177165	0	25658	0	0	0	2604936	0	9661	0	0	0	85216	0	14125527	0	66453	0	14286857	0	85.16	0	38848511	0	174870	13595106	77.744072739750	45620214.0	42812455.0	556245.0	3963944.0	177165.0	25658.0	0.0	2604936.0	38848511.0	93.8	1.2	8.7	0.4	0.1	0.0	5.7	85.2	100	100	100.00	38	4562021400	26.0	24.0	23.9	26.2	0.0	33.4	14.4	bulk
863007	SRR1706563	SRP051076	SRS788251	SRX806618	SRA214041	GEO		Transcriptional profiling of cutaneous Mrgprd free nerve endings and C-LTMRs	Cutaneous C-unmyelinated free nerve endings and hair follicles-innervating C-LTMRs convey two opposite aspects of touch sensation: a sensation of pain and a sensation of pleasant touch. The molecular mechanisms underlying these diametrically opposite functions are unknown. Here we used a mouse model that genetically marks C-LTMRs and the free nerve endings MRGPRD+ neurons in combination with fluorescent cell surface labeling, flow cytometry and RNA deep-sequencing technology. Cluster analysis of the RNA-Seq profiles of the purified neuronal subsets revealed 156 and 184 genes differentially expressed in MRGPRD-expressing neurons and C-LTMRs, respectively. 48 MRGPD- and 67 C-LTMRs-enriched genes were validated using a triple staining experiment approach and the Cav3.3 channel, found to be exclusively expressed in C-LTMRs, was validated using electrophysiology. Furthermore, our study greatly expands the molecular characterization of C-LTMRs and suggests that this particular population of neurons shares common transcriptional signatures with A and A low threshold mechanoreceptors. Overall design: RNA profiles of FACS-sorted subsets of sensory neurons, namely Mrgprd+ neurons (DP, double-positive=IB4+GINIP+), C-LTMRs (IB4-GINIP+) and remaining cells (DN, double-negative=IB4-GINIP-) were generated by deep sequencing in duplicate using Illumina HiSeq 2000.		GSM1564177: C-LTMRs-2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Neurons were sorted directly in RLT-lysis buffer from RNeasy Micro Kit (Qiagen), snap-frozen at -80°C and processed for RNA extraction following manufacturer's recommendations. 50 nanograms of high-quality total RNAs were amplified with the Amino Allyl Message Amp II Amplification kit (Life Technologies, Carlsbad, CA). RNA-Seq libraries were constructed with the TruSeq RNA sample preparation (Low-throughput protocol) kit from Illumina.	Illumina HiSeq 2000	genotype/variation;;GINIP+/mcherry|sensory neuron subset;;C-LTMR (IB4-GINIP+)|source_name;;C-LTMR sensory neurons|tissue;;dorsal root ganglia (DRG)	GEO Accession;;GSM1564177		GSM1564177	C-LTMRs-2	8727791600	43638958	2015-02-02 16:00:02	6027426007	8727791600	43638958	2	43638958	index:0,count:43638958,average:100,stdev:0|index:1,count:43638958,average:100,stdev:0	GSM1564177_r1	GEO					4.42	3.17	0.05	6741863212	6714237889	6082565980	6106970965	99.59	100.4	41009498	39021062	188.432	517.666	148	391778	86.83	96.4	47433583	35608393	47433583	35608393	91.75	92.55	47433583	37627958	47433583	34185344	155024685	2.30	1.10	0	9.33	0	0.37	0	0.06	0	0.00	0	5.60	0	41009498	0	200	0	197.90	0	1.67	0	0.01	0	1.44	0	0.01	0	286.68	0	0.40	0	478118	0	43638958	0	4071859	0	162302	0	24956	0	0	0	2442202	0	9195	0	0	0	82170	0	13174641	0	109925	0	13375931	0	84.64	0	36937639	0	180611	12890527	71.371771376051	43638958.0	41009498.0	478118.0	4071859.0	162302.0	24956.0	0.0	2442202.0	36937639.0	94.0	1.1	9.3	0.4	0.1	0.0	5.6	84.6	100	100	100.00	38	4363895800	26.0	24.0	23.9	26.1	0.0	33.4	14.3	bulk
863015	SRR1706564	SRP051076	SRS788253	SRX806619	SRA214041	GEO		Transcriptional profiling of cutaneous Mrgprd free nerve endings and C-LTMRs	Cutaneous C-unmyelinated free nerve endings and hair follicles-innervating C-LTMRs convey two opposite aspects of touch sensation: a sensation of pain and a sensation of pleasant touch. The molecular mechanisms underlying these diametrically opposite functions are unknown. Here we used a mouse model that genetically marks C-LTMRs and the free nerve endings MRGPRD+ neurons in combination with fluorescent cell surface labeling, flow cytometry and RNA deep-sequencing technology. Cluster analysis of the RNA-Seq profiles of the purified neuronal subsets revealed 156 and 184 genes differentially expressed in MRGPRD-expressing neurons and C-LTMRs, respectively. 48 MRGPD- and 67 C-LTMRs-enriched genes were validated using a triple staining experiment approach and the Cav3.3 channel, found to be exclusively expressed in C-LTMRs, was validated using electrophysiology. Furthermore, our study greatly expands the molecular characterization of C-LTMRs and suggests that this particular population of neurons shares common transcriptional signatures with A and A low threshold mechanoreceptors. Overall design: RNA profiles of FACS-sorted subsets of sensory neurons, namely Mrgprd+ neurons (DP, double-positive=IB4+GINIP+), C-LTMRs (IB4-GINIP+) and remaining cells (DN, double-negative=IB4-GINIP-) were generated by deep sequencing in duplicate using Illumina HiSeq 2000.		GSM1564178: DN-1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Neurons were sorted directly in RLT-lysis buffer from RNeasy Micro Kit (Qiagen), snap-frozen at -80°C and processed for RNA extraction following manufacturer's recommendations. 50 nanograms of high-quality total RNAs were amplified with the Amino Allyl Message Amp II Amplification kit (Life Technologies, Carlsbad, CA). RNA-Seq libraries were constructed with the TruSeq RNA sample preparation (Low-throughput protocol) kit from Illumina.	Illumina HiSeq 2000	genotype/variation;;GINIP+/mcherry|sensory neuron subset;;remaining cells (DN, double-negative=IB4-GINIP-)|source_name;;Remaining sensory neurons|tissue;;dorsal root ganglia (DRG)	GEO Accession;;GSM1564178		GSM1564178	DN-1	10360350000	51801750	2015-02-02 16:00:02	7222802465	10360350000	51801750	2	51801750	index:0,count:51801750,average:100,stdev:0|index:1,count:51801750,average:100,stdev:0	GSM1564178_r1	GEO					4.35	3.34	0.05	8007358064	8015932770	7257286101	7322816840	100.11	100.9	48902471	46510484	188.441	498.359	148	469921	87.13	96.31	56188906	42608728	56188906	42608728	91.44	92.24	56188906	44717276	56188906	40808712	225895586	2.82	1.14	0	8.99	0	0.44	0	0.04	0	0.00	0	5.12	0	48902471	0	200	0	197.85	0	1.56	0	0.01	0	1.42	0	0.01	0	250.32	0	0.41	0	588683	0	51801750	0	4659189	0	228162	0	19936	0	0	0	2651181	0	11144	0	0	0	91475	0	16405186	0	59307	0	16567112	0	85.41	0	44243282	0	200249	15470015	77.253893902092	51801750.0	48902471.0	588683.0	4659189.0	228162.0	19936.0	0.0	2651181.0	44243282.0	94.4	1.1	9.0	0.4	0.0	0.0	5.1	85.4	100	100	100.00	38	5180175000	25.9	24.1	24.0	26.0	0.0	33.6	14.7	bulk
863023	SRR1706565	SRP051076	SRS788252	SRX806620	SRA214041	GEO		Transcriptional profiling of cutaneous Mrgprd free nerve endings and C-LTMRs	Cutaneous C-unmyelinated free nerve endings and hair follicles-innervating C-LTMRs convey two opposite aspects of touch sensation: a sensation of pain and a sensation of pleasant touch. The molecular mechanisms underlying these diametrically opposite functions are unknown. Here we used a mouse model that genetically marks C-LTMRs and the free nerve endings MRGPRD+ neurons in combination with fluorescent cell surface labeling, flow cytometry and RNA deep-sequencing technology. Cluster analysis of the RNA-Seq profiles of the purified neuronal subsets revealed 156 and 184 genes differentially expressed in MRGPRD-expressing neurons and C-LTMRs, respectively. 48 MRGPD- and 67 C-LTMRs-enriched genes were validated using a triple staining experiment approach and the Cav3.3 channel, found to be exclusively expressed in C-LTMRs, was validated using electrophysiology. Furthermore, our study greatly expands the molecular characterization of C-LTMRs and suggests that this particular population of neurons shares common transcriptional signatures with A and A low threshold mechanoreceptors. Overall design: RNA profiles of FACS-sorted subsets of sensory neurons, namely Mrgprd+ neurons (DP, double-positive=IB4+GINIP+), C-LTMRs (IB4-GINIP+) and remaining cells (DN, double-negative=IB4-GINIP-) were generated by deep sequencing in duplicate using Illumina HiSeq 2000.		GSM1564179: DN-2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Neurons were sorted directly in RLT-lysis buffer from RNeasy Micro Kit (Qiagen), snap-frozen at -80°C and processed for RNA extraction following manufacturer's recommendations. 50 nanograms of high-quality total RNAs were amplified with the Amino Allyl Message Amp II Amplification kit (Life Technologies, Carlsbad, CA). RNA-Seq libraries were constructed with the TruSeq RNA sample preparation (Low-throughput protocol) kit from Illumina.	Illumina HiSeq 2000	genotype/variation;;GINIP+/mcherry|sensory neuron subset;;remaining cells (DN, double-negative=IB4-GINIP-)|source_name;;Remaining sensory neurons|tissue;;dorsal root ganglia (DRG)	GEO Accession;;GSM1564179		GSM1564179	DN-2	8609015800	43045079	2015-02-02 16:00:02	5997039778	8609015800	43045079	2	43045079	index:0,count:43045079,average:100,stdev:0|index:1,count:43045079,average:100,stdev:0	GSM1564179_r1	GEO					4.39	3.4	0.07	6688108707	6697269789	6063801911	6122800718	100.14	100.97	40568030	38675887	190.089	485.012	147	384411	87.27	96.42	46582005	35403332	46582005	35403332	91.54	92.41	46582005	37136783	46582005	33932220	186395208	2.79	1.04	0	8.94	0	0.39	0	0.03	0	0.00	0	5.33	0	40568030	0	200	0	197.91	0	1.57	0	0.01	0	1.43	0	0.02	0	264.89	0	0.43	0	445852	0	43045079	0	3849920	0	166833	0	14786	0	0	0	2295430	0	8709	0	0	0	67606	0	12807401	0	49408	0	12933124	0	85.30	0	36718110	0	186949	12239247	65.468373727594	43045079.0	40568030.0	445852.0	3849920.0	166833.0	14786.0	0.0	2295430.0	36718110.0	94.2	1.0	8.9	0.4	0.0	0.0	5.3	85.3	100	100	100.00	38	4304507900	26.1	23.9	23.8	26.2	0.0	33.4	14.5	bulk
465162	SRR1782642	SRP053008	SRS832978	SRX861699	SRA235889	GEO		Identification and Expression Patterns of Novel Long Non-Coding RNAs in Neural Progenitors of the Developing Mammalian Cortex	Long non-coding (lnc)RNAs play key roles in many biological processes. Elucidating the function of lncRNAs in cell type specification during organ development requires knowledge about their expression in individual progenitor types rather than in whole tissues. To achieve this during cortical development, we used a dual-reporter mouse line to isolate coexisting proliferating neural stem cells, differentiating neurogenic progenitors and newborn neurons and assessed the expression of lncRNAs by paired-end, high-throughput sequencing. We identified 379 genomic loci encoding novel lncRNAs and performed a comprehensive assessment of cell-specific expression patterns for all, annotated and novel, lncRNAs described to date. Our study provides a powerful new resource for studying these elusive transcripts during stem cell commitment and neurogenesis. Overall design: mRNA profiles of Proliferating Progenitors, Differentiating Progenitors and Neurons from lateral cortex of E14.5 mouse embryos. Each cell type in three biological replicates.		GSM1598391: S166_RFPminus_1 paired-end; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			E14.5 Btg2GFP/Tubb3GFP cortices were dissociated using the papain-based neural dissociation kit (Miltenyi Biotec) after removal of meninges and ganglionic eminences. FACS was performed at 4˚C in the 4-way purity mode with a flow rate of 20 μl/min using side and forward scatter light to eliminate debris and aggregates and gating established for green (488 nm) and red (561 nm) fluorescence. About 1x106 sorted cells from >3 embryos from different litters were immediately lysed in μMACS™ mRNA Isolation Kit and lysates cleaned on LysateClear Colums (Miltenyi) resulting in ca. 1 µg of poly-A RNAs with a integrity number >9.2 Library preparation and enrichment was performed using 15 µl Sera-Mag Oligo(dT) beads (Thermo Scientific) in 50 µl 10 mM Tris-HCl. Samples were treated with 1U Turbo DNase (Ambion) and purified with Agencourt RNAclean XP beads. Eluted mRNA (18 µl) was chemically fragmented with NEBNext-Mg RNA Fragmentation Module (New England Biolabs), re-purified with RNAclean XP beads and eluted in 13,5 µl nuclease-free water. First strand cDNA synthesis was performed using 0.15 µg/µl Random Primers (New England Biolabs), 1x First Strand Synthesis Reaction Buffer (New England Biolabs), 10 U/uL Superscript II (Invitrogen) with an initial hybridization for 5 min at 65°C with mRNA and primers followed by incubation at 25°C for 10 min, 42°C for 50 min, and 70°C for 15 min. After purification with Agencourt Ampure XP-beads (Beckman Coulter), second strand synthesis was performed using the Second Strand Synthesis module (New England Biolabs) replacing the 2nd strand synthesis buffer with a NTP-free buffer and adding equimolar 2.5 mM of d-nucleotides. Incubation for 2.5 h at 16°C was followed by Ampure XP beads purification as described above. End-Repair was done with the NEBnext End Repair Module (New England Biolabs) followed by XP beads purification and A-Tailing using the NEBnext dA-Tailing Module. Adaptors were ligated  (Adaptor-Oligo 1: 5'-ACA-CTC-TTT-CCC-TAC-ACG-ACG-CTC-TTC-CGA-TCT-3', Adaptor-Oligo 2: 5'-P-GAT-CGG-AAG-AGC-ACA-CGT-CTG-AAC-TCC-AGT-CAC-3') using 1x NEBnext Quick Ligation Buffer (New England Biolabs), 0.3 uM DNA Adaptors, 1 uL Quick T4 DNA Ligase (New England Biolabs) in 50 µl. XP beads purification was followed by dUTP cleavage with 1 U USER enzyme mix (New England Biolabs) per sample and direct enrichment using the PCR Enrich Adaptor Ligated cDNA Library module (New England Biolabs) with indexed primers.	Illumina HiSeq 2000	cell type;;Proliferating Progenitors Btg2 negative|developmental stage;;Embryonic day 14.5|genotype;;Btg2GFP/Tubb3GFP|source_name;;Lateral cortex of the brain|strain;;C57BL/6	GEO Accession;;GSM1598391		GSM1598391	S166_RFPminus_1 paired-end	3712246600	18561233	2015-04-23 16:23:12	2666592844	3712246600	18561233	2	18561233	index:0,count:18561233,average:100,stdev:0|index:1,count:18561233,average:100,stdev:0	GSM1598391_r1	GEO					1.27	3.34	0.13	3144814419	3133232008	2942654337	2944915592	99.63	100.08	17631903	15824124	231.612	905.031	175	128239	82.59	88.28	19886554	14562131	19886554	14562131	85.11	85.01	19886554	15005853	19886554	14023304	360059658	11.45	0.90	0	6.12	0	0.29	0	0.06	0	0.00	0	4.66	0	17631903	0	200	0	194.84	0	1.01	0	0.45	0	1.26	0	0.00	0	206.24	0	0.31	0	166511	0	18561233	0	1136068	0	53372	0	10254	0	0	0	865704	0	5201	0	0	0	43567	0	6059875	0	218213	0	6326856	0	88.87	0	16495835	0	203594	6784509	33.323717791291	18561233.0	17631903.0	166511.0	1136068.0	53372.0	10254.0	0.0	865704.0	16495835.0	95.0	0.9	6.1	0.3	0.1	0.0	4.7	88.9	100	100	100.00	38	1856123300	24.2	25.5	25.2	25.1	0.0	34.1	17.3	bulk
465166	SRR1782643	SRP053008	SRS832978	SRX861699	SRA235889	GEO		Identification and Expression Patterns of Novel Long Non-Coding RNAs in Neural Progenitors of the Developing Mammalian Cortex	Long non-coding (lnc)RNAs play key roles in many biological processes. Elucidating the function of lncRNAs in cell type specification during organ development requires knowledge about their expression in individual progenitor types rather than in whole tissues. To achieve this during cortical development, we used a dual-reporter mouse line to isolate coexisting proliferating neural stem cells, differentiating neurogenic progenitors and newborn neurons and assessed the expression of lncRNAs by paired-end, high-throughput sequencing. We identified 379 genomic loci encoding novel lncRNAs and performed a comprehensive assessment of cell-specific expression patterns for all, annotated and novel, lncRNAs described to date. Our study provides a powerful new resource for studying these elusive transcripts during stem cell commitment and neurogenesis. Overall design: mRNA profiles of Proliferating Progenitors, Differentiating Progenitors and Neurons from lateral cortex of E14.5 mouse embryos. Each cell type in three biological replicates.		GSM1598391: S166_RFPminus_1 paired-end; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			E14.5 Btg2GFP/Tubb3GFP cortices were dissociated using the papain-based neural dissociation kit (Miltenyi Biotec) after removal of meninges and ganglionic eminences. FACS was performed at 4˚C in the 4-way purity mode with a flow rate of 20 μl/min using side and forward scatter light to eliminate debris and aggregates and gating established for green (488 nm) and red (561 nm) fluorescence. About 1x106 sorted cells from >3 embryos from different litters were immediately lysed in μMACS™ mRNA Isolation Kit and lysates cleaned on LysateClear Colums (Miltenyi) resulting in ca. 1 µg of poly-A RNAs with a integrity number >9.2 Library preparation and enrichment was performed using 15 µl Sera-Mag Oligo(dT) beads (Thermo Scientific) in 50 µl 10 mM Tris-HCl. Samples were treated with 1U Turbo DNase (Ambion) and purified with Agencourt RNAclean XP beads. Eluted mRNA (18 µl) was chemically fragmented with NEBNext-Mg RNA Fragmentation Module (New England Biolabs), re-purified with RNAclean XP beads and eluted in 13,5 µl nuclease-free water. First strand cDNA synthesis was performed using 0.15 µg/µl Random Primers (New England Biolabs), 1x First Strand Synthesis Reaction Buffer (New England Biolabs), 10 U/uL Superscript II (Invitrogen) with an initial hybridization for 5 min at 65°C with mRNA and primers followed by incubation at 25°C for 10 min, 42°C for 50 min, and 70°C for 15 min. After purification with Agencourt Ampure XP-beads (Beckman Coulter), second strand synthesis was performed using the Second Strand Synthesis module (New England Biolabs) replacing the 2nd strand synthesis buffer with a NTP-free buffer and adding equimolar 2.5 mM of d-nucleotides. Incubation for 2.5 h at 16°C was followed by Ampure XP beads purification as described above. End-Repair was done with the NEBnext End Repair Module (New England Biolabs) followed by XP beads purification and A-Tailing using the NEBnext dA-Tailing Module. Adaptors were ligated  (Adaptor-Oligo 1: 5'-ACA-CTC-TTT-CCC-TAC-ACG-ACG-CTC-TTC-CGA-TCT-3', Adaptor-Oligo 2: 5'-P-GAT-CGG-AAG-AGC-ACA-CGT-CTG-AAC-TCC-AGT-CAC-3') using 1x NEBnext Quick Ligation Buffer (New England Biolabs), 0.3 uM DNA Adaptors, 1 uL Quick T4 DNA Ligase (New England Biolabs) in 50 µl. XP beads purification was followed by dUTP cleavage with 1 U USER enzyme mix (New England Biolabs) per sample and direct enrichment using the PCR Enrich Adaptor Ligated cDNA Library module (New England Biolabs) with indexed primers.	Illumina HiSeq 2000	cell type;;Proliferating Progenitors Btg2 negative|developmental stage;;Embryonic day 14.5|genotype;;Btg2GFP/Tubb3GFP|source_name;;Lateral cortex of the brain|strain;;C57BL/6	GEO Accession;;GSM1598391		GSM1598391	S166_RFPminus_1 paired-end	3722293000	18611465	2015-04-23 16:23:12	2683593036	3722293000	18611465	2	18611465	index:0,count:18611465,average:100,stdev:0|index:1,count:18611465,average:100,stdev:0	GSM1598391_r2	GEO					1.28	3.34	0.12	3153373778	3141665827	2950545224	2952728531	99.63	100.07	17682383	15865987	231.637	907.579	173	128662	82.59	88.28	19941980	14603306	19941980	14603306	85.12	85.02	19941980	15050423	19941980	14064458	360849547	11.44	0.89	0	6.12	0	0.28	0	0.05	0	0.00	0	4.65	0	17682383	0	200	0	194.82	0	1.01	0	0.45	0	1.26	0	0.00	0	116.93	0	0.32	0	166188	0	18611465	0	1139820	0	52934	0	10029	0	0	0	866119	0	5149	0	0	0	43459	0	6074202	0	218399	0	6341209	0	88.88	0	16542563	0	203884	6799936	33.351984461753	18611465.0	17682383.0	166188.0	1139820.0	52934.0	10029.0	0.0	866119.0	16542563.0	95.0	0.9	6.1	0.3	0.1	0.0	4.7	88.9	100	100	100.00	38	1861146500	24.2	25.5	25.2	25.1	0.0	34.0	17.1	bulk
465174	SRR1782645	SRP053008	SRS832980	SRX861701	SRA235889	GEO		Identification and Expression Patterns of Novel Long Non-Coding RNAs in Neural Progenitors of the Developing Mammalian Cortex	Long non-coding (lnc)RNAs play key roles in many biological processes. Elucidating the function of lncRNAs in cell type specification during organ development requires knowledge about their expression in individual progenitor types rather than in whole tissues. To achieve this during cortical development, we used a dual-reporter mouse line to isolate coexisting proliferating neural stem cells, differentiating neurogenic progenitors and newborn neurons and assessed the expression of lncRNAs by paired-end, high-throughput sequencing. We identified 379 genomic loci encoding novel lncRNAs and performed a comprehensive assessment of cell-specific expression patterns for all, annotated and novel, lncRNAs described to date. Our study provides a powerful new resource for studying these elusive transcripts during stem cell commitment and neurogenesis. Overall design: mRNA profiles of Proliferating Progenitors, Differentiating Progenitors and Neurons from lateral cortex of E14.5 mouse embryos. Each cell type in three biological replicates.		GSM1598393: S167_RFPplus_1 paired-end; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			E14.5 Btg2GFP/Tubb3GFP cortices were dissociated using the papain-based neural dissociation kit (Miltenyi Biotec) after removal of meninges and ganglionic eminences. FACS was performed at 4˚C in the 4-way purity mode with a flow rate of 20 μl/min using side and forward scatter light to eliminate debris and aggregates and gating established for green (488 nm) and red (561 nm) fluorescence. About 1x106 sorted cells from >3 embryos from different litters were immediately lysed in μMACS™ mRNA Isolation Kit and lysates cleaned on LysateClear Colums (Miltenyi) resulting in ca. 1 µg of poly-A RNAs with a integrity number >9.2 Library preparation and enrichment was performed using 15 µl Sera-Mag Oligo(dT) beads (Thermo Scientific) in 50 µl 10 mM Tris-HCl. Samples were treated with 1U Turbo DNase (Ambion) and purified with Agencourt RNAclean XP beads. Eluted mRNA (18 µl) was chemically fragmented with NEBNext-Mg RNA Fragmentation Module (New England Biolabs), re-purified with RNAclean XP beads and eluted in 13,5 µl nuclease-free water. First strand cDNA synthesis was performed using 0.15 µg/µl Random Primers (New England Biolabs), 1x First Strand Synthesis Reaction Buffer (New England Biolabs), 10 U/uL Superscript II (Invitrogen) with an initial hybridization for 5 min at 65°C with mRNA and primers followed by incubation at 25°C for 10 min, 42°C for 50 min, and 70°C for 15 min. After purification with Agencourt Ampure XP-beads (Beckman Coulter), second strand synthesis was performed using the Second Strand Synthesis module (New England Biolabs) replacing the 2nd strand synthesis buffer with a NTP-free buffer and adding equimolar 2.5 mM of d-nucleotides. Incubation for 2.5 h at 16°C was followed by Ampure XP beads purification as described above. End-Repair was done with the NEBnext End Repair Module (New England Biolabs) followed by XP beads purification and A-Tailing using the NEBnext dA-Tailing Module. Adaptors were ligated  (Adaptor-Oligo 1: 5'-ACA-CTC-TTT-CCC-TAC-ACG-ACG-CTC-TTC-CGA-TCT-3', Adaptor-Oligo 2: 5'-P-GAT-CGG-AAG-AGC-ACA-CGT-CTG-AAC-TCC-AGT-CAC-3') using 1x NEBnext Quick Ligation Buffer (New England Biolabs), 0.3 uM DNA Adaptors, 1 uL Quick T4 DNA Ligase (New England Biolabs) in 50 µl. XP beads purification was followed by dUTP cleavage with 1 U USER enzyme mix (New England Biolabs) per sample and direct enrichment using the PCR Enrich Adaptor Ligated cDNA Library module (New England Biolabs) with indexed primers.	Illumina HiSeq 2000	cell type;;Differentiating Progenitors Btg2 positive|developmental stage;;Embryonic day 14.5|genotype;;Btg2GFP/Tubb3GFP|source_name;;Lateral cortex of the brain|strain;;C57BL/6	GEO Accession;;GSM1598393		GSM1598393	S167_RFPplus_1 paired-end	4314695400	21573477	2015-04-23 16:23:12	3090308196	4314695400	21573477	2	21573477	index:0,count:21573477,average:100,stdev:0|index:1,count:21573477,average:100,stdev:0	GSM1598393_r1	GEO					1.4	3.49	0.13	3536280158	3527424321	3378970795	3385079064	99.75	100.18	20257147	18388467	218.187	832.996	164	163344	84.44	88.4	21832760	17104568	21832760	17104568	84.94	85.12	21832760	17206645	21832760	16469774	411436113	11.63	0.95	0	4.21	0	0.27	0	0.05	0	0.00	0	5.78	0	20257147	0	200	0	194.85	0	1.00	0	0.45	0	1.25	0	0.00	0	181.46	0	0.31	0	204862	0	21573477	0	908368	0	59246	0	10675	0	0	0	1246409	0	5836	0	0	0	50634	0	7137317	0	242300	0	7436087	0	89.69	0	19348779	0	212206	7146816	33.678670725616	21573477.0	20257147.0	204862.0	908368.0	59246.0	10675.0	0.0	1246409.0	19348779.0	93.9	0.9	4.2	0.3	0.0	0.0	5.8	89.7	100	100	100.00	38	2157347700	24.1	25.7	25.2	25.0	0.0	33.9	16.8	bulk
465178	SRR1782646	SRP053008	SRS832980	SRX861701	SRA235889	GEO		Identification and Expression Patterns of Novel Long Non-Coding RNAs in Neural Progenitors of the Developing Mammalian Cortex	Long non-coding (lnc)RNAs play key roles in many biological processes. Elucidating the function of lncRNAs in cell type specification during organ development requires knowledge about their expression in individual progenitor types rather than in whole tissues. To achieve this during cortical development, we used a dual-reporter mouse line to isolate coexisting proliferating neural stem cells, differentiating neurogenic progenitors and newborn neurons and assessed the expression of lncRNAs by paired-end, high-throughput sequencing. We identified 379 genomic loci encoding novel lncRNAs and performed a comprehensive assessment of cell-specific expression patterns for all, annotated and novel, lncRNAs described to date. Our study provides a powerful new resource for studying these elusive transcripts during stem cell commitment and neurogenesis. Overall design: mRNA profiles of Proliferating Progenitors, Differentiating Progenitors and Neurons from lateral cortex of E14.5 mouse embryos. Each cell type in three biological replicates.		GSM1598393: S167_RFPplus_1 paired-end; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			E14.5 Btg2GFP/Tubb3GFP cortices were dissociated using the papain-based neural dissociation kit (Miltenyi Biotec) after removal of meninges and ganglionic eminences. FACS was performed at 4˚C in the 4-way purity mode with a flow rate of 20 μl/min using side and forward scatter light to eliminate debris and aggregates and gating established for green (488 nm) and red (561 nm) fluorescence. About 1x106 sorted cells from >3 embryos from different litters were immediately lysed in μMACS™ mRNA Isolation Kit and lysates cleaned on LysateClear Colums (Miltenyi) resulting in ca. 1 µg of poly-A RNAs with a integrity number >9.2 Library preparation and enrichment was performed using 15 µl Sera-Mag Oligo(dT) beads (Thermo Scientific) in 50 µl 10 mM Tris-HCl. Samples were treated with 1U Turbo DNase (Ambion) and purified with Agencourt RNAclean XP beads. Eluted mRNA (18 µl) was chemically fragmented with NEBNext-Mg RNA Fragmentation Module (New England Biolabs), re-purified with RNAclean XP beads and eluted in 13,5 µl nuclease-free water. First strand cDNA synthesis was performed using 0.15 µg/µl Random Primers (New England Biolabs), 1x First Strand Synthesis Reaction Buffer (New England Biolabs), 10 U/uL Superscript II (Invitrogen) with an initial hybridization for 5 min at 65°C with mRNA and primers followed by incubation at 25°C for 10 min, 42°C for 50 min, and 70°C for 15 min. After purification with Agencourt Ampure XP-beads (Beckman Coulter), second strand synthesis was performed using the Second Strand Synthesis module (New England Biolabs) replacing the 2nd strand synthesis buffer with a NTP-free buffer and adding equimolar 2.5 mM of d-nucleotides. Incubation for 2.5 h at 16°C was followed by Ampure XP beads purification as described above. End-Repair was done with the NEBnext End Repair Module (New England Biolabs) followed by XP beads purification and A-Tailing using the NEBnext dA-Tailing Module. Adaptors were ligated  (Adaptor-Oligo 1: 5'-ACA-CTC-TTT-CCC-TAC-ACG-ACG-CTC-TTC-CGA-TCT-3', Adaptor-Oligo 2: 5'-P-GAT-CGG-AAG-AGC-ACA-CGT-CTG-AAC-TCC-AGT-CAC-3') using 1x NEBnext Quick Ligation Buffer (New England Biolabs), 0.3 uM DNA Adaptors, 1 uL Quick T4 DNA Ligase (New England Biolabs) in 50 µl. XP beads purification was followed by dUTP cleavage with 1 U USER enzyme mix (New England Biolabs) per sample and direct enrichment using the PCR Enrich Adaptor Ligated cDNA Library module (New England Biolabs) with indexed primers.	Illumina HiSeq 2000	cell type;;Differentiating Progenitors Btg2 positive|developmental stage;;Embryonic day 14.5|genotype;;Btg2GFP/Tubb3GFP|source_name;;Lateral cortex of the brain|strain;;C57BL/6	GEO Accession;;GSM1598393		GSM1598393	S167_RFPplus_1 paired-end	4328662600	21643313	2015-04-23 16:23:12	3111300096	4328662600	21643313	2	21643313	index:0,count:21643313,average:100,stdev:0|index:1,count:21643313,average:100,stdev:0	GSM1598393_r2	GEO					1.41	3.48	0.13	3548272325	3539382389	3390154851	3396184612	99.75	100.18	20325207	18446670	218.248	834.008	164	163978	84.45	88.42	21903004	17164639	21903004	17164639	84.97	85.15	21903004	17269946	21903004	16528723	412153620	11.62	0.94	0	4.22	0	0.27	0	0.05	0	0.00	0	5.77	0	20325207	0	200	0	194.84	0	1.00	0	0.45	0	1.25	0	0.00	0	184.63	0	0.31	0	204348	0	21643313	0	913059	0	59350	0	10907	0	0	0	1247849	0	5664	0	0	0	50673	0	7156358	0	242755	0	7455450	0	89.69	0	19412148	0	212265	7166659	33.762791793277	21643313.0	20325207.0	204348.0	913059.0	59350.0	10907.0	0.0	1247849.0	19412148.0	93.9	0.9	4.2	0.3	0.1	0.0	5.8	89.7	100	100	100.00	38	2164331300	24.1	25.7	25.2	25.0	0.0	33.8	16.6	bulk
465186	SRR1782648	SRP053008	SRS832983	SRX861703	SRA235889	GEO		Identification and Expression Patterns of Novel Long Non-Coding RNAs in Neural Progenitors of the Developing Mammalian Cortex	Long non-coding (lnc)RNAs play key roles in many biological processes. Elucidating the function of lncRNAs in cell type specification during organ development requires knowledge about their expression in individual progenitor types rather than in whole tissues. To achieve this during cortical development, we used a dual-reporter mouse line to isolate coexisting proliferating neural stem cells, differentiating neurogenic progenitors and newborn neurons and assessed the expression of lncRNAs by paired-end, high-throughput sequencing. We identified 379 genomic loci encoding novel lncRNAs and performed a comprehensive assessment of cell-specific expression patterns for all, annotated and novel, lncRNAs described to date. Our study provides a powerful new resource for studying these elusive transcripts during stem cell commitment and neurogenesis. Overall design: mRNA profiles of Proliferating Progenitors, Differentiating Progenitors and Neurons from lateral cortex of E14.5 mouse embryos. Each cell type in three biological replicates.		GSM1598395: S168_GFPplus_1 paired-end; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			E14.5 Btg2GFP/Tubb3GFP cortices were dissociated using the papain-based neural dissociation kit (Miltenyi Biotec) after removal of meninges and ganglionic eminences. FACS was performed at 4˚C in the 4-way purity mode with a flow rate of 20 μl/min using side and forward scatter light to eliminate debris and aggregates and gating established for green (488 nm) and red (561 nm) fluorescence. About 1x106 sorted cells from >3 embryos from different litters were immediately lysed in μMACS™ mRNA Isolation Kit and lysates cleaned on LysateClear Colums (Miltenyi) resulting in ca. 1 µg of poly-A RNAs with a integrity number >9.2 Library preparation and enrichment was performed using 15 µl Sera-Mag Oligo(dT) beads (Thermo Scientific) in 50 µl 10 mM Tris-HCl. Samples were treated with 1U Turbo DNase (Ambion) and purified with Agencourt RNAclean XP beads. Eluted mRNA (18 µl) was chemically fragmented with NEBNext-Mg RNA Fragmentation Module (New England Biolabs), re-purified with RNAclean XP beads and eluted in 13,5 µl nuclease-free water. First strand cDNA synthesis was performed using 0.15 µg/µl Random Primers (New England Biolabs), 1x First Strand Synthesis Reaction Buffer (New England Biolabs), 10 U/uL Superscript II (Invitrogen) with an initial hybridization for 5 min at 65°C with mRNA and primers followed by incubation at 25°C for 10 min, 42°C for 50 min, and 70°C for 15 min. After purification with Agencourt Ampure XP-beads (Beckman Coulter), second strand synthesis was performed using the Second Strand Synthesis module (New England Biolabs) replacing the 2nd strand synthesis buffer with a NTP-free buffer and adding equimolar 2.5 mM of d-nucleotides. Incubation for 2.5 h at 16°C was followed by Ampure XP beads purification as described above. End-Repair was done with the NEBnext End Repair Module (New England Biolabs) followed by XP beads purification and A-Tailing using the NEBnext dA-Tailing Module. Adaptors were ligated  (Adaptor-Oligo 1: 5'-ACA-CTC-TTT-CCC-TAC-ACG-ACG-CTC-TTC-CGA-TCT-3', Adaptor-Oligo 2: 5'-P-GAT-CGG-AAG-AGC-ACA-CGT-CTG-AAC-TCC-AGT-CAC-3') using 1x NEBnext Quick Ligation Buffer (New England Biolabs), 0.3 uM DNA Adaptors, 1 uL Quick T4 DNA Ligase (New England Biolabs) in 50 µl. XP beads purification was followed by dUTP cleavage with 1 U USER enzyme mix (New England Biolabs) per sample and direct enrichment using the PCR Enrich Adaptor Ligated cDNA Library module (New England Biolabs) with indexed primers.	Illumina HiSeq 2000	cell type;;Neurons Tubb3 positive|developmental stage;;Embryonic day 14.5|genotype;;Btg2GFP/Tubb3GFP|source_name;;Lateral cortex of the brain|strain;;C57BL/6	GEO Accession;;GSM1598395		GSM1598395	S168_GFPplus_1 paired-end	4761948400	23809742	2015-04-23 16:23:12	3397156964	4761948400	23809742	2	23809742	index:0,count:23809742,average:100,stdev:0|index:1,count:23809742,average:100,stdev:0	GSM1598395_r1	GEO					1.78	3.38	0.08	3866057435	3841189093	3703329104	3692863303	99.36	99.72	22242005	20316447	214.221	884.943	160	185798	83.68	87.39	23768464	18611153	23768464	18611153	84.2	84.3	23768464	18728462	23768464	17953647	475316784	12.29	0.80	0	3.97	0	0.17	0	0.07	0	0.00	0	6.35	0	22242005	0	200	0	195.22	0	1.00	0	0.46	0	1.24	0	0.00	0	185.13	0	0.29	0	189408	0	23809742	0	944544	0	39562	0	16070	0	0	0	1512105	0	5407	0	0	0	52412	0	7426231	0	246614	0	7730664	0	89.45	0	21297461	0	211506	7398485	34.980024207351	23809742.0	22242005.0	189408.0	944544.0	39562.0	16070.0	0.0	1512105.0	21297461.0	93.4	0.8	4.0	0.2	0.1	0.0	6.4	89.4	100	100	100.00	38	2380974200	24.0	25.6	25.3	25.1	0.0	33.9	16.8	bulk
465191	SRR1782649	SRP053008	SRS832983	SRX861703	SRA235889	GEO		Identification and Expression Patterns of Novel Long Non-Coding RNAs in Neural Progenitors of the Developing Mammalian Cortex	Long non-coding (lnc)RNAs play key roles in many biological processes. Elucidating the function of lncRNAs in cell type specification during organ development requires knowledge about their expression in individual progenitor types rather than in whole tissues. To achieve this during cortical development, we used a dual-reporter mouse line to isolate coexisting proliferating neural stem cells, differentiating neurogenic progenitors and newborn neurons and assessed the expression of lncRNAs by paired-end, high-throughput sequencing. We identified 379 genomic loci encoding novel lncRNAs and performed a comprehensive assessment of cell-specific expression patterns for all, annotated and novel, lncRNAs described to date. Our study provides a powerful new resource for studying these elusive transcripts during stem cell commitment and neurogenesis. Overall design: mRNA profiles of Proliferating Progenitors, Differentiating Progenitors and Neurons from lateral cortex of E14.5 mouse embryos. Each cell type in three biological replicates.		GSM1598395: S168_GFPplus_1 paired-end; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			E14.5 Btg2GFP/Tubb3GFP cortices were dissociated using the papain-based neural dissociation kit (Miltenyi Biotec) after removal of meninges and ganglionic eminences. FACS was performed at 4˚C in the 4-way purity mode with a flow rate of 20 μl/min using side and forward scatter light to eliminate debris and aggregates and gating established for green (488 nm) and red (561 nm) fluorescence. About 1x106 sorted cells from >3 embryos from different litters were immediately lysed in μMACS™ mRNA Isolation Kit and lysates cleaned on LysateClear Colums (Miltenyi) resulting in ca. 1 µg of poly-A RNAs with a integrity number >9.2 Library preparation and enrichment was performed using 15 µl Sera-Mag Oligo(dT) beads (Thermo Scientific) in 50 µl 10 mM Tris-HCl. Samples were treated with 1U Turbo DNase (Ambion) and purified with Agencourt RNAclean XP beads. Eluted mRNA (18 µl) was chemically fragmented with NEBNext-Mg RNA Fragmentation Module (New England Biolabs), re-purified with RNAclean XP beads and eluted in 13,5 µl nuclease-free water. First strand cDNA synthesis was performed using 0.15 µg/µl Random Primers (New England Biolabs), 1x First Strand Synthesis Reaction Buffer (New England Biolabs), 10 U/uL Superscript II (Invitrogen) with an initial hybridization for 5 min at 65°C with mRNA and primers followed by incubation at 25°C for 10 min, 42°C for 50 min, and 70°C for 15 min. After purification with Agencourt Ampure XP-beads (Beckman Coulter), second strand synthesis was performed using the Second Strand Synthesis module (New England Biolabs) replacing the 2nd strand synthesis buffer with a NTP-free buffer and adding equimolar 2.5 mM of d-nucleotides. Incubation for 2.5 h at 16°C was followed by Ampure XP beads purification as described above. End-Repair was done with the NEBnext End Repair Module (New England Biolabs) followed by XP beads purification and A-Tailing using the NEBnext dA-Tailing Module. Adaptors were ligated  (Adaptor-Oligo 1: 5'-ACA-CTC-TTT-CCC-TAC-ACG-ACG-CTC-TTC-CGA-TCT-3', Adaptor-Oligo 2: 5'-P-GAT-CGG-AAG-AGC-ACA-CGT-CTG-AAC-TCC-AGT-CAC-3') using 1x NEBnext Quick Ligation Buffer (New England Biolabs), 0.3 uM DNA Adaptors, 1 uL Quick T4 DNA Ligase (New England Biolabs) in 50 µl. XP beads purification was followed by dUTP cleavage with 1 U USER enzyme mix (New England Biolabs) per sample and direct enrichment using the PCR Enrich Adaptor Ligated cDNA Library module (New England Biolabs) with indexed primers.	Illumina HiSeq 2000	cell type;;Neurons Tubb3 positive|developmental stage;;Embryonic day 14.5|genotype;;Btg2GFP/Tubb3GFP|source_name;;Lateral cortex of the brain|strain;;C57BL/6	GEO Accession;;GSM1598395		GSM1598395	S168_GFPplus_1 paired-end	4774813200	23874066	2015-04-23 16:23:12	3418475508	4774813200	23874066	2	23874066	index:0,count:23874066,average:100,stdev:0|index:1,count:23874066,average:100,stdev:0	GSM1598395_r2	GEO					1.79	3.39	0.08	3876723706	3851568910	3713582390	3702834359	99.35	99.71	22305044	20370264	214.261	886.323	161	187388	83.67	87.38	23832798	18663364	23832798	18663364	84.21	84.3	23832798	18782817	23832798	18005571	476798561	12.30	0.79	0	3.97	0	0.17	0	0.07	0	0.00	0	6.34	0	22305044	0	200	0	195.21	0	1.00	0	0.46	0	1.24	0	0.00	0	172.93	0	0.29	0	188680	0	23874066	0	946814	0	39682	0	16002	0	0	0	1513338	0	5454	0	0	0	53252	0	7437557	0	245507	0	7741770	0	89.46	0	21358230	0	211744	7408588	34.988419978842	23874066.0	22305044.0	188680.0	946814.0	39682.0	16002.0	0.0	1513338.0	21358230.0	93.4	0.8	4.0	0.2	0.1	0.0	6.3	89.5	100	100	100.00	38	2387406600	24.0	25.6	25.3	25.1	0.0	33.8	16.6	bulk
465223	SRR1782651	SRP053008	SRS832985	SRX861705	SRA235889	GEO		Identification and Expression Patterns of Novel Long Non-Coding RNAs in Neural Progenitors of the Developing Mammalian Cortex	Long non-coding (lnc)RNAs play key roles in many biological processes. Elucidating the function of lncRNAs in cell type specification during organ development requires knowledge about their expression in individual progenitor types rather than in whole tissues. To achieve this during cortical development, we used a dual-reporter mouse line to isolate coexisting proliferating neural stem cells, differentiating neurogenic progenitors and newborn neurons and assessed the expression of lncRNAs by paired-end, high-throughput sequencing. We identified 379 genomic loci encoding novel lncRNAs and performed a comprehensive assessment of cell-specific expression patterns for all, annotated and novel, lncRNAs described to date. Our study provides a powerful new resource for studying these elusive transcripts during stem cell commitment and neurogenesis. Overall design: mRNA profiles of Proliferating Progenitors, Differentiating Progenitors and Neurons from lateral cortex of E14.5 mouse embryos. Each cell type in three biological replicates.		GSM1598397: S334_RFPminus_2 paired-end; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			E14.5 Btg2GFP/Tubb3GFP cortices were dissociated using the papain-based neural dissociation kit (Miltenyi Biotec) after removal of meninges and ganglionic eminences. FACS was performed at 4˚C in the 4-way purity mode with a flow rate of 20 μl/min using side and forward scatter light to eliminate debris and aggregates and gating established for green (488 nm) and red (561 nm) fluorescence. About 1x106 sorted cells from >3 embryos from different litters were immediately lysed in μMACS™ mRNA Isolation Kit and lysates cleaned on LysateClear Colums (Miltenyi) resulting in ca. 1 µg of poly-A RNAs with a integrity number >9.2 Library preparation and enrichment was performed using 15 µl Sera-Mag Oligo(dT) beads (Thermo Scientific) in 50 µl 10 mM Tris-HCl. Samples were treated with 1U Turbo DNase (Ambion) and purified with Agencourt RNAclean XP beads. Eluted mRNA (18 µl) was chemically fragmented with NEBNext-Mg RNA Fragmentation Module (New England Biolabs), re-purified with RNAclean XP beads and eluted in 13,5 µl nuclease-free water. First strand cDNA synthesis was performed using 0.15 µg/µl Random Primers (New England Biolabs), 1x First Strand Synthesis Reaction Buffer (New England Biolabs), 10 U/uL Superscript II (Invitrogen) with an initial hybridization for 5 min at 65°C with mRNA and primers followed by incubation at 25°C for 10 min, 42°C for 50 min, and 70°C for 15 min. After purification with Agencourt Ampure XP-beads (Beckman Coulter), second strand synthesis was performed using the Second Strand Synthesis module (New England Biolabs) replacing the 2nd strand synthesis buffer with a NTP-free buffer and adding equimolar 2.5 mM of d-nucleotides. Incubation for 2.5 h at 16°C was followed by Ampure XP beads purification as described above. End-Repair was done with the NEBnext End Repair Module (New England Biolabs) followed by XP beads purification and A-Tailing using the NEBnext dA-Tailing Module. Adaptors were ligated  (Adaptor-Oligo 1: 5'-ACA-CTC-TTT-CCC-TAC-ACG-ACG-CTC-TTC-CGA-TCT-3', Adaptor-Oligo 2: 5'-P-GAT-CGG-AAG-AGC-ACA-CGT-CTG-AAC-TCC-AGT-CAC-3') using 1x NEBnext Quick Ligation Buffer (New England Biolabs), 0.3 uM DNA Adaptors, 1 uL Quick T4 DNA Ligase (New England Biolabs) in 50 µl. XP beads purification was followed by dUTP cleavage with 1 U USER enzyme mix (New England Biolabs) per sample and direct enrichment using the PCR Enrich Adaptor Ligated cDNA Library module (New England Biolabs) with indexed primers.	Illumina HiSeq 2000	cell type;;Proliferating Progenitors Btg2 negative|developmental stage;;Embryonic day 14.5|genotype;;Btg2GFP/Tubb3GFP|source_name;;Lateral cortex of the brain|strain;;C57BL/6	GEO Accession;;GSM1598397		GSM1598397	S334_RFPminus_2 paired-end	4602887200	23014436	2015-04-23 16:23:12	3310183087	4602887200	23014436	2	23014436	index:0,count:23014436,average:100,stdev:0|index:1,count:23014436,average:100,stdev:0	GSM1598397_r1	GEO					1.38	3.33	0.1	3806596135	3791444241	3592006141	3593596128	99.6	100.04	21739760	19738413	221.450	838.837	164	169173	82.52	87.47	24085695	17940539	24085695	17940539	84.25	84.25	24085695	18316158	24085695	17278236	470267788	12.35	0.96	0	5.35	0	0.32	0	0.06	0	0.00	0	5.16	0	21739760	0	200	0	194.96	0	1.00	0	0.45	0	1.28	0	0.00	0	172.61	0	0.31	0	221601	0	23014436	0	1230356	0	73835	0	13695	0	0	0	1187146	0	6382	0	0	0	52631	0	7360548	0	254968	0	7674529	0	89.12	0	20509404	0	216706	7819186	36.082000498371	23014436.0	21739760.0	221601.0	1230356.0	73835.0	13695.0	0.0	1187146.0	20509404.0	94.5	1.0	5.3	0.3	0.1	0.0	5.2	89.1	100	100	100.00	38	2301443600	24.2	25.7	25.1	25.1	0.0	34.0	17.0	bulk
465226	SRR1782652	SRP053008	SRS832985	SRX861705	SRA235889	GEO		Identification and Expression Patterns of Novel Long Non-Coding RNAs in Neural Progenitors of the Developing Mammalian Cortex	Long non-coding (lnc)RNAs play key roles in many biological processes. Elucidating the function of lncRNAs in cell type specification during organ development requires knowledge about their expression in individual progenitor types rather than in whole tissues. To achieve this during cortical development, we used a dual-reporter mouse line to isolate coexisting proliferating neural stem cells, differentiating neurogenic progenitors and newborn neurons and assessed the expression of lncRNAs by paired-end, high-throughput sequencing. We identified 379 genomic loci encoding novel lncRNAs and performed a comprehensive assessment of cell-specific expression patterns for all, annotated and novel, lncRNAs described to date. Our study provides a powerful new resource for studying these elusive transcripts during stem cell commitment and neurogenesis. Overall design: mRNA profiles of Proliferating Progenitors, Differentiating Progenitors and Neurons from lateral cortex of E14.5 mouse embryos. Each cell type in three biological replicates.		GSM1598397: S334_RFPminus_2 paired-end; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			E14.5 Btg2GFP/Tubb3GFP cortices were dissociated using the papain-based neural dissociation kit (Miltenyi Biotec) after removal of meninges and ganglionic eminences. FACS was performed at 4˚C in the 4-way purity mode with a flow rate of 20 μl/min using side and forward scatter light to eliminate debris and aggregates and gating established for green (488 nm) and red (561 nm) fluorescence. About 1x106 sorted cells from >3 embryos from different litters were immediately lysed in μMACS™ mRNA Isolation Kit and lysates cleaned on LysateClear Colums (Miltenyi) resulting in ca. 1 µg of poly-A RNAs with a integrity number >9.2 Library preparation and enrichment was performed using 15 µl Sera-Mag Oligo(dT) beads (Thermo Scientific) in 50 µl 10 mM Tris-HCl. Samples were treated with 1U Turbo DNase (Ambion) and purified with Agencourt RNAclean XP beads. Eluted mRNA (18 µl) was chemically fragmented with NEBNext-Mg RNA Fragmentation Module (New England Biolabs), re-purified with RNAclean XP beads and eluted in 13,5 µl nuclease-free water. First strand cDNA synthesis was performed using 0.15 µg/µl Random Primers (New England Biolabs), 1x First Strand Synthesis Reaction Buffer (New England Biolabs), 10 U/uL Superscript II (Invitrogen) with an initial hybridization for 5 min at 65°C with mRNA and primers followed by incubation at 25°C for 10 min, 42°C for 50 min, and 70°C for 15 min. After purification with Agencourt Ampure XP-beads (Beckman Coulter), second strand synthesis was performed using the Second Strand Synthesis module (New England Biolabs) replacing the 2nd strand synthesis buffer with a NTP-free buffer and adding equimolar 2.5 mM of d-nucleotides. Incubation for 2.5 h at 16°C was followed by Ampure XP beads purification as described above. End-Repair was done with the NEBnext End Repair Module (New England Biolabs) followed by XP beads purification and A-Tailing using the NEBnext dA-Tailing Module. Adaptors were ligated  (Adaptor-Oligo 1: 5'-ACA-CTC-TTT-CCC-TAC-ACG-ACG-CTC-TTC-CGA-TCT-3', Adaptor-Oligo 2: 5'-P-GAT-CGG-AAG-AGC-ACA-CGT-CTG-AAC-TCC-AGT-CAC-3') using 1x NEBnext Quick Ligation Buffer (New England Biolabs), 0.3 uM DNA Adaptors, 1 uL Quick T4 DNA Ligase (New England Biolabs) in 50 µl. XP beads purification was followed by dUTP cleavage with 1 U USER enzyme mix (New England Biolabs) per sample and direct enrichment using the PCR Enrich Adaptor Ligated cDNA Library module (New England Biolabs) with indexed primers.	Illumina HiSeq 2000	cell type;;Proliferating Progenitors Btg2 negative|developmental stage;;Embryonic day 14.5|genotype;;Btg2GFP/Tubb3GFP|source_name;;Lateral cortex of the brain|strain;;C57BL/6	GEO Accession;;GSM1598397		GSM1598397	S334_RFPminus_2 paired-end	4618824000	23094120	2015-04-23 16:23:12	3333733388	4618824000	23094120	2	23094120	index:0,count:23094120,average:100,stdev:0|index:1,count:23094120,average:100,stdev:0	GSM1598397_r2	GEO					1.39	3.32	0.1	3820264712	3805275846	3605323688	3606946528	99.61	100.05	21817754	19805870	221.502	837.676	163	169774	82.54	87.48	24166558	18008271	24166558	18008271	84.26	84.25	24166558	18383485	24166558	17343245	471737742	12.35	0.96	0	5.34	0	0.32	0	0.06	0	0.00	0	5.15	0	21817754	0	200	0	194.93	0	1.00	0	0.45	0	1.28	0	0.00	0	183.94	0	0.32	0	220906	0	23094120	0	1232240	0	74205	0	13548	0	0	0	1188613	0	6546	0	0	0	53030	0	7379206	0	256354	0	7695136	0	89.14	0	20585514	0	216738	7843854	36.190488054702	23094120.0	21817754.0	220906.0	1232240.0	74205.0	13548.0	0.0	1188613.0	20585514.0	94.5	1.0	5.3	0.3	0.1	0.0	5.1	89.1	100	100	100.00	38	2309412000	24.2	25.6	25.1	25.1	0.0	33.9	16.8	bulk
465234	SRR1782654	SRP053008	SRS832987	SRX861707	SRA235889	GEO		Identification and Expression Patterns of Novel Long Non-Coding RNAs in Neural Progenitors of the Developing Mammalian Cortex	Long non-coding (lnc)RNAs play key roles in many biological processes. Elucidating the function of lncRNAs in cell type specification during organ development requires knowledge about their expression in individual progenitor types rather than in whole tissues. To achieve this during cortical development, we used a dual-reporter mouse line to isolate coexisting proliferating neural stem cells, differentiating neurogenic progenitors and newborn neurons and assessed the expression of lncRNAs by paired-end, high-throughput sequencing. We identified 379 genomic loci encoding novel lncRNAs and performed a comprehensive assessment of cell-specific expression patterns for all, annotated and novel, lncRNAs described to date. Our study provides a powerful new resource for studying these elusive transcripts during stem cell commitment and neurogenesis. Overall design: mRNA profiles of Proliferating Progenitors, Differentiating Progenitors and Neurons from lateral cortex of E14.5 mouse embryos. Each cell type in three biological replicates.		GSM1598399: S335_RFPplus_2 paired-end; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			E14.5 Btg2GFP/Tubb3GFP cortices were dissociated using the papain-based neural dissociation kit (Miltenyi Biotec) after removal of meninges and ganglionic eminences. FACS was performed at 4˚C in the 4-way purity mode with a flow rate of 20 μl/min using side and forward scatter light to eliminate debris and aggregates and gating established for green (488 nm) and red (561 nm) fluorescence. About 1x106 sorted cells from >3 embryos from different litters were immediately lysed in μMACS™ mRNA Isolation Kit and lysates cleaned on LysateClear Colums (Miltenyi) resulting in ca. 1 µg of poly-A RNAs with a integrity number >9.2 Library preparation and enrichment was performed using 15 µl Sera-Mag Oligo(dT) beads (Thermo Scientific) in 50 µl 10 mM Tris-HCl. Samples were treated with 1U Turbo DNase (Ambion) and purified with Agencourt RNAclean XP beads. Eluted mRNA (18 µl) was chemically fragmented with NEBNext-Mg RNA Fragmentation Module (New England Biolabs), re-purified with RNAclean XP beads and eluted in 13,5 µl nuclease-free water. First strand cDNA synthesis was performed using 0.15 µg/µl Random Primers (New England Biolabs), 1x First Strand Synthesis Reaction Buffer (New England Biolabs), 10 U/uL Superscript II (Invitrogen) with an initial hybridization for 5 min at 65°C with mRNA and primers followed by incubation at 25°C for 10 min, 42°C for 50 min, and 70°C for 15 min. After purification with Agencourt Ampure XP-beads (Beckman Coulter), second strand synthesis was performed using the Second Strand Synthesis module (New England Biolabs) replacing the 2nd strand synthesis buffer with a NTP-free buffer and adding equimolar 2.5 mM of d-nucleotides. Incubation for 2.5 h at 16°C was followed by Ampure XP beads purification as described above. End-Repair was done with the NEBnext End Repair Module (New England Biolabs) followed by XP beads purification and A-Tailing using the NEBnext dA-Tailing Module. Adaptors were ligated  (Adaptor-Oligo 1: 5'-ACA-CTC-TTT-CCC-TAC-ACG-ACG-CTC-TTC-CGA-TCT-3', Adaptor-Oligo 2: 5'-P-GAT-CGG-AAG-AGC-ACA-CGT-CTG-AAC-TCC-AGT-CAC-3') using 1x NEBnext Quick Ligation Buffer (New England Biolabs), 0.3 uM DNA Adaptors, 1 uL Quick T4 DNA Ligase (New England Biolabs) in 50 µl. XP beads purification was followed by dUTP cleavage with 1 U USER enzyme mix (New England Biolabs) per sample and direct enrichment using the PCR Enrich Adaptor Ligated cDNA Library module (New England Biolabs) with indexed primers.	Illumina HiSeq 2000	cell type;;Differentiating Progenitors Btg2 positive|developmental stage;;Embryonic day 14.5|genotype;;Btg2GFP/Tubb3GFP|source_name;;Lateral cortex of the brain|strain;;C57BL/6	GEO Accession;;GSM1598399		GSM1598399	S335_RFPplus_2 paired-end	5083234800	25416174	2015-04-23 16:23:12	3640824969	5083234800	25416174	2	25416174	index:0,count:25416174,average:100,stdev:0|index:1,count:25416174,average:100,stdev:0	GSM1598399_r1	GEO					1.54	3.42	0.1	4168740352	4153051337	3981123810	3982997302	99.62	100.05	24118369	22033880	214.343	800.594	157	200260	83.29	87.26	25982211	20089358	25982211	20089358	83.91	84.04	25982211	20236606	25982211	19350021	530297659	12.72	0.75	0	4.31	0	0.27	0	0.05	0	0.00	0	4.78	0	24118369	0	200	0	195.20	0	1.00	0	0.45	0	1.28	0	0.00	0	170.71	0	0.29	0	190967	0	25416174	0	1094728	0	68259	0	13407	0	0	0	1216139	0	6369	0	0	0	58241	0	8143655	0	267829	0	8476094	0	90.59	0	23023641	0	222183	8110600	36.504142981236	25416174.0	24118369.0	190967.0	1094728.0	68259.0	13407.0	0.0	1216139.0	23023641.0	94.9	0.8	4.3	0.3	0.1	0.0	4.8	90.6	100	100	100.00	38	2541617400	24.0	25.7	25.0	25.3	0.0	34.1	17.3	bulk
465238	SRR1782655	SRP053008	SRS832987	SRX861707	SRA235889	GEO		Identification and Expression Patterns of Novel Long Non-Coding RNAs in Neural Progenitors of the Developing Mammalian Cortex	Long non-coding (lnc)RNAs play key roles in many biological processes. Elucidating the function of lncRNAs in cell type specification during organ development requires knowledge about their expression in individual progenitor types rather than in whole tissues. To achieve this during cortical development, we used a dual-reporter mouse line to isolate coexisting proliferating neural stem cells, differentiating neurogenic progenitors and newborn neurons and assessed the expression of lncRNAs by paired-end, high-throughput sequencing. We identified 379 genomic loci encoding novel lncRNAs and performed a comprehensive assessment of cell-specific expression patterns for all, annotated and novel, lncRNAs described to date. Our study provides a powerful new resource for studying these elusive transcripts during stem cell commitment and neurogenesis. Overall design: mRNA profiles of Proliferating Progenitors, Differentiating Progenitors and Neurons from lateral cortex of E14.5 mouse embryos. Each cell type in three biological replicates.		GSM1598399: S335_RFPplus_2 paired-end; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			E14.5 Btg2GFP/Tubb3GFP cortices were dissociated using the papain-based neural dissociation kit (Miltenyi Biotec) after removal of meninges and ganglionic eminences. FACS was performed at 4˚C in the 4-way purity mode with a flow rate of 20 μl/min using side and forward scatter light to eliminate debris and aggregates and gating established for green (488 nm) and red (561 nm) fluorescence. About 1x106 sorted cells from >3 embryos from different litters were immediately lysed in μMACS™ mRNA Isolation Kit and lysates cleaned on LysateClear Colums (Miltenyi) resulting in ca. 1 µg of poly-A RNAs with a integrity number >9.2 Library preparation and enrichment was performed using 15 µl Sera-Mag Oligo(dT) beads (Thermo Scientific) in 50 µl 10 mM Tris-HCl. Samples were treated with 1U Turbo DNase (Ambion) and purified with Agencourt RNAclean XP beads. Eluted mRNA (18 µl) was chemically fragmented with NEBNext-Mg RNA Fragmentation Module (New England Biolabs), re-purified with RNAclean XP beads and eluted in 13,5 µl nuclease-free water. First strand cDNA synthesis was performed using 0.15 µg/µl Random Primers (New England Biolabs), 1x First Strand Synthesis Reaction Buffer (New England Biolabs), 10 U/uL Superscript II (Invitrogen) with an initial hybridization for 5 min at 65°C with mRNA and primers followed by incubation at 25°C for 10 min, 42°C for 50 min, and 70°C for 15 min. After purification with Agencourt Ampure XP-beads (Beckman Coulter), second strand synthesis was performed using the Second Strand Synthesis module (New England Biolabs) replacing the 2nd strand synthesis buffer with a NTP-free buffer and adding equimolar 2.5 mM of d-nucleotides. Incubation for 2.5 h at 16°C was followed by Ampure XP beads purification as described above. End-Repair was done with the NEBnext End Repair Module (New England Biolabs) followed by XP beads purification and A-Tailing using the NEBnext dA-Tailing Module. Adaptors were ligated  (Adaptor-Oligo 1: 5'-ACA-CTC-TTT-CCC-TAC-ACG-ACG-CTC-TTC-CGA-TCT-3', Adaptor-Oligo 2: 5'-P-GAT-CGG-AAG-AGC-ACA-CGT-CTG-AAC-TCC-AGT-CAC-3') using 1x NEBnext Quick Ligation Buffer (New England Biolabs), 0.3 uM DNA Adaptors, 1 uL Quick T4 DNA Ligase (New England Biolabs) in 50 µl. XP beads purification was followed by dUTP cleavage with 1 U USER enzyme mix (New England Biolabs) per sample and direct enrichment using the PCR Enrich Adaptor Ligated cDNA Library module (New England Biolabs) with indexed primers.	Illumina HiSeq 2000	cell type;;Differentiating Progenitors Btg2 positive|developmental stage;;Embryonic day 14.5|genotype;;Btg2GFP/Tubb3GFP|source_name;;Lateral cortex of the brain|strain;;C57BL/6	GEO Accession;;GSM1598399		GSM1598399	S335_RFPplus_2 paired-end	5095594400	25477972	2015-04-23 16:23:12	3663347248	5095594400	25477972	2	25477972	index:0,count:25477972,average:100,stdev:0|index:1,count:25477972,average:100,stdev:0	GSM1598399_r2	GEO					1.54	3.41	0.1	4179074966	4163405129	3990676920	3992687725	99.63	100.05	24180613	22084964	214.420	798.192	157	200311	83.28	87.25	26054326	20137608	26054326	20137608	83.9	84.04	26054326	20287097	26054326	19396978	532067640	12.73	0.75	0	4.32	0	0.27	0	0.05	0	0.00	0	4.77	0	24180613	0	200	0	195.18	0	1.00	0	0.45	0	1.27	0	0.00	0	197.25	0	0.30	0	190068	0	25477972	0	1099464	0	68456	0	13404	0	0	0	1215499	0	6575	0	0	0	58239	0	8161074	0	269421	0	8495309	0	90.59	0	23081149	0	222173	8130076	36.593447448610	25477972.0	24180613.0	190068.0	1099464.0	68456.0	13404.0	0.0	1215499.0	23081149.0	94.9	0.7	4.3	0.3	0.1	0.0	4.8	90.6	100	100	100.00	38	2547797200	24.0	25.7	25.0	25.3	0.0	34.0	17.1	bulk
465247	SRR1782657	SRP053008	SRS832988	SRX861709	SRA235889	GEO		Identification and Expression Patterns of Novel Long Non-Coding RNAs in Neural Progenitors of the Developing Mammalian Cortex	Long non-coding (lnc)RNAs play key roles in many biological processes. Elucidating the function of lncRNAs in cell type specification during organ development requires knowledge about their expression in individual progenitor types rather than in whole tissues. To achieve this during cortical development, we used a dual-reporter mouse line to isolate coexisting proliferating neural stem cells, differentiating neurogenic progenitors and newborn neurons and assessed the expression of lncRNAs by paired-end, high-throughput sequencing. We identified 379 genomic loci encoding novel lncRNAs and performed a comprehensive assessment of cell-specific expression patterns for all, annotated and novel, lncRNAs described to date. Our study provides a powerful new resource for studying these elusive transcripts during stem cell commitment and neurogenesis. Overall design: mRNA profiles of Proliferating Progenitors, Differentiating Progenitors and Neurons from lateral cortex of E14.5 mouse embryos. Each cell type in three biological replicates.		GSM1598401: S336_GFPplus_2 paired-end; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			E14.5 Btg2GFP/Tubb3GFP cortices were dissociated using the papain-based neural dissociation kit (Miltenyi Biotec) after removal of meninges and ganglionic eminences. FACS was performed at 4˚C in the 4-way purity mode with a flow rate of 20 μl/min using side and forward scatter light to eliminate debris and aggregates and gating established for green (488 nm) and red (561 nm) fluorescence. About 1x106 sorted cells from >3 embryos from different litters were immediately lysed in μMACS™ mRNA Isolation Kit and lysates cleaned on LysateClear Colums (Miltenyi) resulting in ca. 1 µg of poly-A RNAs with a integrity number >9.2 Library preparation and enrichment was performed using 15 µl Sera-Mag Oligo(dT) beads (Thermo Scientific) in 50 µl 10 mM Tris-HCl. Samples were treated with 1U Turbo DNase (Ambion) and purified with Agencourt RNAclean XP beads. Eluted mRNA (18 µl) was chemically fragmented with NEBNext-Mg RNA Fragmentation Module (New England Biolabs), re-purified with RNAclean XP beads and eluted in 13,5 µl nuclease-free water. First strand cDNA synthesis was performed using 0.15 µg/µl Random Primers (New England Biolabs), 1x First Strand Synthesis Reaction Buffer (New England Biolabs), 10 U/uL Superscript II (Invitrogen) with an initial hybridization for 5 min at 65°C with mRNA and primers followed by incubation at 25°C for 10 min, 42°C for 50 min, and 70°C for 15 min. After purification with Agencourt Ampure XP-beads (Beckman Coulter), second strand synthesis was performed using the Second Strand Synthesis module (New England Biolabs) replacing the 2nd strand synthesis buffer with a NTP-free buffer and adding equimolar 2.5 mM of d-nucleotides. Incubation for 2.5 h at 16°C was followed by Ampure XP beads purification as described above. End-Repair was done with the NEBnext End Repair Module (New England Biolabs) followed by XP beads purification and A-Tailing using the NEBnext dA-Tailing Module. Adaptors were ligated  (Adaptor-Oligo 1: 5'-ACA-CTC-TTT-CCC-TAC-ACG-ACG-CTC-TTC-CGA-TCT-3', Adaptor-Oligo 2: 5'-P-GAT-CGG-AAG-AGC-ACA-CGT-CTG-AAC-TCC-AGT-CAC-3') using 1x NEBnext Quick Ligation Buffer (New England Biolabs), 0.3 uM DNA Adaptors, 1 uL Quick T4 DNA Ligase (New England Biolabs) in 50 µl. XP beads purification was followed by dUTP cleavage with 1 U USER enzyme mix (New England Biolabs) per sample and direct enrichment using the PCR Enrich Adaptor Ligated cDNA Library module (New England Biolabs) with indexed primers.	Illumina HiSeq 2000	cell type;;Neurons Tubb3 positive|developmental stage;;Embryonic day 14.5|genotype;;Btg2GFP/Tubb3GFP|source_name;;Lateral cortex of the brain|strain;;C57BL/6	GEO Accession;;GSM1598401		GSM1598401	S336_GFPplus_2 paired-end	5342437200	26712186	2015-04-23 16:23:12	3818313469	5342437200	26712186	2	26712186	index:0,count:26712186,average:100,stdev:0|index:1,count:26712186,average:100,stdev:0	GSM1598401_r1	GEO					1.8	3.29	0.06	4348327805	4320190111	4166289663	4154187571	99.35	99.71	25060330	22924211	214.334	884.889	157	207818	83.03	86.68	26755662	20806528	26755662	20806528	83.51	83.57	26755662	20927674	26755662	20061157	565784100	13.01	0.73	0	3.95	0	0.16	0	0.08	0	0.00	0	5.94	0	25060330	0	200	0	195.38	0	1.00	0	0.46	0	1.26	0	0.00	0	144.61	0	0.29	0	194532	0	26712186	0	1056107	0	42178	0	21850	0	0	0	1587828	0	5890	0	0	0	57879	0	8112909	0	268049	0	8444727	0	89.86	0	24004223	0	219218	8073264	36.827559780675	26712186.0	25060330.0	194532.0	1056107.0	42178.0	21850.0	0.0	1587828.0	24004223.0	93.8	0.7	4.0	0.2	0.1	0.0	5.9	89.9	100	100	100.00	38	2671218600	24.1	25.7	25.2	25.0	0.0	33.9	16.8	bulk
465251	SRR1782658	SRP053008	SRS832988	SRX861709	SRA235889	GEO		Identification and Expression Patterns of Novel Long Non-Coding RNAs in Neural Progenitors of the Developing Mammalian Cortex	Long non-coding (lnc)RNAs play key roles in many biological processes. Elucidating the function of lncRNAs in cell type specification during organ development requires knowledge about their expression in individual progenitor types rather than in whole tissues. To achieve this during cortical development, we used a dual-reporter mouse line to isolate coexisting proliferating neural stem cells, differentiating neurogenic progenitors and newborn neurons and assessed the expression of lncRNAs by paired-end, high-throughput sequencing. We identified 379 genomic loci encoding novel lncRNAs and performed a comprehensive assessment of cell-specific expression patterns for all, annotated and novel, lncRNAs described to date. Our study provides a powerful new resource for studying these elusive transcripts during stem cell commitment and neurogenesis. Overall design: mRNA profiles of Proliferating Progenitors, Differentiating Progenitors and Neurons from lateral cortex of E14.5 mouse embryos. Each cell type in three biological replicates.		GSM1598401: S336_GFPplus_2 paired-end; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			E14.5 Btg2GFP/Tubb3GFP cortices were dissociated using the papain-based neural dissociation kit (Miltenyi Biotec) after removal of meninges and ganglionic eminences. FACS was performed at 4˚C in the 4-way purity mode with a flow rate of 20 μl/min using side and forward scatter light to eliminate debris and aggregates and gating established for green (488 nm) and red (561 nm) fluorescence. About 1x106 sorted cells from >3 embryos from different litters were immediately lysed in μMACS™ mRNA Isolation Kit and lysates cleaned on LysateClear Colums (Miltenyi) resulting in ca. 1 µg of poly-A RNAs with a integrity number >9.2 Library preparation and enrichment was performed using 15 µl Sera-Mag Oligo(dT) beads (Thermo Scientific) in 50 µl 10 mM Tris-HCl. Samples were treated with 1U Turbo DNase (Ambion) and purified with Agencourt RNAclean XP beads. Eluted mRNA (18 µl) was chemically fragmented with NEBNext-Mg RNA Fragmentation Module (New England Biolabs), re-purified with RNAclean XP beads and eluted in 13,5 µl nuclease-free water. First strand cDNA synthesis was performed using 0.15 µg/µl Random Primers (New England Biolabs), 1x First Strand Synthesis Reaction Buffer (New England Biolabs), 10 U/uL Superscript II (Invitrogen) with an initial hybridization for 5 min at 65°C with mRNA and primers followed by incubation at 25°C for 10 min, 42°C for 50 min, and 70°C for 15 min. After purification with Agencourt Ampure XP-beads (Beckman Coulter), second strand synthesis was performed using the Second Strand Synthesis module (New England Biolabs) replacing the 2nd strand synthesis buffer with a NTP-free buffer and adding equimolar 2.5 mM of d-nucleotides. Incubation for 2.5 h at 16°C was followed by Ampure XP beads purification as described above. End-Repair was done with the NEBnext End Repair Module (New England Biolabs) followed by XP beads purification and A-Tailing using the NEBnext dA-Tailing Module. Adaptors were ligated  (Adaptor-Oligo 1: 5'-ACA-CTC-TTT-CCC-TAC-ACG-ACG-CTC-TTC-CGA-TCT-3', Adaptor-Oligo 2: 5'-P-GAT-CGG-AAG-AGC-ACA-CGT-CTG-AAC-TCC-AGT-CAC-3') using 1x NEBnext Quick Ligation Buffer (New England Biolabs), 0.3 uM DNA Adaptors, 1 uL Quick T4 DNA Ligase (New England Biolabs) in 50 µl. XP beads purification was followed by dUTP cleavage with 1 U USER enzyme mix (New England Biolabs) per sample and direct enrichment using the PCR Enrich Adaptor Ligated cDNA Library module (New England Biolabs) with indexed primers.	Illumina HiSeq 2000	cell type;;Neurons Tubb3 positive|developmental stage;;Embryonic day 14.5|genotype;;Btg2GFP/Tubb3GFP|source_name;;Lateral cortex of the brain|strain;;C57BL/6	GEO Accession;;GSM1598401		GSM1598401	S336_GFPplus_2 paired-end	5356187400	26780937	2015-04-23 16:23:12	3842165904	5356187400	26780937	2	26780937	index:0,count:26780937,average:100,stdev:0|index:1,count:26780937,average:100,stdev:0	GSM1598401_r2	GEO					1.8	3.29	0.06	4359620980	4331603557	4177218154	4165307736	99.36	99.71	25127609	22980344	214.352	886.310	157	207731	83.03	86.68	26828792	20862702	26828792	20862702	83.5	83.57	26828792	20982517	26828792	20115512	567251868	13.01	0.72	0	3.95	0	0.16	0	0.08	0	0.00	0	5.93	0	25127609	0	200	0	195.36	0	1.00	0	0.46	0	1.25	0	0.00	0	151.12	0	0.30	0	194040	0	26780937	0	1058506	0	42015	0	22274	0	0	0	1589039	0	5875	0	0	0	58241	0	8130152	0	269191	0	8463459	0	89.87	0	24069103	0	219489	8092361	36.869095945583	26780937.0	25127609.0	194040.0	1058506.0	42015.0	22274.0	0.0	1589039.0	24069103.0	93.8	0.7	4.0	0.2	0.1	0.0	5.9	89.9	100	100	100.00	38	2678093700	24.0	25.7	25.2	25.0	0.0	33.8	16.6	bulk
465282	SRR1782660	SRP053008	SRS832992	SRX861711	SRA235889	GEO		Identification and Expression Patterns of Novel Long Non-Coding RNAs in Neural Progenitors of the Developing Mammalian Cortex	Long non-coding (lnc)RNAs play key roles in many biological processes. Elucidating the function of lncRNAs in cell type specification during organ development requires knowledge about their expression in individual progenitor types rather than in whole tissues. To achieve this during cortical development, we used a dual-reporter mouse line to isolate coexisting proliferating neural stem cells, differentiating neurogenic progenitors and newborn neurons and assessed the expression of lncRNAs by paired-end, high-throughput sequencing. We identified 379 genomic loci encoding novel lncRNAs and performed a comprehensive assessment of cell-specific expression patterns for all, annotated and novel, lncRNAs described to date. Our study provides a powerful new resource for studying these elusive transcripts during stem cell commitment and neurogenesis. Overall design: mRNA profiles of Proliferating Progenitors, Differentiating Progenitors and Neurons from lateral cortex of E14.5 mouse embryos. Each cell type in three biological replicates.		GSM1598403: S353_RFPminus_3 paired-end; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			E14.5 Btg2GFP/Tubb3GFP cortices were dissociated using the papain-based neural dissociation kit (Miltenyi Biotec) after removal of meninges and ganglionic eminences. FACS was performed at 4˚C in the 4-way purity mode with a flow rate of 20 μl/min using side and forward scatter light to eliminate debris and aggregates and gating established for green (488 nm) and red (561 nm) fluorescence. About 1x106 sorted cells from >3 embryos from different litters were immediately lysed in μMACS™ mRNA Isolation Kit and lysates cleaned on LysateClear Colums (Miltenyi) resulting in ca. 1 µg of poly-A RNAs with a integrity number >9.2 Library preparation and enrichment was performed using 15 µl Sera-Mag Oligo(dT) beads (Thermo Scientific) in 50 µl 10 mM Tris-HCl. Samples were treated with 1U Turbo DNase (Ambion) and purified with Agencourt RNAclean XP beads. Eluted mRNA (18 µl) was chemically fragmented with NEBNext-Mg RNA Fragmentation Module (New England Biolabs), re-purified with RNAclean XP beads and eluted in 13,5 µl nuclease-free water. First strand cDNA synthesis was performed using 0.15 µg/µl Random Primers (New England Biolabs), 1x First Strand Synthesis Reaction Buffer (New England Biolabs), 10 U/uL Superscript II (Invitrogen) with an initial hybridization for 5 min at 65°C with mRNA and primers followed by incubation at 25°C for 10 min, 42°C for 50 min, and 70°C for 15 min. After purification with Agencourt Ampure XP-beads (Beckman Coulter), second strand synthesis was performed using the Second Strand Synthesis module (New England Biolabs) replacing the 2nd strand synthesis buffer with a NTP-free buffer and adding equimolar 2.5 mM of d-nucleotides. Incubation for 2.5 h at 16°C was followed by Ampure XP beads purification as described above. End-Repair was done with the NEBnext End Repair Module (New England Biolabs) followed by XP beads purification and A-Tailing using the NEBnext dA-Tailing Module. Adaptors were ligated  (Adaptor-Oligo 1: 5'-ACA-CTC-TTT-CCC-TAC-ACG-ACG-CTC-TTC-CGA-TCT-3', Adaptor-Oligo 2: 5'-P-GAT-CGG-AAG-AGC-ACA-CGT-CTG-AAC-TCC-AGT-CAC-3') using 1x NEBnext Quick Ligation Buffer (New England Biolabs), 0.3 uM DNA Adaptors, 1 uL Quick T4 DNA Ligase (New England Biolabs) in 50 µl. XP beads purification was followed by dUTP cleavage with 1 U USER enzyme mix (New England Biolabs) per sample and direct enrichment using the PCR Enrich Adaptor Ligated cDNA Library module (New England Biolabs) with indexed primers.	Illumina HiSeq 2000	cell type;;Proliferating Progenitors Btg2 negative|developmental stage;;Embryonic day 14.5|genotype;;Btg2GFP/Tubb3GFP|source_name;;Lateral cortex of the brain|strain;;C57BL/6	GEO Accession;;GSM1598403		GSM1598403	S353_RFPminus_3 paired-end	4728663800	23643319	2015-04-23 16:23:12	3418372907	4728663800	23643319	2	23643319	index:0,count:23643319,average:100,stdev:0|index:1,count:23643319,average:100,stdev:0	GSM1598403_r1	GEO					1.35	3.34	0.13	4020874238	3999489997	3808976887	3806450727	99.47	99.93	22734844	20600886	226.931	844.902	166	167925	81.4	85.95	25050360	18505830	25050360	18505830	82.79	82.76	25050360	18821140	25050360	17819593	563155470	14.01	0.98	0	5.09	0	0.32	0	0.07	0	0.00	0	3.45	0	22734844	0	200	0	194.96	0	1.00	0	0.45	0	1.26	0	0.00	0	211.73	0	0.32	0	231256	0	23643319	0	1202801	0	76281	0	16416	0	0	0	815778	0	6238	0	0	0	51949	0	7396906	0	263580	0	7718673	0	91.07	0	21532043	0	224577	7924260	35.285269640257	23643319.0	22734844.0	231256.0	1202801.0	76281.0	16416.0	0.0	815778.0	21532043.0	96.2	1.0	5.1	0.3	0.1	0.0	3.5	91.1	100	100	100.00	38	2364331900	24.4	25.5	25.1	25.0	0.0	34.2	17.7	bulk
465286	SRR1782661	SRP053008	SRS832992	SRX861711	SRA235889	GEO		Identification and Expression Patterns of Novel Long Non-Coding RNAs in Neural Progenitors of the Developing Mammalian Cortex	Long non-coding (lnc)RNAs play key roles in many biological processes. Elucidating the function of lncRNAs in cell type specification during organ development requires knowledge about their expression in individual progenitor types rather than in whole tissues. To achieve this during cortical development, we used a dual-reporter mouse line to isolate coexisting proliferating neural stem cells, differentiating neurogenic progenitors and newborn neurons and assessed the expression of lncRNAs by paired-end, high-throughput sequencing. We identified 379 genomic loci encoding novel lncRNAs and performed a comprehensive assessment of cell-specific expression patterns for all, annotated and novel, lncRNAs described to date. Our study provides a powerful new resource for studying these elusive transcripts during stem cell commitment and neurogenesis. Overall design: mRNA profiles of Proliferating Progenitors, Differentiating Progenitors and Neurons from lateral cortex of E14.5 mouse embryos. Each cell type in three biological replicates.		GSM1598403: S353_RFPminus_3 paired-end; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			E14.5 Btg2GFP/Tubb3GFP cortices were dissociated using the papain-based neural dissociation kit (Miltenyi Biotec) after removal of meninges and ganglionic eminences. FACS was performed at 4˚C in the 4-way purity mode with a flow rate of 20 μl/min using side and forward scatter light to eliminate debris and aggregates and gating established for green (488 nm) and red (561 nm) fluorescence. About 1x106 sorted cells from >3 embryos from different litters were immediately lysed in μMACS™ mRNA Isolation Kit and lysates cleaned on LysateClear Colums (Miltenyi) resulting in ca. 1 µg of poly-A RNAs with a integrity number >9.2 Library preparation and enrichment was performed using 15 µl Sera-Mag Oligo(dT) beads (Thermo Scientific) in 50 µl 10 mM Tris-HCl. Samples were treated with 1U Turbo DNase (Ambion) and purified with Agencourt RNAclean XP beads. Eluted mRNA (18 µl) was chemically fragmented with NEBNext-Mg RNA Fragmentation Module (New England Biolabs), re-purified with RNAclean XP beads and eluted in 13,5 µl nuclease-free water. First strand cDNA synthesis was performed using 0.15 µg/µl Random Primers (New England Biolabs), 1x First Strand Synthesis Reaction Buffer (New England Biolabs), 10 U/uL Superscript II (Invitrogen) with an initial hybridization for 5 min at 65°C with mRNA and primers followed by incubation at 25°C for 10 min, 42°C for 50 min, and 70°C for 15 min. After purification with Agencourt Ampure XP-beads (Beckman Coulter), second strand synthesis was performed using the Second Strand Synthesis module (New England Biolabs) replacing the 2nd strand synthesis buffer with a NTP-free buffer and adding equimolar 2.5 mM of d-nucleotides. Incubation for 2.5 h at 16°C was followed by Ampure XP beads purification as described above. End-Repair was done with the NEBnext End Repair Module (New England Biolabs) followed by XP beads purification and A-Tailing using the NEBnext dA-Tailing Module. Adaptors were ligated  (Adaptor-Oligo 1: 5'-ACA-CTC-TTT-CCC-TAC-ACG-ACG-CTC-TTC-CGA-TCT-3', Adaptor-Oligo 2: 5'-P-GAT-CGG-AAG-AGC-ACA-CGT-CTG-AAC-TCC-AGT-CAC-3') using 1x NEBnext Quick Ligation Buffer (New England Biolabs), 0.3 uM DNA Adaptors, 1 uL Quick T4 DNA Ligase (New England Biolabs) in 50 µl. XP beads purification was followed by dUTP cleavage with 1 U USER enzyme mix (New England Biolabs) per sample and direct enrichment using the PCR Enrich Adaptor Ligated cDNA Library module (New England Biolabs) with indexed primers.	Illumina HiSeq 2000	cell type;;Proliferating Progenitors Btg2 negative|developmental stage;;Embryonic day 14.5|genotype;;Btg2GFP/Tubb3GFP|source_name;;Lateral cortex of the brain|strain;;C57BL/6	GEO Accession;;GSM1598403		GSM1598403	S353_RFPminus_3 paired-end	4738956600	23694783	2015-04-23 16:23:12	3439092101	4738956600	23694783	2	23694783	index:0,count:23694783,average:100,stdev:0|index:1,count:23694783,average:100,stdev:0	GSM1598403_r2	GEO					1.35	3.34	0.13	4029833458	4008604998	3817244988	3814953075	99.47	99.94	22786012	20642095	226.957	846.152	166	169002	81.41	85.96	25109346	18550394	25109346	18550394	82.79	82.77	25109346	18864515	25109346	17860622	563453031	13.98	0.97	0	5.09	0	0.32	0	0.07	0	0.00	0	3.44	0	22786012	0	200	0	194.93	0	1.00	0	0.45	0	1.26	0	0.00	0	159.44	0	0.32	0	230584	0	23694783	0	1206250	0	76081	0	16411	0	0	0	816279	0	6121	0	0	0	52482	0	7413475	0	262967	0	7735045	0	91.07	0	21579762	0	224641	7940451	35.347291901300	23694783.0	22786012.0	230584.0	1206250.0	76081.0	16411.0	0.0	816279.0	21579762.0	96.2	1.0	5.1	0.3	0.1	0.0	3.4	91.1	100	100	100.00	38	2369478300	24.4	25.4	25.1	25.0	0.0	34.1	17.5	bulk
465307	SRR1782666	SRP053008	SRS832996	SRX861715	SRA235889	GEO		Identification and Expression Patterns of Novel Long Non-Coding RNAs in Neural Progenitors of the Developing Mammalian Cortex	Long non-coding (lnc)RNAs play key roles in many biological processes. Elucidating the function of lncRNAs in cell type specification during organ development requires knowledge about their expression in individual progenitor types rather than in whole tissues. To achieve this during cortical development, we used a dual-reporter mouse line to isolate coexisting proliferating neural stem cells, differentiating neurogenic progenitors and newborn neurons and assessed the expression of lncRNAs by paired-end, high-throughput sequencing. We identified 379 genomic loci encoding novel lncRNAs and performed a comprehensive assessment of cell-specific expression patterns for all, annotated and novel, lncRNAs described to date. Our study provides a powerful new resource for studying these elusive transcripts during stem cell commitment and neurogenesis. Overall design: mRNA profiles of Proliferating Progenitors, Differentiating Progenitors and Neurons from lateral cortex of E14.5 mouse embryos. Each cell type in three biological replicates.		GSM1598407: S355_GFPplus_3 paired-end; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			E14.5 Btg2GFP/Tubb3GFP cortices were dissociated using the papain-based neural dissociation kit (Miltenyi Biotec) after removal of meninges and ganglionic eminences. FACS was performed at 4˚C in the 4-way purity mode with a flow rate of 20 μl/min using side and forward scatter light to eliminate debris and aggregates and gating established for green (488 nm) and red (561 nm) fluorescence. About 1x106 sorted cells from >3 embryos from different litters were immediately lysed in μMACS™ mRNA Isolation Kit and lysates cleaned on LysateClear Colums (Miltenyi) resulting in ca. 1 µg of poly-A RNAs with a integrity number >9.2 Library preparation and enrichment was performed using 15 µl Sera-Mag Oligo(dT) beads (Thermo Scientific) in 50 µl 10 mM Tris-HCl. Samples were treated with 1U Turbo DNase (Ambion) and purified with Agencourt RNAclean XP beads. Eluted mRNA (18 µl) was chemically fragmented with NEBNext-Mg RNA Fragmentation Module (New England Biolabs), re-purified with RNAclean XP beads and eluted in 13,5 µl nuclease-free water. First strand cDNA synthesis was performed using 0.15 µg/µl Random Primers (New England Biolabs), 1x First Strand Synthesis Reaction Buffer (New England Biolabs), 10 U/uL Superscript II (Invitrogen) with an initial hybridization for 5 min at 65°C with mRNA and primers followed by incubation at 25°C for 10 min, 42°C for 50 min, and 70°C for 15 min. After purification with Agencourt Ampure XP-beads (Beckman Coulter), second strand synthesis was performed using the Second Strand Synthesis module (New England Biolabs) replacing the 2nd strand synthesis buffer with a NTP-free buffer and adding equimolar 2.5 mM of d-nucleotides. Incubation for 2.5 h at 16°C was followed by Ampure XP beads purification as described above. End-Repair was done with the NEBnext End Repair Module (New England Biolabs) followed by XP beads purification and A-Tailing using the NEBnext dA-Tailing Module. Adaptors were ligated  (Adaptor-Oligo 1: 5'-ACA-CTC-TTT-CCC-TAC-ACG-ACG-CTC-TTC-CGA-TCT-3', Adaptor-Oligo 2: 5'-P-GAT-CGG-AAG-AGC-ACA-CGT-CTG-AAC-TCC-AGT-CAC-3') using 1x NEBnext Quick Ligation Buffer (New England Biolabs), 0.3 uM DNA Adaptors, 1 uL Quick T4 DNA Ligase (New England Biolabs) in 50 µl. XP beads purification was followed by dUTP cleavage with 1 U USER enzyme mix (New England Biolabs) per sample and direct enrichment using the PCR Enrich Adaptor Ligated cDNA Library module (New England Biolabs) with indexed primers.	Illumina HiSeq 2000	cell type;;Neurons Tubb3 positive|developmental stage;;Embryonic day 14.5|genotype;;Btg2GFP/Tubb3GFP|source_name;;Lateral cortex of the brain|strain;;C57BL/6	GEO Accession;;GSM1598407		GSM1598407	S355_GFPplus_3 paired-end	3970763800	19853819	2015-04-23 16:23:12	2858546902	3970763800	19853819	2	19853819	index:0,count:19853819,average:100,stdev:0|index:1,count:19853819,average:100,stdev:0	GSM1598407_r1	GEO					1.94	3.37	0.07	3366866181	3338092436	3227820482	3212841285	99.15	99.54	19049852	17308423	222.684	926.914	166	145832	82.58	86.16	20312639	15731229	20312639	15731229	83.06	83.16	20312639	15823702	20312639	15182320	452762984	13.45	0.64	0	3.99	0	0.16	0	0.08	0	0.00	0	3.80	0	19049852	0	200	0	195.44	0	1.00	0	0.46	0	1.24	0	0.00	0	199.65	0	0.29	0	126809	0	19853819	0	792158	0	32432	0	16410	0	0	0	755125	0	4350	0	0	0	42265	0	5995610	0	205908	0	6248133	0	91.96	0	18257694	0	204911	6001770	29.289642820542	19853819.0	19049852.0	126809.0	792158.0	32432.0	16410.0	0.0	755125.0	18257694.0	96.0	0.6	4.0	0.2	0.1	0.0	3.8	92.0	100	100	100.00	38	1985381900	24.2	25.4	25.1	25.3	0.0	34.2	17.6	bulk
465310	SRR1782667	SRP053008	SRS832996	SRX861715	SRA235889	GEO		Identification and Expression Patterns of Novel Long Non-Coding RNAs in Neural Progenitors of the Developing Mammalian Cortex	Long non-coding (lnc)RNAs play key roles in many biological processes. Elucidating the function of lncRNAs in cell type specification during organ development requires knowledge about their expression in individual progenitor types rather than in whole tissues. To achieve this during cortical development, we used a dual-reporter mouse line to isolate coexisting proliferating neural stem cells, differentiating neurogenic progenitors and newborn neurons and assessed the expression of lncRNAs by paired-end, high-throughput sequencing. We identified 379 genomic loci encoding novel lncRNAs and performed a comprehensive assessment of cell-specific expression patterns for all, annotated and novel, lncRNAs described to date. Our study provides a powerful new resource for studying these elusive transcripts during stem cell commitment and neurogenesis. Overall design: mRNA profiles of Proliferating Progenitors, Differentiating Progenitors and Neurons from lateral cortex of E14.5 mouse embryos. Each cell type in three biological replicates.		GSM1598407: S355_GFPplus_3 paired-end; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			E14.5 Btg2GFP/Tubb3GFP cortices were dissociated using the papain-based neural dissociation kit (Miltenyi Biotec) after removal of meninges and ganglionic eminences. FACS was performed at 4˚C in the 4-way purity mode with a flow rate of 20 μl/min using side and forward scatter light to eliminate debris and aggregates and gating established for green (488 nm) and red (561 nm) fluorescence. About 1x106 sorted cells from >3 embryos from different litters were immediately lysed in μMACS™ mRNA Isolation Kit and lysates cleaned on LysateClear Colums (Miltenyi) resulting in ca. 1 µg of poly-A RNAs with a integrity number >9.2 Library preparation and enrichment was performed using 15 µl Sera-Mag Oligo(dT) beads (Thermo Scientific) in 50 µl 10 mM Tris-HCl. Samples were treated with 1U Turbo DNase (Ambion) and purified with Agencourt RNAclean XP beads. Eluted mRNA (18 µl) was chemically fragmented with NEBNext-Mg RNA Fragmentation Module (New England Biolabs), re-purified with RNAclean XP beads and eluted in 13,5 µl nuclease-free water. First strand cDNA synthesis was performed using 0.15 µg/µl Random Primers (New England Biolabs), 1x First Strand Synthesis Reaction Buffer (New England Biolabs), 10 U/uL Superscript II (Invitrogen) with an initial hybridization for 5 min at 65°C with mRNA and primers followed by incubation at 25°C for 10 min, 42°C for 50 min, and 70°C for 15 min. After purification with Agencourt Ampure XP-beads (Beckman Coulter), second strand synthesis was performed using the Second Strand Synthesis module (New England Biolabs) replacing the 2nd strand synthesis buffer with a NTP-free buffer and adding equimolar 2.5 mM of d-nucleotides. Incubation for 2.5 h at 16°C was followed by Ampure XP beads purification as described above. End-Repair was done with the NEBnext End Repair Module (New England Biolabs) followed by XP beads purification and A-Tailing using the NEBnext dA-Tailing Module. Adaptors were ligated  (Adaptor-Oligo 1: 5'-ACA-CTC-TTT-CCC-TAC-ACG-ACG-CTC-TTC-CGA-TCT-3', Adaptor-Oligo 2: 5'-P-GAT-CGG-AAG-AGC-ACA-CGT-CTG-AAC-TCC-AGT-CAC-3') using 1x NEBnext Quick Ligation Buffer (New England Biolabs), 0.3 uM DNA Adaptors, 1 uL Quick T4 DNA Ligase (New England Biolabs) in 50 µl. XP beads purification was followed by dUTP cleavage with 1 U USER enzyme mix (New England Biolabs) per sample and direct enrichment using the PCR Enrich Adaptor Ligated cDNA Library module (New England Biolabs) with indexed primers.	Illumina HiSeq 2000	cell type;;Neurons Tubb3 positive|developmental stage;;Embryonic day 14.5|genotype;;Btg2GFP/Tubb3GFP|source_name;;Lateral cortex of the brain|strain;;C57BL/6	GEO Accession;;GSM1598407		GSM1598407	S355_GFPplus_3 paired-end	3981876200	19909381	2015-04-23 16:23:12	2876837898	3981876200	19909381	2	19909381	index:0,count:19909381,average:100,stdev:0|index:1,count:19909381,average:100,stdev:0	GSM1598407_r2	GEO					1.94	3.37	0.07	3376636511	3347708069	3237064549	3221894823	99.14	99.53	19106682	17357807	222.675	929.260	164	146311	82.59	86.17	20373972	15779264	20373972	15779264	83.08	83.17	20373972	15872931	20373972	15228979	453728795	13.44	0.64	0	3.99	0	0.16	0	0.08	0	0.00	0	3.79	0	19106682	0	200	0	195.42	0	1.00	0	0.46	0	1.25	0	0.00	0	252.37	0	0.30	0	126476	0	19909381	0	795182	0	32732	0	16130	0	0	0	753837	0	4367	0	0	0	42476	0	6011967	0	206174	0	6264984	0	91.97	0	18311500	0	205241	6023602	29.348921511784	19909381.0	19106682.0	126476.0	795182.0	32732.0	16130.0	0.0	753837.0	18311500.0	96.0	0.6	4.0	0.2	0.1	0.0	3.8	92.0	100	100	100.00	38	1990938100	24.2	25.4	25.1	25.3	0.0	34.1	17.4	bulk
930588	SRR1782663	SRP053008	SRS832993	SRX861713	SRA235889	GEO		Identification and Expression Patterns of Novel Long Non-Coding RNAs in Neural Progenitors of the Developing Mammalian Cortex	Long non-coding (lnc)RNAs play key roles in many biological processes. Elucidating the function of lncRNAs in cell type specification during organ development requires knowledge about their expression in individual progenitor types rather than in whole tissues. To achieve this during cortical development, we used a dual-reporter mouse line to isolate coexisting proliferating neural stem cells, differentiating neurogenic progenitors and newborn neurons and assessed the expression of lncRNAs by paired-end, high-throughput sequencing. We identified 379 genomic loci encoding novel lncRNAs and performed a comprehensive assessment of cell-specific expression patterns for all, annotated and novel, lncRNAs described to date. Our study provides a powerful new resource for studying these elusive transcripts during stem cell commitment and neurogenesis. Overall design: mRNA profiles of Proliferating Progenitors, Differentiating Progenitors and Neurons from lateral cortex of E14.5 mouse embryos. Each cell type in three biological replicates.		GSM1598405: S354_RFPplus_3 paired-end; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			E14.5 Btg2GFP/Tubb3GFP cortices were dissociated using the papain-based neural dissociation kit (Miltenyi Biotec) after removal of meninges and ganglionic eminences. FACS was performed at 4˚C in the 4-way purity mode with a flow rate of 20 μl/min using side and forward scatter light to eliminate debris and aggregates and gating established for green (488 nm) and red (561 nm) fluorescence. About 1x106 sorted cells from >3 embryos from different litters were immediately lysed in μMACS™ mRNA Isolation Kit and lysates cleaned on LysateClear Colums (Miltenyi) resulting in ca. 1 µg of poly-A RNAs with a integrity number >9.2 Library preparation and enrichment was performed using 15 µl Sera-Mag Oligo(dT) beads (Thermo Scientific) in 50 µl 10 mM Tris-HCl. Samples were treated with 1U Turbo DNase (Ambion) and purified with Agencourt RNAclean XP beads. Eluted mRNA (18 µl) was chemically fragmented with NEBNext-Mg RNA Fragmentation Module (New England Biolabs), re-purified with RNAclean XP beads and eluted in 13,5 µl nuclease-free water. First strand cDNA synthesis was performed using 0.15 µg/µl Random Primers (New England Biolabs), 1x First Strand Synthesis Reaction Buffer (New England Biolabs), 10 U/uL Superscript II (Invitrogen) with an initial hybridization for 5 min at 65°C with mRNA and primers followed by incubation at 25°C for 10 min, 42°C for 50 min, and 70°C for 15 min. After purification with Agencourt Ampure XP-beads (Beckman Coulter), second strand synthesis was performed using the Second Strand Synthesis module (New England Biolabs) replacing the 2nd strand synthesis buffer with a NTP-free buffer and adding equimolar 2.5 mM of d-nucleotides. Incubation for 2.5 h at 16°C was followed by Ampure XP beads purification as described above. End-Repair was done with the NEBnext End Repair Module (New England Biolabs) followed by XP beads purification and A-Tailing using the NEBnext dA-Tailing Module. Adaptors were ligated  (Adaptor-Oligo 1: 5'-ACA-CTC-TTT-CCC-TAC-ACG-ACG-CTC-TTC-CGA-TCT-3', Adaptor-Oligo 2: 5'-P-GAT-CGG-AAG-AGC-ACA-CGT-CTG-AAC-TCC-AGT-CAC-3') using 1x NEBnext Quick Ligation Buffer (New England Biolabs), 0.3 uM DNA Adaptors, 1 uL Quick T4 DNA Ligase (New England Biolabs) in 50 µl. XP beads purification was followed by dUTP cleavage with 1 U USER enzyme mix (New England Biolabs) per sample and direct enrichment using the PCR Enrich Adaptor Ligated cDNA Library module (New England Biolabs) with indexed primers.	Illumina HiSeq 2000	cell type;;Differentiating Progenitors Btg2 positive|developmental stage;;Embryonic day 14.5|genotype;;Btg2GFP/Tubb3GFP|source_name;;Lateral cortex of the brain|strain;;C57BL/6	GEO Accession;;GSM1598405		GSM1598405	S354_RFPplus_3 paired-end	4090281200	20451406	2015-04-23 16:23:12	2956345621	4090281200	20451406	2	20451406	index:0,count:20451406,average:100,stdev:0|index:1,count:20451406,average:100,stdev:0	GSM1598405_r1	GEO					1.66	3.46	0.12	3506226600	3484401499	3360422036	3354890776	99.38	99.84	19706122	17851383	228.004	848.066	167	143294	81.59	85.16	21112867	16078920	21112867	16078920	81.94	82.06	21112867	16146255	21112867	15493142	524284596	14.95	0.79	0	4.03	0	0.27	0	0.06	0	0.00	0	3.31	0	19706122	0	200	0	195.23	0	1.00	0	0.46	0	1.25	0	0.00	0	196.33	0	0.31	0	160616	0	20451406	0	825125	0	55207	0	12802	0	0	0	677275	0	4864	0	0	0	44589	0	6246497	0	220533	0	6516483	0	92.32	0	18880997	0	213413	6280949	29.430957814191	20451406.0	19706122.0	160616.0	825125.0	55207.0	12802.0	0.0	677275.0	18880997.0	96.4	0.8	4.0	0.3	0.1	0.0	3.3	92.3	100	100	100.00	38	2045140600	24.4	25.4	24.8	25.4	0.0	34.2	17.7	bulk
930597	SRR1782664	SRP053008	SRS832993	SRX861713	SRA235889	GEO		Identification and Expression Patterns of Novel Long Non-Coding RNAs in Neural Progenitors of the Developing Mammalian Cortex	Long non-coding (lnc)RNAs play key roles in many biological processes. Elucidating the function of lncRNAs in cell type specification during organ development requires knowledge about their expression in individual progenitor types rather than in whole tissues. To achieve this during cortical development, we used a dual-reporter mouse line to isolate coexisting proliferating neural stem cells, differentiating neurogenic progenitors and newborn neurons and assessed the expression of lncRNAs by paired-end, high-throughput sequencing. We identified 379 genomic loci encoding novel lncRNAs and performed a comprehensive assessment of cell-specific expression patterns for all, annotated and novel, lncRNAs described to date. Our study provides a powerful new resource for studying these elusive transcripts during stem cell commitment and neurogenesis. Overall design: mRNA profiles of Proliferating Progenitors, Differentiating Progenitors and Neurons from lateral cortex of E14.5 mouse embryos. Each cell type in three biological replicates.		GSM1598405: S354_RFPplus_3 paired-end; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			E14.5 Btg2GFP/Tubb3GFP cortices were dissociated using the papain-based neural dissociation kit (Miltenyi Biotec) after removal of meninges and ganglionic eminences. FACS was performed at 4˚C in the 4-way purity mode with a flow rate of 20 μl/min using side and forward scatter light to eliminate debris and aggregates and gating established for green (488 nm) and red (561 nm) fluorescence. About 1x106 sorted cells from >3 embryos from different litters were immediately lysed in μMACS™ mRNA Isolation Kit and lysates cleaned on LysateClear Colums (Miltenyi) resulting in ca. 1 µg of poly-A RNAs with a integrity number >9.2 Library preparation and enrichment was performed using 15 µl Sera-Mag Oligo(dT) beads (Thermo Scientific) in 50 µl 10 mM Tris-HCl. Samples were treated with 1U Turbo DNase (Ambion) and purified with Agencourt RNAclean XP beads. Eluted mRNA (18 µl) was chemically fragmented with NEBNext-Mg RNA Fragmentation Module (New England Biolabs), re-purified with RNAclean XP beads and eluted in 13,5 µl nuclease-free water. First strand cDNA synthesis was performed using 0.15 µg/µl Random Primers (New England Biolabs), 1x First Strand Synthesis Reaction Buffer (New England Biolabs), 10 U/uL Superscript II (Invitrogen) with an initial hybridization for 5 min at 65°C with mRNA and primers followed by incubation at 25°C for 10 min, 42°C for 50 min, and 70°C for 15 min. After purification with Agencourt Ampure XP-beads (Beckman Coulter), second strand synthesis was performed using the Second Strand Synthesis module (New England Biolabs) replacing the 2nd strand synthesis buffer with a NTP-free buffer and adding equimolar 2.5 mM of d-nucleotides. Incubation for 2.5 h at 16°C was followed by Ampure XP beads purification as described above. End-Repair was done with the NEBnext End Repair Module (New England Biolabs) followed by XP beads purification and A-Tailing using the NEBnext dA-Tailing Module. Adaptors were ligated  (Adaptor-Oligo 1: 5'-ACA-CTC-TTT-CCC-TAC-ACG-ACG-CTC-TTC-CGA-TCT-3', Adaptor-Oligo 2: 5'-P-GAT-CGG-AAG-AGC-ACA-CGT-CTG-AAC-TCC-AGT-CAC-3') using 1x NEBnext Quick Ligation Buffer (New England Biolabs), 0.3 uM DNA Adaptors, 1 uL Quick T4 DNA Ligase (New England Biolabs) in 50 µl. XP beads purification was followed by dUTP cleavage with 1 U USER enzyme mix (New England Biolabs) per sample and direct enrichment using the PCR Enrich Adaptor Ligated cDNA Library module (New England Biolabs) with indexed primers.	Illumina HiSeq 2000	cell type;;Differentiating Progenitors Btg2 positive|developmental stage;;Embryonic day 14.5|genotype;;Btg2GFP/Tubb3GFP|source_name;;Lateral cortex of the brain|strain;;C57BL/6	GEO Accession;;GSM1598405		GSM1598405	S354_RFPplus_3 paired-end	4097388200	20486941	2015-04-23 16:23:12	2972541937	4097388200	20486941	2	20486941	index:0,count:20486941,average:100,stdev:0|index:1,count:20486941,average:100,stdev:0	GSM1598405_r2	GEO					1.66	3.45	0.12	3511829205	3490000543	3365655853	3360211811	99.38	99.84	19740790	17882008	228.028	852.055	166	143830	81.59	85.16	21152313	16106640	21152313	16106640	81.93	82.06	21152313	16174544	21152313	15519575	525078159	14.95	0.78	0	4.04	0	0.27	0	0.06	0	0.00	0	3.31	0	19740790	0	200	0	195.21	0	1.00	0	0.46	0	1.25	0	0.00	0	232.66	0	0.31	0	159371	0	20486941	0	827346	0	54842	0	12721	0	0	0	678588	0	4822	0	0	0	44487	0	6250826	0	220814	0	6520949	0	92.32	0	18913444	0	213221	6286244	29.482293019918	20486941.0	19740790.0	159371.0	827346.0	54842.0	12721.0	0.0	678588.0	18913444.0	96.4	0.8	4.0	0.3	0.1	0.0	3.3	92.3	100	100	100.00	38	2048694100	24.4	25.4	24.8	25.3	0.0	34.1	17.5	bulk
466971	SRR1783806	SRP053038	SRS833778	SRX862820	SRA236037	GEO		Purification and transcriptomic analysis of mouse fetal Leydig cells reveals candidate genes for disorders of sex development	To examine the transcriptome of early testicular somatic cells during gonadogenesis at 12.5dpc RNA sequencing (RNA-Seq) was performed on murine primary testicular cell lineages isolated from the Sf1-eGFP line by FACS. The three main somatic cell lineages of the testis were isolated: the Sertoli cells which direct male development; the fetal Leydig cells (FLCs) that produce steroid hormones and virilise the XY individual and a heterogenous population of interstitial cells, some of which give rise to the adult Leydig cells (ALCs). This dataset provides a platform for exploring the biology of FLCs and understanding the role of these cells in testicular development and masculinization of the embryo, and a basis for targeted studies designed to identify causes of idiopathic XY DSD. Overall design: RNA-Seq of 3 enriched cell populations from 12.5dpc mouse gonad (Sertoli cells, Leydig cells and Interstitial cells isolated by FACS-sorting) on an Illumina HiSeq 1500, in triplicate.		GSM1598863: Sertoli repC; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted (Micro RNeasy kit without carrier RNA, Qiagen) from CD31-treated FACS-sorted cells. Each sample represented approximately 10 sorting experiments conducted on different days with 4-10 litters of Sf1-eGFP embryos in each experiment. We prepared sample A, sample B and Sample A+B (a mix of samples A and B), with 100ng of total RNA in each sample. Libraries were prepared using TruSeq Stranded Total RNA Libraries  (Illumina protocol 15031048 Rev C, Sep 2012), with multiplexing, Ribosomal depletion,with all sample run over the 4 rapid lanes	Illumina HiSeq 1500	age;;12.5 dpc|source_name;;Enriched Sertoli cells|strain;;Sf1-eGFP|tissue;;gonad	GEO Accession;;GSM1598863		GSM1598863	Sertoli repC	3118141892	15436346	2015-05-21 16:54:12	1871727505	3118141892	15436346	2	15436346	index:0,count:15436346,average:101,stdev:0|index:1,count:15436346,average:101,stdev:0	GSM1598863_r1	GEO			in_mesa	25855264	12.32	3.34	0.18	2542891185	2496949455	2392191275	2361915729	98.19	98.73	14859807	14476035	181.371	368.463	139	169290	65.32	69.46	16349484	9705880	16349484	9705880	67.02	66.97	16349484	9959338	16349484	9357870	720955597	28.35	0.17	0	5.75	0	0.21	0	0.22	0	0.00	0	3.31	0	14859807	0	202	0	200.94	0	2.12	0	0.01	0	2.00	0	0.01	0	219.65	0	0.20	0	26517	0	15436346	0	886983	0	32361	0	33701	0	0	0	510477	0	2477	0	0	0	32041	0	3673707	0	13002	0	3721227	0	90.52	0	13972824	0	173105	3531909	20.403275468646	15436346.0	14859807.0	26517.0	886983.0	32361.0	33701.0	0.0	510477.0	13972824.0	96.3	0.2	5.7	0.2	0.2	0.0	3.3	90.5	101	101	101.00	38	1559070946	25.9	23.6	22.8	27.7	0.0	37.3	29.0	bulk
466975	SRR1783807	SRP053038	SRS833778	SRX862820	SRA236037	GEO		Purification and transcriptomic analysis of mouse fetal Leydig cells reveals candidate genes for disorders of sex development	To examine the transcriptome of early testicular somatic cells during gonadogenesis at 12.5dpc RNA sequencing (RNA-Seq) was performed on murine primary testicular cell lineages isolated from the Sf1-eGFP line by FACS. The three main somatic cell lineages of the testis were isolated: the Sertoli cells which direct male development; the fetal Leydig cells (FLCs) that produce steroid hormones and virilise the XY individual and a heterogenous population of interstitial cells, some of which give rise to the adult Leydig cells (ALCs). This dataset provides a platform for exploring the biology of FLCs and understanding the role of these cells in testicular development and masculinization of the embryo, and a basis for targeted studies designed to identify causes of idiopathic XY DSD. Overall design: RNA-Seq of 3 enriched cell populations from 12.5dpc mouse gonad (Sertoli cells, Leydig cells and Interstitial cells isolated by FACS-sorting) on an Illumina HiSeq 1500, in triplicate.		GSM1598863: Sertoli repC; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted (Micro RNeasy kit without carrier RNA, Qiagen) from CD31-treated FACS-sorted cells. Each sample represented approximately 10 sorting experiments conducted on different days with 4-10 litters of Sf1-eGFP embryos in each experiment. We prepared sample A, sample B and Sample A+B (a mix of samples A and B), with 100ng of total RNA in each sample. Libraries were prepared using TruSeq Stranded Total RNA Libraries  (Illumina protocol 15031048 Rev C, Sep 2012), with multiplexing, Ribosomal depletion,with all sample run over the 4 rapid lanes	Illumina HiSeq 1500	age;;12.5 dpc|source_name;;Enriched Sertoli cells|strain;;Sf1-eGFP|tissue;;gonad	GEO Accession;;GSM1598863		GSM1598863	Sertoli repC	3117720116	15434258	2015-05-21 16:54:12	1876798734	3117720116	15434258	2	15434258	index:0,count:15434258,average:101,stdev:0|index:1,count:15434258,average:101,stdev:0	GSM1598863_r2	GEO			in_mesa	25855264	12.29	3.34	0.18	2542880209	2497024640	2392659396	2362379628	98.2	98.73	14855878	14473243	181.382	369.877	139	169216	65.34	69.47	16338214	9707003	16338214	9707003	67.05	67.0	16338214	9961060	16338214	9361280	721214873	28.36	0.17	0	5.73	0	0.21	0	0.22	0	0.00	0	3.32	0	14855878	0	202	0	200.95	0	2.12	0	0.01	0	2.00	0	0.01	0	306.98	0	0.20	0	25998	0	15434258	0	883710	0	32552	0	33346	0	0	0	512482	0	2578	0	0	0	31511	0	3668741	0	12842	0	3715672	0	90.53	0	13972168	0	172225	3530625	20.500072579475	15434258.0	14855878.0	25998.0	883710.0	32552.0	33346.0	0.0	512482.0	13972168.0	96.3	0.2	5.7	0.2	0.2	0.0	3.3	90.5	101	101	101.00	38	1558860058	25.9	23.6	22.8	27.7	0.0	37.3	29.1	bulk
466979	SRR1783808	SRP053038	SRS833778	SRX862820	SRA236037	GEO		Purification and transcriptomic analysis of mouse fetal Leydig cells reveals candidate genes for disorders of sex development	To examine the transcriptome of early testicular somatic cells during gonadogenesis at 12.5dpc RNA sequencing (RNA-Seq) was performed on murine primary testicular cell lineages isolated from the Sf1-eGFP line by FACS. The three main somatic cell lineages of the testis were isolated: the Sertoli cells which direct male development; the fetal Leydig cells (FLCs) that produce steroid hormones and virilise the XY individual and a heterogenous population of interstitial cells, some of which give rise to the adult Leydig cells (ALCs). This dataset provides a platform for exploring the biology of FLCs and understanding the role of these cells in testicular development and masculinization of the embryo, and a basis for targeted studies designed to identify causes of idiopathic XY DSD. Overall design: RNA-Seq of 3 enriched cell populations from 12.5dpc mouse gonad (Sertoli cells, Leydig cells and Interstitial cells isolated by FACS-sorting) on an Illumina HiSeq 1500, in triplicate.		GSM1598863: Sertoli repC; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted (Micro RNeasy kit without carrier RNA, Qiagen) from CD31-treated FACS-sorted cells. Each sample represented approximately 10 sorting experiments conducted on different days with 4-10 litters of Sf1-eGFP embryos in each experiment. We prepared sample A, sample B and Sample A+B (a mix of samples A and B), with 100ng of total RNA in each sample. Libraries were prepared using TruSeq Stranded Total RNA Libraries  (Illumina protocol 15031048 Rev C, Sep 2012), with multiplexing, Ribosomal depletion,with all sample run over the 4 rapid lanes	Illumina HiSeq 1500	age;;12.5 dpc|source_name;;Enriched Sertoli cells|strain;;Sf1-eGFP|tissue;;gonad	GEO Accession;;GSM1598863		GSM1598863	Sertoli repC	3076746234	15231417	2015-05-21 16:54:12	1835780129	3076746234	15231417	2	15231417	index:0,count:15231417,average:101,stdev:0|index:1,count:15231417,average:101,stdev:0	GSM1598863_r3	GEO			in_mesa	25855264	12.29	3.34	0.18	2519078791	2473260176	2370199449	2339859485	98.18	98.72	14713759	14334903	181.417	368.412	139	167396	65.3	69.43	16179985	9608201	16179985	9608201	67.01	66.95	16179985	9859345	16179985	9265000	714760056	28.37	0.17	0	5.75	0	0.21	0	0.22	0	0.00	0	2.97	0	14713759	0	202	0	201.00	0	2.11	0	0.01	0	1.99	0	0.01	0	293.23	0	0.20	0	26196	0	15231417	0	875614	0	31884	0	33413	0	0	0	452361	0	2611	0	0	0	31423	0	3635656	0	13065	0	3682755	0	90.85	0	13838145	0	172144	3490643	20.277459568733	15231417.0	14713759.0	26196.0	875614.0	31884.0	33413.0	0.0	452361.0	13838145.0	96.6	0.2	5.7	0.2	0.2	0.0	3.0	90.9	101	101	101.00	38	1538373117	25.9	23.6	22.8	27.7	0.0	37.3	29.4	bulk
466982	SRR1783809	SRP053038	SRS833778	SRX862820	SRA236037	GEO		Purification and transcriptomic analysis of mouse fetal Leydig cells reveals candidate genes for disorders of sex development	To examine the transcriptome of early testicular somatic cells during gonadogenesis at 12.5dpc RNA sequencing (RNA-Seq) was performed on murine primary testicular cell lineages isolated from the Sf1-eGFP line by FACS. The three main somatic cell lineages of the testis were isolated: the Sertoli cells which direct male development; the fetal Leydig cells (FLCs) that produce steroid hormones and virilise the XY individual and a heterogenous population of interstitial cells, some of which give rise to the adult Leydig cells (ALCs). This dataset provides a platform for exploring the biology of FLCs and understanding the role of these cells in testicular development and masculinization of the embryo, and a basis for targeted studies designed to identify causes of idiopathic XY DSD. Overall design: RNA-Seq of 3 enriched cell populations from 12.5dpc mouse gonad (Sertoli cells, Leydig cells and Interstitial cells isolated by FACS-sorting) on an Illumina HiSeq 1500, in triplicate.		GSM1598863: Sertoli repC; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted (Micro RNeasy kit without carrier RNA, Qiagen) from CD31-treated FACS-sorted cells. Each sample represented approximately 10 sorting experiments conducted on different days with 4-10 litters of Sf1-eGFP embryos in each experiment. We prepared sample A, sample B and Sample A+B (a mix of samples A and B), with 100ng of total RNA in each sample. Libraries were prepared using TruSeq Stranded Total RNA Libraries  (Illumina protocol 15031048 Rev C, Sep 2012), with multiplexing, Ribosomal depletion,with all sample run over the 4 rapid lanes	Illumina HiSeq 1500	age;;12.5 dpc|source_name;;Enriched Sertoli cells|strain;;Sf1-eGFP|tissue;;gonad	GEO Accession;;GSM1598863		GSM1598863	Sertoli repC	3057815400	15137700	2015-05-21 16:54:12	1814202601	3057815400	15137700	2	15137700	index:0,count:15137700,average:101,stdev:0|index:1,count:15137700,average:101,stdev:0	GSM1598863_r4	GEO			in_mesa	25855264	12.28	3.34	0.18	2503765589	2458491755	2355750098	2325788571	98.19	98.73	14623255	14247924	181.404	371.058	139	167167	65.32	69.45	16082398	9551487	16082398	9551487	67.02	66.98	16082398	9800689	16082398	9211266	710401961	28.37	0.17	0	5.75	0	0.21	0	0.22	0	0.00	0	2.96	0	14623255	0	202	0	201.01	0	2.10	0	0.01	0	1.98	0	0.01	0	122.19	0	0.20	0	25996	0	15137700	0	870465	0	32077	0	33542	0	0	0	448826	0	2577	0	0	0	31045	0	3612626	0	12904	0	3659152	0	90.85	0	13752790	0	171873	3468480	20.180482100155	15137700.0	14623255.0	25996.0	870465.0	32077.0	33542.0	0.0	448826.0	13752790.0	96.6	0.2	5.8	0.2	0.2	0.0	3.0	90.9	101	101	101.00	38	1528907700	25.9	23.6	22.8	27.7	0.0	37.4	29.6	bulk
467011	SRR1783810	SRP053038	SRS833777	SRX862821	SRA236037	GEO		Purification and transcriptomic analysis of mouse fetal Leydig cells reveals candidate genes for disorders of sex development	To examine the transcriptome of early testicular somatic cells during gonadogenesis at 12.5dpc RNA sequencing (RNA-Seq) was performed on murine primary testicular cell lineages isolated from the Sf1-eGFP line by FACS. The three main somatic cell lineages of the testis were isolated: the Sertoli cells which direct male development; the fetal Leydig cells (FLCs) that produce steroid hormones and virilise the XY individual and a heterogenous population of interstitial cells, some of which give rise to the adult Leydig cells (ALCs). This dataset provides a platform for exploring the biology of FLCs and understanding the role of these cells in testicular development and masculinization of the embryo, and a basis for targeted studies designed to identify causes of idiopathic XY DSD. Overall design: RNA-Seq of 3 enriched cell populations from 12.5dpc mouse gonad (Sertoli cells, Leydig cells and Interstitial cells isolated by FACS-sorting) on an Illumina HiSeq 1500, in triplicate.		GSM1598864: Leydig repA; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted (Micro RNeasy kit without carrier RNA, Qiagen) from CD31-treated FACS-sorted cells. Each sample represented approximately 10 sorting experiments conducted on different days with 4-10 litters of Sf1-eGFP embryos in each experiment. We prepared sample A, sample B and Sample A+B (a mix of samples A and B), with 100ng of total RNA in each sample. Libraries were prepared using TruSeq Stranded Total RNA Libraries  (Illumina protocol 15031048 Rev C, Sep 2012), with multiplexing, Ribosomal depletion,with all sample run over the 4 rapid lanes	Illumina HiSeq 1500	age;;12.5 dpc|source_name;;Enriched Leydig cells|strain;;Sf1-eGFP|tissue;;gonad	GEO Accession;;GSM1598864		GSM1598864	Leydig repA	2716970094	13450347	2015-05-21 16:54:12	1653758467	2716970094	13450347	2	13450347	index:0,count:13450347,average:101,stdev:0|index:1,count:13450347,average:101,stdev:0	GSM1598864_r1	GEO			in_mesa	25855264	10.76	3.26	0.13	2127188532	2085229792	1986570994	1958298684	98.03	98.58	12505341	12179679	180.360	381.045	139	146453	64.87	69.51	13908324	8111634	13908324	8111634	66.42	66.6	13908324	8306513	13908324	7772189	590552403	27.76	0.22	0	6.21	0	0.22	0	0.22	0	0.00	0	6.59	0	12505341	0	202	0	200.67	0	2.18	0	0.01	0	2.40	0	0.02	0	156.20	0	0.25	0	29423	0	13450347	0	835101	0	29188	0	29015	0	0	0	886803	0	2426	0	0	0	27132	0	3141719	0	10899	0	3182176	0	86.77	0	11670240	0	167889	3009383	17.924837243655	13450347.0	12505341.0	29423.0	835101.0	29188.0	29015.0	0.0	886803.0	11670240.0	93.0	0.2	6.2	0.2	0.2	0.0	6.6	86.8	101	101	101.00	38	1358485047	25.4	24.0	23.5	27.1	0.0	37.2	28.7	bulk
467015	SRR1783811	SRP053038	SRS833777	SRX862821	SRA236037	GEO		Purification and transcriptomic analysis of mouse fetal Leydig cells reveals candidate genes for disorders of sex development	To examine the transcriptome of early testicular somatic cells during gonadogenesis at 12.5dpc RNA sequencing (RNA-Seq) was performed on murine primary testicular cell lineages isolated from the Sf1-eGFP line by FACS. The three main somatic cell lineages of the testis were isolated: the Sertoli cells which direct male development; the fetal Leydig cells (FLCs) that produce steroid hormones and virilise the XY individual and a heterogenous population of interstitial cells, some of which give rise to the adult Leydig cells (ALCs). This dataset provides a platform for exploring the biology of FLCs and understanding the role of these cells in testicular development and masculinization of the embryo, and a basis for targeted studies designed to identify causes of idiopathic XY DSD. Overall design: RNA-Seq of 3 enriched cell populations from 12.5dpc mouse gonad (Sertoli cells, Leydig cells and Interstitial cells isolated by FACS-sorting) on an Illumina HiSeq 1500, in triplicate.		GSM1598864: Leydig repA; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted (Micro RNeasy kit without carrier RNA, Qiagen) from CD31-treated FACS-sorted cells. Each sample represented approximately 10 sorting experiments conducted on different days with 4-10 litters of Sf1-eGFP embryos in each experiment. We prepared sample A, sample B and Sample A+B (a mix of samples A and B), with 100ng of total RNA in each sample. Libraries were prepared using TruSeq Stranded Total RNA Libraries  (Illumina protocol 15031048 Rev C, Sep 2012), with multiplexing, Ribosomal depletion,with all sample run over the 4 rapid lanes	Illumina HiSeq 1500	age;;12.5 dpc|source_name;;Enriched Leydig cells|strain;;Sf1-eGFP|tissue;;gonad	GEO Accession;;GSM1598864		GSM1598864	Leydig repA	2706295606	13397503	2015-05-21 16:54:12	1651037438	2706295606	13397503	2	13397503	index:0,count:13397503,average:101,stdev:0|index:1,count:13397503,average:101,stdev:0	GSM1598864_r2	GEO			in_mesa	25855264	10.77	3.27	0.12	2119493100	2077922932	1979778792	1951758936	98.04	98.58	12456778	12130633	180.445	378.961	139	145451	64.87	69.5	13847486	8080880	13847486	8080880	66.41	66.59	13847486	8272816	13847486	7742141	588786744	27.78	0.22	0	6.19	0	0.22	0	0.22	0	0.00	0	6.59	0	12456778	0	202	0	200.68	0	2.17	0	0.01	0	2.41	0	0.02	0	241.16	0	0.25	0	29072	0	13397503	0	829400	0	29204	0	28835	0	0	0	882686	0	2269	0	0	0	27064	0	3134931	0	10627	0	3174891	0	86.79	0	11627378	0	168077	3000474	17.851782218864	13397503.0	12456778.0	29072.0	829400.0	29204.0	28835.0	0.0	882686.0	11627378.0	93.0	0.2	6.2	0.2	0.2	0.0	6.6	86.8	101	101	101.00	38	1353147803	25.4	24.0	23.5	27.1	0.0	37.2	28.8	bulk
467047	SRR1783819	SRP053038	SRS833781	SRX862823	SRA236037	GEO		Purification and transcriptomic analysis of mouse fetal Leydig cells reveals candidate genes for disorders of sex development	To examine the transcriptome of early testicular somatic cells during gonadogenesis at 12.5dpc RNA sequencing (RNA-Seq) was performed on murine primary testicular cell lineages isolated from the Sf1-eGFP line by FACS. The three main somatic cell lineages of the testis were isolated: the Sertoli cells which direct male development; the fetal Leydig cells (FLCs) that produce steroid hormones and virilise the XY individual and a heterogenous population of interstitial cells, some of which give rise to the adult Leydig cells (ALCs). This dataset provides a platform for exploring the biology of FLCs and understanding the role of these cells in testicular development and masculinization of the embryo, and a basis for targeted studies designed to identify causes of idiopathic XY DSD. Overall design: RNA-Seq of 3 enriched cell populations from 12.5dpc mouse gonad (Sertoli cells, Leydig cells and Interstitial cells isolated by FACS-sorting) on an Illumina HiSeq 1500, in triplicate.		GSM1598866: Leydig repC; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted (Micro RNeasy kit without carrier RNA, Qiagen) from CD31-treated FACS-sorted cells. Each sample represented approximately 10 sorting experiments conducted on different days with 4-10 litters of Sf1-eGFP embryos in each experiment. We prepared sample A, sample B and Sample A+B (a mix of samples A and B), with 100ng of total RNA in each sample. Libraries were prepared using TruSeq Stranded Total RNA Libraries  (Illumina protocol 15031048 Rev C, Sep 2012), with multiplexing, Ribosomal depletion,with all sample run over the 4 rapid lanes	Illumina HiSeq 1500	age;;12.5 dpc|source_name;;Enriched Leydig cells|strain;;Sf1-eGFP|tissue;;gonad	GEO Accession;;GSM1598866		GSM1598866	Leydig repC	3027388140	14987070	2015-05-21 16:54:12	1831914999	3027388140	14987070	2	14987070	index:0,count:14987070,average:101,stdev:0|index:1,count:14987070,average:101,stdev:0	GSM1598866_r2	GEO			in_mesa	25855264	10.85	3.31	0.13	2457559999	2410517643	2305833901	2274237295	98.09	98.63	14282927	13920672	182.535	375.404	151	155507	64.25	68.51	15784368	9176413	15784368	9176413	65.76	65.75	15784368	9392838	15784368	8806741	712225856	28.98	0.17	0	5.93	0	0.22	0	0.23	0	0.00	0	4.25	0	14282927	0	202	0	200.81	0	2.19	0	0.01	0	2.21	0	0.02	0	233.56	0	0.22	0	26183	0	14987070	0	889341	0	32654	0	34543	0	0	0	636946	0	2686	0	0	0	30768	0	3514063	0	12296	0	3559813	0	89.37	0	13393586	0	174215	3401271	19.523410728123	14987070.0	14282927.0	26183.0	889341.0	32654.0	34543.0	0.0	636946.0	13393586.0	95.3	0.2	5.9	0.2	0.2	0.0	4.2	89.4	101	101	101.00	38	1513694070	25.7	23.8	23.0	27.4	0.0	37.2	28.9	bulk
467075	SRR1783820	SRP053038	SRS833781	SRX862823	SRA236037	GEO		Purification and transcriptomic analysis of mouse fetal Leydig cells reveals candidate genes for disorders of sex development	To examine the transcriptome of early testicular somatic cells during gonadogenesis at 12.5dpc RNA sequencing (RNA-Seq) was performed on murine primary testicular cell lineages isolated from the Sf1-eGFP line by FACS. The three main somatic cell lineages of the testis were isolated: the Sertoli cells which direct male development; the fetal Leydig cells (FLCs) that produce steroid hormones and virilise the XY individual and a heterogenous population of interstitial cells, some of which give rise to the adult Leydig cells (ALCs). This dataset provides a platform for exploring the biology of FLCs and understanding the role of these cells in testicular development and masculinization of the embryo, and a basis for targeted studies designed to identify causes of idiopathic XY DSD. Overall design: RNA-Seq of 3 enriched cell populations from 12.5dpc mouse gonad (Sertoli cells, Leydig cells and Interstitial cells isolated by FACS-sorting) on an Illumina HiSeq 1500, in triplicate.		GSM1598866: Leydig repC; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted (Micro RNeasy kit without carrier RNA, Qiagen) from CD31-treated FACS-sorted cells. Each sample represented approximately 10 sorting experiments conducted on different days with 4-10 litters of Sf1-eGFP embryos in each experiment. We prepared sample A, sample B and Sample A+B (a mix of samples A and B), with 100ng of total RNA in each sample. Libraries were prepared using TruSeq Stranded Total RNA Libraries  (Illumina protocol 15031048 Rev C, Sep 2012), with multiplexing, Ribosomal depletion,with all sample run over the 4 rapid lanes	Illumina HiSeq 1500	age;;12.5 dpc|source_name;;Enriched Leydig cells|strain;;Sf1-eGFP|tissue;;gonad	GEO Accession;;GSM1598866		GSM1598866	Leydig repC	2952950736	14618568	2015-05-21 16:54:12	1772070402	2952950736	14618568	2	14618568	index:0,count:14618568,average:101,stdev:0|index:1,count:14618568,average:101,stdev:0	GSM1598866_r3	GEO			in_mesa	25855264	10.87	3.33	0.13	2405496738	2359482256	2257351183	2226359602	98.09	98.63	13978543	13625675	182.501	373.223	151	153004	64.22	68.47	15445273	8977199	15445273	8977199	65.73	65.72	15445273	9188343	15445273	8616524	698434601	29.03	0.18	0	5.94	0	0.22	0	0.23	0	0.00	0	3.93	0	13978543	0	202	0	200.88	0	2.20	0	0.01	0	2.19	0	0.02	0	234.94	0	0.22	0	26014	0	14618568	0	868248	0	31808	0	33797	0	0	0	574420	0	2559	0	0	0	29790	0	3430471	0	12241	0	3475061	0	89.68	0	13110295	0	173527	3318768	19.125369539034	14618568.0	13978543.0	26014.0	868248.0	31808.0	33797.0	0.0	574420.0	13110295.0	95.6	0.2	5.9	0.2	0.2	0.0	3.9	89.7	101	101	101.00	38	1476475368	25.8	23.8	23.0	27.4	0.0	37.3	29.3	bulk
467079	SRR1783821	SRP053038	SRS833781	SRX862823	SRA236037	GEO		Purification and transcriptomic analysis of mouse fetal Leydig cells reveals candidate genes for disorders of sex development	To examine the transcriptome of early testicular somatic cells during gonadogenesis at 12.5dpc RNA sequencing (RNA-Seq) was performed on murine primary testicular cell lineages isolated from the Sf1-eGFP line by FACS. The three main somatic cell lineages of the testis were isolated: the Sertoli cells which direct male development; the fetal Leydig cells (FLCs) that produce steroid hormones and virilise the XY individual and a heterogenous population of interstitial cells, some of which give rise to the adult Leydig cells (ALCs). This dataset provides a platform for exploring the biology of FLCs and understanding the role of these cells in testicular development and masculinization of the embryo, and a basis for targeted studies designed to identify causes of idiopathic XY DSD. Overall design: RNA-Seq of 3 enriched cell populations from 12.5dpc mouse gonad (Sertoli cells, Leydig cells and Interstitial cells isolated by FACS-sorting) on an Illumina HiSeq 1500, in triplicate.		GSM1598866: Leydig repC; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted (Micro RNeasy kit without carrier RNA, Qiagen) from CD31-treated FACS-sorted cells. Each sample represented approximately 10 sorting experiments conducted on different days with 4-10 litters of Sf1-eGFP embryos in each experiment. We prepared sample A, sample B and Sample A+B (a mix of samples A and B), with 100ng of total RNA in each sample. Libraries were prepared using TruSeq Stranded Total RNA Libraries  (Illumina protocol 15031048 Rev C, Sep 2012), with multiplexing, Ribosomal depletion,with all sample run over the 4 rapid lanes	Illumina HiSeq 1500	age;;12.5 dpc|source_name;;Enriched Leydig cells|strain;;Sf1-eGFP|tissue;;gonad	GEO Accession;;GSM1598866		GSM1598866	Leydig repC	2943491480	14571740	2015-05-21 16:54:12	1756445730	2943491480	14571740	2	14571740	index:0,count:14571740,average:101,stdev:0|index:1,count:14571740,average:101,stdev:0	GSM1598866_r4	GEO			in_mesa	25855264	10.87	3.32	0.13	2398496299	2352328630	2250799139	2219593924	98.08	98.61	13937140	13585150	182.494	375.155	151	152225	64.23	68.48	15399770	8951893	15399770	8951893	65.74	65.73	15399770	9162744	15399770	8591775	695804748	29.01	0.18	0	5.94	0	0.22	0	0.23	0	0.00	0	3.91	0	13937140	0	202	0	200.88	0	2.19	0	0.01	0	2.20	0	0.02	0	214.99	0	0.22	0	25949	0	14571740	0	865559	0	31606	0	33781	0	0	0	569213	0	2527	0	0	0	30098	0	3421883	0	12359	0	3466867	0	89.71	0	13071581	0	173413	3312167	19.099877171838	14571740.0	13937140.0	25949.0	865559.0	31606.0	33781.0	0.0	569213.0	13071581.0	95.6	0.2	5.9	0.2	0.2	0.0	3.9	89.7	101	101	101.00	38	1471745740	25.8	23.8	23.0	27.4	0.0	37.3	29.4	bulk
467082	SRR1783822	SRP053038	SRS833780	SRX862824	SRA236037	GEO		Purification and transcriptomic analysis of mouse fetal Leydig cells reveals candidate genes for disorders of sex development	To examine the transcriptome of early testicular somatic cells during gonadogenesis at 12.5dpc RNA sequencing (RNA-Seq) was performed on murine primary testicular cell lineages isolated from the Sf1-eGFP line by FACS. The three main somatic cell lineages of the testis were isolated: the Sertoli cells which direct male development; the fetal Leydig cells (FLCs) that produce steroid hormones and virilise the XY individual and a heterogenous population of interstitial cells, some of which give rise to the adult Leydig cells (ALCs). This dataset provides a platform for exploring the biology of FLCs and understanding the role of these cells in testicular development and masculinization of the embryo, and a basis for targeted studies designed to identify causes of idiopathic XY DSD. Overall design: RNA-Seq of 3 enriched cell populations from 12.5dpc mouse gonad (Sertoli cells, Leydig cells and Interstitial cells isolated by FACS-sorting) on an Illumina HiSeq 1500, in triplicate.		GSM1598867: Interstitial repA; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted (Micro RNeasy kit without carrier RNA, Qiagen) from CD31-treated FACS-sorted cells. Each sample represented approximately 10 sorting experiments conducted on different days with 4-10 litters of Sf1-eGFP embryos in each experiment. We prepared sample A, sample B and Sample A+B (a mix of samples A and B), with 100ng of total RNA in each sample. Libraries were prepared using TruSeq Stranded Total RNA Libraries  (Illumina protocol 15031048 Rev C, Sep 2012), with multiplexing, Ribosomal depletion,with all sample run over the 4 rapid lanes	Illumina HiSeq 1500	age;;12.5 dpc|source_name;;Enriched Interstitial cells|strain;;Sf1-eGFP|tissue;;gonad	GEO Accession;;GSM1598867		GSM1598867	Interstitial repA	3232000000	16000000	2015-05-21 16:54:12	1964246536	3232000000	16000000	2	16000000	index:0,count:16000000,average:101,stdev:0|index:1,count:16000000,average:101,stdev:0	GSM1598867_r1	GEO			in_mesa	25855264	8.81	2.99	0.14	2559437634	2498711556	2367573665	2323240666	97.63	98.13	14971828	14584825	181.697	378.970	151	170077	62.71	67.85	16937892	9389073	16937892	9389073	64.65	64.57	16937892	9679320	16937892	8934799	728538362	28.46	0.25	0	7.09	0	0.27	0	0.23	0	0.00	0	5.92	0	14971828	0	202	0	200.39	0	2.27	0	0.01	0	2.90	0	0.02	0	186.41	0	0.30	0	39779	0	16000000	0	1134516	0	43218	0	37543	0	0	0	947411	0	2784	0	0	0	35097	0	3806998	0	13027	0	3857906	0	86.48	0	13837312	0	182772	3830613	20.958423609743	16000000.0	14971828.0	39779.0	1134516.0	43218.0	37543.0	0.0	947411.0	13837312.0	93.6	0.2	7.1	0.3	0.2	0.0	5.9	86.5	101	101	101.00	38	1616000000	25.1	24.3	24.0	26.6	0.0	37.1	28.6	bulk
467087	SRR1783823	SRP053038	SRS833780	SRX862824	SRA236037	GEO		Purification and transcriptomic analysis of mouse fetal Leydig cells reveals candidate genes for disorders of sex development	To examine the transcriptome of early testicular somatic cells during gonadogenesis at 12.5dpc RNA sequencing (RNA-Seq) was performed on murine primary testicular cell lineages isolated from the Sf1-eGFP line by FACS. The three main somatic cell lineages of the testis were isolated: the Sertoli cells which direct male development; the fetal Leydig cells (FLCs) that produce steroid hormones and virilise the XY individual and a heterogenous population of interstitial cells, some of which give rise to the adult Leydig cells (ALCs). This dataset provides a platform for exploring the biology of FLCs and understanding the role of these cells in testicular development and masculinization of the embryo, and a basis for targeted studies designed to identify causes of idiopathic XY DSD. Overall design: RNA-Seq of 3 enriched cell populations from 12.5dpc mouse gonad (Sertoli cells, Leydig cells and Interstitial cells isolated by FACS-sorting) on an Illumina HiSeq 1500, in triplicate.		GSM1598867: Interstitial repA; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted (Micro RNeasy kit without carrier RNA, Qiagen) from CD31-treated FACS-sorted cells. Each sample represented approximately 10 sorting experiments conducted on different days with 4-10 litters of Sf1-eGFP embryos in each experiment. We prepared sample A, sample B and Sample A+B (a mix of samples A and B), with 100ng of total RNA in each sample. Libraries were prepared using TruSeq Stranded Total RNA Libraries  (Illumina protocol 15031048 Rev C, Sep 2012), with multiplexing, Ribosomal depletion,with all sample run over the 4 rapid lanes	Illumina HiSeq 1500	age;;12.5 dpc|source_name;;Enriched Interstitial cells|strain;;Sf1-eGFP|tissue;;gonad	GEO Accession;;GSM1598867		GSM1598867	Interstitial repA	3232000000	16000000	2015-05-21 16:54:12	1969571309	3232000000	16000000	2	16000000	index:0,count:16000000,average:101,stdev:0|index:1,count:16000000,average:101,stdev:0	GSM1598867_r2	GEO			in_mesa	25855264	8.81	2.99	0.13	2559561173	2498690845	2367781249	2323385161	97.62	98.12	14968385	14582014	181.773	374.510	151	169907	62.73	67.87	16938224	9389331	16938224	9389331	64.67	64.58	16938224	9679772	16938224	8934713	727924726	28.44	0.25	0	7.09	0	0.27	0	0.24	0	0.00	0	5.94	0	14968385	0	202	0	200.40	0	2.28	0	0.01	0	2.90	0	0.02	0	184.62	0	0.30	0	39804	0	16000000	0	1133932	0	43313	0	37700	0	0	0	950602	0	2928	0	0	0	35401	0	3805771	0	12723	0	3856823	0	86.47	0	13834453	0	182961	3824443	20.903050376856	16000000.0	14968385.0	39804.0	1133932.0	43313.0	37700.0	0.0	950602.0	13834453.0	93.6	0.2	7.1	0.3	0.2	0.0	5.9	86.5	101	101	101.00	38	1616000000	25.2	24.3	24.0	26.6	0.0	37.1	28.6	bulk
467091	SRR1783824	SRP053038	SRS833780	SRX862824	SRA236037	GEO		Purification and transcriptomic analysis of mouse fetal Leydig cells reveals candidate genes for disorders of sex development	To examine the transcriptome of early testicular somatic cells during gonadogenesis at 12.5dpc RNA sequencing (RNA-Seq) was performed on murine primary testicular cell lineages isolated from the Sf1-eGFP line by FACS. The three main somatic cell lineages of the testis were isolated: the Sertoli cells which direct male development; the fetal Leydig cells (FLCs) that produce steroid hormones and virilise the XY individual and a heterogenous population of interstitial cells, some of which give rise to the adult Leydig cells (ALCs). This dataset provides a platform for exploring the biology of FLCs and understanding the role of these cells in testicular development and masculinization of the embryo, and a basis for targeted studies designed to identify causes of idiopathic XY DSD. Overall design: RNA-Seq of 3 enriched cell populations from 12.5dpc mouse gonad (Sertoli cells, Leydig cells and Interstitial cells isolated by FACS-sorting) on an Illumina HiSeq 1500, in triplicate.		GSM1598867: Interstitial repA; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted (Micro RNeasy kit without carrier RNA, Qiagen) from CD31-treated FACS-sorted cells. Each sample represented approximately 10 sorting experiments conducted on different days with 4-10 litters of Sf1-eGFP embryos in each experiment. We prepared sample A, sample B and Sample A+B (a mix of samples A and B), with 100ng of total RNA in each sample. Libraries were prepared using TruSeq Stranded Total RNA Libraries  (Illumina protocol 15031048 Rev C, Sep 2012), with multiplexing, Ribosomal depletion,with all sample run over the 4 rapid lanes	Illumina HiSeq 1500	age;;12.5 dpc|source_name;;Enriched Interstitial cells|strain;;Sf1-eGFP|tissue;;gonad	GEO Accession;;GSM1598867		GSM1598867	Interstitial repA	3244764986	16063193	2015-05-21 16:54:12	1964009005	3244764986	16063193	2	16063193	index:0,count:16063193,average:101,stdev:0|index:1,count:16063193,average:101,stdev:0	GSM1598867_r3	GEO			in_mesa	25855264	8.81	2.99	0.13	2581664130	2520374713	2388363467	2343571657	97.63	98.12	15096550	14708100	181.701	376.787	151	171459	62.7	67.83	17080957	9465310	17080957	9465310	64.64	64.56	17080957	9758324	17080957	9007911	735328039	28.48	0.25	0	7.12	0	0.27	0	0.23	0	0.00	0	5.52	0	15096550	0	202	0	200.46	0	2.28	0	0.01	0	2.88	0	0.02	0	259.32	0	0.30	0	40162	0	16063193	0	1142976	0	42882	0	37739	0	0	0	886022	0	2988	0	0	0	35633	0	3836199	0	12976	0	3887796	0	86.87	0	13953574	0	182998	3853581	21.058049814752	16063193.0	15096550.0	40162.0	1142976.0	42882.0	37739.0	0.0	886022.0	13953574.0	94.0	0.3	7.1	0.3	0.2	0.0	5.5	86.9	101	101	101.00	38	1622382493	25.2	24.3	24.0	26.6	0.0	37.1	29.0	bulk
467095	SRR1783825	SRP053038	SRS833780	SRX862824	SRA236037	GEO		Purification and transcriptomic analysis of mouse fetal Leydig cells reveals candidate genes for disorders of sex development	To examine the transcriptome of early testicular somatic cells during gonadogenesis at 12.5dpc RNA sequencing (RNA-Seq) was performed on murine primary testicular cell lineages isolated from the Sf1-eGFP line by FACS. The three main somatic cell lineages of the testis were isolated: the Sertoli cells which direct male development; the fetal Leydig cells (FLCs) that produce steroid hormones and virilise the XY individual and a heterogenous population of interstitial cells, some of which give rise to the adult Leydig cells (ALCs). This dataset provides a platform for exploring the biology of FLCs and understanding the role of these cells in testicular development and masculinization of the embryo, and a basis for targeted studies designed to identify causes of idiopathic XY DSD. Overall design: RNA-Seq of 3 enriched cell populations from 12.5dpc mouse gonad (Sertoli cells, Leydig cells and Interstitial cells isolated by FACS-sorting) on an Illumina HiSeq 1500, in triplicate.		GSM1598867: Interstitial repA; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted (Micro RNeasy kit without carrier RNA, Qiagen) from CD31-treated FACS-sorted cells. Each sample represented approximately 10 sorting experiments conducted on different days with 4-10 litters of Sf1-eGFP embryos in each experiment. We prepared sample A, sample B and Sample A+B (a mix of samples A and B), with 100ng of total RNA in each sample. Libraries were prepared using TruSeq Stranded Total RNA Libraries  (Illumina protocol 15031048 Rev C, Sep 2012), with multiplexing, Ribosomal depletion,with all sample run over the 4 rapid lanes	Illumina HiSeq 1500	age;;12.5 dpc|source_name;;Enriched Interstitial cells|strain;;Sf1-eGFP|tissue;;gonad	GEO Accession;;GSM1598867		GSM1598867	Interstitial repA	3224476308	15962754	2015-05-21 16:54:12	1940109206	3224476308	15962754	2	15962754	index:0,count:15962754,average:101,stdev:0|index:1,count:15962754,average:101,stdev:0	GSM1598867_r4	GEO			in_mesa	25855264	8.79	2.98	0.13	2566003356	2505016886	2374244936	2329625534	97.62	98.12	15003077	14616351	181.767	377.174	151	169836	62.71	67.84	16970303	9408665	16970303	9408665	64.63	64.55	16970303	9697210	16970303	8953275	730696984	28.48	0.25	0	7.10	0	0.27	0	0.24	0	0.00	0	5.51	0	15003077	0	202	0	200.46	0	2.26	0	0.01	0	2.87	0	0.02	0	280.32	0	0.29	0	40071	0	15962754	0	1133649	0	42854	0	38035	0	0	0	878788	0	2890	0	0	0	35500	0	3814979	0	12752	0	3866121	0	86.89	0	13869428	0	183217	3839379	20.955364403958	15962754.0	15003077.0	40071.0	1133649.0	42854.0	38035.0	0.0	878788.0	13869428.0	94.0	0.3	7.1	0.3	0.2	0.0	5.5	86.9	101	101	101.00	38	1612238154	25.2	24.3	24.0	26.6	0.0	37.2	29.1	bulk
467099	SRR1783826	SRP053038	SRS833783	SRX862825	SRA236037	GEO		Purification and transcriptomic analysis of mouse fetal Leydig cells reveals candidate genes for disorders of sex development	To examine the transcriptome of early testicular somatic cells during gonadogenesis at 12.5dpc RNA sequencing (RNA-Seq) was performed on murine primary testicular cell lineages isolated from the Sf1-eGFP line by FACS. The three main somatic cell lineages of the testis were isolated: the Sertoli cells which direct male development; the fetal Leydig cells (FLCs) that produce steroid hormones and virilise the XY individual and a heterogenous population of interstitial cells, some of which give rise to the adult Leydig cells (ALCs). This dataset provides a platform for exploring the biology of FLCs and understanding the role of these cells in testicular development and masculinization of the embryo, and a basis for targeted studies designed to identify causes of idiopathic XY DSD. Overall design: RNA-Seq of 3 enriched cell populations from 12.5dpc mouse gonad (Sertoli cells, Leydig cells and Interstitial cells isolated by FACS-sorting) on an Illumina HiSeq 1500, in triplicate.		GSM1598868: Interstitial repB; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted (Micro RNeasy kit without carrier RNA, Qiagen) from CD31-treated FACS-sorted cells. Each sample represented approximately 10 sorting experiments conducted on different days with 4-10 litters of Sf1-eGFP embryos in each experiment. We prepared sample A, sample B and Sample A+B (a mix of samples A and B), with 100ng of total RNA in each sample. Libraries were prepared using TruSeq Stranded Total RNA Libraries  (Illumina protocol 15031048 Rev C, Sep 2012), with multiplexing, Ribosomal depletion,with all sample run over the 4 rapid lanes	Illumina HiSeq 1500	age;;12.5 dpc|source_name;;Enriched Interstitial cells|strain;;Sf1-eGFP|tissue;;gonad	GEO Accession;;GSM1598868		GSM1598868	Interstitial repB	2889579498	14304849	2015-05-21 16:54:12	1762485717	2889579498	14304849	2	14304849	index:0,count:14304849,average:101,stdev:0|index:1,count:14304849,average:101,stdev:0	GSM1598868_r1	GEO			in_mesa	25855264	9.99	2.94	0.14	2169801533	2113567080	2027784656	1985622375	97.41	97.92	12891718	12544134	178.673	376.070	139	156260	64.75	69.35	14437942	8346896	14437942	8346896	66.5	66.33	14437942	8573602	14437942	7982917	591499573	27.26	0.27	0	5.99	0	0.27	0	0.23	0	0.00	0	9.38	0	12891718	0	202	0	200.41	0	2.41	0	0.02	0	2.99	0	0.02	0	156.53	0	0.29	0	39112	0	14304849	0	856472	0	38694	0	32224	0	0	0	1342213	0	2561	0	0	0	29477	0	3360797	0	11851	0	3404686	0	84.13	0	12035246	0	177925	3309391	18.599921315161	14304849.0	12891718.0	39112.0	856472.0	38694.0	32224.0	0.0	1342213.0	12035246.0	90.1	0.3	6.0	0.3	0.2	0.0	9.4	84.1	101	101	101.00	38	1444789749	24.3	25.0	24.7	26.0	0.0	37.0	28.1	bulk
467151	SRR1783833	SRP053038	SRS833782	SRX862826	SRA236037	GEO		Purification and transcriptomic analysis of mouse fetal Leydig cells reveals candidate genes for disorders of sex development	To examine the transcriptome of early testicular somatic cells during gonadogenesis at 12.5dpc RNA sequencing (RNA-Seq) was performed on murine primary testicular cell lineages isolated from the Sf1-eGFP line by FACS. The three main somatic cell lineages of the testis were isolated: the Sertoli cells which direct male development; the fetal Leydig cells (FLCs) that produce steroid hormones and virilise the XY individual and a heterogenous population of interstitial cells, some of which give rise to the adult Leydig cells (ALCs). This dataset provides a platform for exploring the biology of FLCs and understanding the role of these cells in testicular development and masculinization of the embryo, and a basis for targeted studies designed to identify causes of idiopathic XY DSD. Overall design: RNA-Seq of 3 enriched cell populations from 12.5dpc mouse gonad (Sertoli cells, Leydig cells and Interstitial cells isolated by FACS-sorting) on an Illumina HiSeq 1500, in triplicate.		GSM1598869: Interstitial repC; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted (Micro RNeasy kit without carrier RNA, Qiagen) from CD31-treated FACS-sorted cells. Each sample represented approximately 10 sorting experiments conducted on different days with 4-10 litters of Sf1-eGFP embryos in each experiment. We prepared sample A, sample B and Sample A+B (a mix of samples A and B), with 100ng of total RNA in each sample. Libraries were prepared using TruSeq Stranded Total RNA Libraries  (Illumina protocol 15031048 Rev C, Sep 2012), with multiplexing, Ribosomal depletion,with all sample run over the 4 rapid lanes	Illumina HiSeq 1500	age;;12.5 dpc|source_name;;Enriched Interstitial cells|strain;;Sf1-eGFP|tissue;;gonad	GEO Accession;;GSM1598869		GSM1598869	Interstitial repC	3079999848	15247524	2015-05-21 16:54:12	1825290679	3079999848	15247524	2	15247524	index:0,count:15247524,average:101,stdev:0|index:1,count:15247524,average:101,stdev:0	GSM1598869_r4	GEO			in_mesa	25855264	10.25	3.14	0.14	2495433477	2453284090	2321267380	2294602396	98.31	98.85	14690902	14306216	180.129	376.541	139	167668	64.39	69.26	16499086	9459821	16499086	9459821	66.71	66.46	16499086	9799826	16499086	9076795	706211255	28.30	0.19	0	6.77	0	0.29	0	0.26	0	0.00	0	3.10	0	14690902	0	202	0	200.92	0	2.25	0	0.01	0	1.95	0	0.01	0	250.64	0	0.20	0	29015	0	15247524	0	1032974	0	44816	0	38962	0	0	0	472844	0	2882	0	0	0	34014	0	3744502	0	13031	0	3794429	0	89.57	0	13657928	0	181633	3719814	20.479835712673	15247524.0	14690902.0	29015.0	1032974.0	44816.0	38962.0	0.0	472844.0	13657928.0	96.3	0.2	6.8	0.3	0.3	0.0	3.1	89.6	101	101	101.00	38	1539999924	25.9	23.7	22.8	27.5	0.0	37.4	29.4	bulk
933062	SRR1783798	SRP053038	SRS833776	SRX862818	SRA236037	GEO		Purification and transcriptomic analysis of mouse fetal Leydig cells reveals candidate genes for disorders of sex development	To examine the transcriptome of early testicular somatic cells during gonadogenesis at 12.5dpc RNA sequencing (RNA-Seq) was performed on murine primary testicular cell lineages isolated from the Sf1-eGFP line by FACS. The three main somatic cell lineages of the testis were isolated: the Sertoli cells which direct male development; the fetal Leydig cells (FLCs) that produce steroid hormones and virilise the XY individual and a heterogenous population of interstitial cells, some of which give rise to the adult Leydig cells (ALCs). This dataset provides a platform for exploring the biology of FLCs and understanding the role of these cells in testicular development and masculinization of the embryo, and a basis for targeted studies designed to identify causes of idiopathic XY DSD. Overall design: RNA-Seq of 3 enriched cell populations from 12.5dpc mouse gonad (Sertoli cells, Leydig cells and Interstitial cells isolated by FACS-sorting) on an Illumina HiSeq 1500, in triplicate.		GSM1598861: Sertoli repA; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted (Micro RNeasy kit without carrier RNA, Qiagen) from CD31-treated FACS-sorted cells. Each sample represented approximately 10 sorting experiments conducted on different days with 4-10 litters of Sf1-eGFP embryos in each experiment. We prepared sample A, sample B and Sample A+B (a mix of samples A and B), with 100ng of total RNA in each sample. Libraries were prepared using TruSeq Stranded Total RNA Libraries  (Illumina protocol 15031048 Rev C, Sep 2012), with multiplexing, Ribosomal depletion,with all sample run over the 4 rapid lanes	Illumina HiSeq 1500	age;;12.5 dpc|source_name;;Enriched Sertoli cells|strain;;Sf1-eGFP|tissue;;gonad	GEO Accession;;GSM1598861		GSM1598861	Sertoli repA	3138327550	15536275	2015-05-21 16:54:12	1911675606	3138327550	15536275	2	15536275	index:0,count:15536275,average:101,stdev:0|index:1,count:15536275,average:101,stdev:0	GSM1598861_r1	GEO			in_mesa	25855264	10.84	3.11	0.15	2443146392	2378848666	2271229688	2223799126	97.37	97.91	14390059	14018360	179.984	368.300	151	167935	64.43	69.38	16093473	9270823	16093473	9270823	65.63	66.07	16093473	9444330	16093473	8829208	653437028	26.75	0.30	0	6.61	0	0.21	0	0.19	0	0.00	0	6.98	0	14390059	0	202	0	200.26	0	2.13	0	0.01	0	3.08	0	0.03	0	159.80	0	0.31	0	46290	0	15536275	0	1027376	0	32542	0	29432	0	0	0	1084242	0	2492	0	0	0	31564	0	3568946	0	12076	0	3615078	0	86.01	0	13362683	0	171204	3418015	19.964574425831	15536275.0	14390059.0	46290.0	1027376.0	32542.0	29432.0	0.0	1084242.0	13362683.0	92.6	0.3	6.6	0.2	0.2	0.0	7.0	86.0	101	101	101.00	38	1569163775	25.0	24.2	24.3	26.5	0.0	37.0	28.4	bulk
933069	SRR1783799	SRP053038	SRS833776	SRX862818	SRA236037	GEO		Purification and transcriptomic analysis of mouse fetal Leydig cells reveals candidate genes for disorders of sex development	To examine the transcriptome of early testicular somatic cells during gonadogenesis at 12.5dpc RNA sequencing (RNA-Seq) was performed on murine primary testicular cell lineages isolated from the Sf1-eGFP line by FACS. The three main somatic cell lineages of the testis were isolated: the Sertoli cells which direct male development; the fetal Leydig cells (FLCs) that produce steroid hormones and virilise the XY individual and a heterogenous population of interstitial cells, some of which give rise to the adult Leydig cells (ALCs). This dataset provides a platform for exploring the biology of FLCs and understanding the role of these cells in testicular development and masculinization of the embryo, and a basis for targeted studies designed to identify causes of idiopathic XY DSD. Overall design: RNA-Seq of 3 enriched cell populations from 12.5dpc mouse gonad (Sertoli cells, Leydig cells and Interstitial cells isolated by FACS-sorting) on an Illumina HiSeq 1500, in triplicate.		GSM1598861: Sertoli repA; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted (Micro RNeasy kit without carrier RNA, Qiagen) from CD31-treated FACS-sorted cells. Each sample represented approximately 10 sorting experiments conducted on different days with 4-10 litters of Sf1-eGFP embryos in each experiment. We prepared sample A, sample B and Sample A+B (a mix of samples A and B), with 100ng of total RNA in each sample. Libraries were prepared using TruSeq Stranded Total RNA Libraries  (Illumina protocol 15031048 Rev C, Sep 2012), with multiplexing, Ribosomal depletion,with all sample run over the 4 rapid lanes	Illumina HiSeq 1500	age;;12.5 dpc|source_name;;Enriched Sertoli cells|strain;;Sf1-eGFP|tissue;;gonad	GEO Accession;;GSM1598861		GSM1598861	Sertoli repA	3127175736	15481068	2015-05-21 16:54:12	1910046415	3127175736	15481068	2	15481068	index:0,count:15481068,average:101,stdev:0|index:1,count:15481068,average:101,stdev:0	GSM1598861_r2	GEO			in_mesa	25855264	10.83	3.11	0.15	2435559328	2371372798	2264164768	2216807432	97.36	97.91	14339847	13970102	180.081	368.665	151	166240	64.42	69.38	16039831	9238426	16039831	9238426	65.63	66.07	16039831	9411607	16039831	8798327	651224691	26.74	0.29	0	6.61	0	0.22	0	0.19	0	0.00	0	6.97	0	14339847	0	202	0	200.27	0	2.12	0	0.01	0	3.08	0	0.03	0	195.55	0	0.31	0	45598	0	15481068	0	1023634	0	33387	0	29302	0	0	0	1078532	0	2550	0	0	0	31244	0	3556874	0	11888	0	3602556	0	86.02	0	13316213	0	171468	3414189	19.911522849745	15481068.0	14339847.0	45598.0	1023634.0	33387.0	29302.0	0.0	1078532.0	13316213.0	92.6	0.3	6.6	0.2	0.2	0.0	7.0	86.0	101	101	101.00	38	1563587868	25.0	24.2	24.3	26.6	0.0	37.0	28.5	bulk
933893	SRR1783800	SRP053038	SRS833776	SRX862818	SRA236037	GEO		Purification and transcriptomic analysis of mouse fetal Leydig cells reveals candidate genes for disorders of sex development	To examine the transcriptome of early testicular somatic cells during gonadogenesis at 12.5dpc RNA sequencing (RNA-Seq) was performed on murine primary testicular cell lineages isolated from the Sf1-eGFP line by FACS. The three main somatic cell lineages of the testis were isolated: the Sertoli cells which direct male development; the fetal Leydig cells (FLCs) that produce steroid hormones and virilise the XY individual and a heterogenous population of interstitial cells, some of which give rise to the adult Leydig cells (ALCs). This dataset provides a platform for exploring the biology of FLCs and understanding the role of these cells in testicular development and masculinization of the embryo, and a basis for targeted studies designed to identify causes of idiopathic XY DSD. Overall design: RNA-Seq of 3 enriched cell populations from 12.5dpc mouse gonad (Sertoli cells, Leydig cells and Interstitial cells isolated by FACS-sorting) on an Illumina HiSeq 1500, in triplicate.		GSM1598861: Sertoli repA; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted (Micro RNeasy kit without carrier RNA, Qiagen) from CD31-treated FACS-sorted cells. Each sample represented approximately 10 sorting experiments conducted on different days with 4-10 litters of Sf1-eGFP embryos in each experiment. We prepared sample A, sample B and Sample A+B (a mix of samples A and B), with 100ng of total RNA in each sample. Libraries were prepared using TruSeq Stranded Total RNA Libraries  (Illumina protocol 15031048 Rev C, Sep 2012), with multiplexing, Ribosomal depletion,with all sample run over the 4 rapid lanes	Illumina HiSeq 1500	age;;12.5 dpc|source_name;;Enriched Sertoli cells|strain;;Sf1-eGFP|tissue;;gonad	GEO Accession;;GSM1598861		GSM1598861	Sertoli repA	3076663212	15231006	2015-05-21 16:54:12	1860712071	3076663212	15231006	2	15231006	index:0,count:15231006,average:101,stdev:0|index:1,count:15231006,average:101,stdev:0	GSM1598861_r3	GEO			in_mesa	25855264	10.84	3.1	0.16	2408128952	2344415919	2239423579	2192342769	97.35	97.9	14177560	13812238	180.039	366.856	150	164455	64.41	69.34	15853310	9131437	15853310	9131437	65.61	66.03	15853310	9302587	15853310	8696506	644801938	26.78	0.30	0	6.62	0	0.21	0	0.19	0	0.00	0	6.52	0	14177560	0	202	0	200.32	0	2.13	0	0.01	0	3.06	0	0.03	0	197.24	0	0.31	0	45402	0	15231006	0	1007818	0	32087	0	28738	0	0	0	992621	0	2446	0	0	0	30784	0	3516035	0	12207	0	3561472	0	86.47	0	13169742	0	170516	3372709	19.779428323442	15231006.0	14177560.0	45402.0	1007818.0	32087.0	28738.0	0.0	992621.0	13169742.0	93.1	0.3	6.6	0.2	0.2	0.0	6.5	86.5	101	101	101.00	38	1538331606	25.0	24.2	24.3	26.5	0.0	37.1	28.9	bulk
933901	SRR1783801	SRP053038	SRS833776	SRX862818	SRA236037	GEO		Purification and transcriptomic analysis of mouse fetal Leydig cells reveals candidate genes for disorders of sex development	To examine the transcriptome of early testicular somatic cells during gonadogenesis at 12.5dpc RNA sequencing (RNA-Seq) was performed on murine primary testicular cell lineages isolated from the Sf1-eGFP line by FACS. The three main somatic cell lineages of the testis were isolated: the Sertoli cells which direct male development; the fetal Leydig cells (FLCs) that produce steroid hormones and virilise the XY individual and a heterogenous population of interstitial cells, some of which give rise to the adult Leydig cells (ALCs). This dataset provides a platform for exploring the biology of FLCs and understanding the role of these cells in testicular development and masculinization of the embryo, and a basis for targeted studies designed to identify causes of idiopathic XY DSD. Overall design: RNA-Seq of 3 enriched cell populations from 12.5dpc mouse gonad (Sertoli cells, Leydig cells and Interstitial cells isolated by FACS-sorting) on an Illumina HiSeq 1500, in triplicate.		GSM1598861: Sertoli repA; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted (Micro RNeasy kit without carrier RNA, Qiagen) from CD31-treated FACS-sorted cells. Each sample represented approximately 10 sorting experiments conducted on different days with 4-10 litters of Sf1-eGFP embryos in each experiment. We prepared sample A, sample B and Sample A+B (a mix of samples A and B), with 100ng of total RNA in each sample. Libraries were prepared using TruSeq Stranded Total RNA Libraries  (Illumina protocol 15031048 Rev C, Sep 2012), with multiplexing, Ribosomal depletion,with all sample run over the 4 rapid lanes	Illumina HiSeq 1500	age;;12.5 dpc|source_name;;Enriched Sertoli cells|strain;;Sf1-eGFP|tissue;;gonad	GEO Accession;;GSM1598861		GSM1598861	Sertoli repA	3058975284	15143442	2015-05-21 16:54:12	1839457729	3058975284	15143442	2	15143442	index:0,count:15143442,average:101,stdev:0|index:1,count:15143442,average:101,stdev:0	GSM1598861_r4	GEO			in_mesa	25855264	10.83	3.11	0.15	2394733135	2331437901	2226998645	2180261618	97.36	97.9	14097306	13735342	180.069	366.424	151	164023	64.41	69.34	15763366	9080136	15763366	9080136	65.61	66.04	15763366	9249333	15763366	8647835	641114729	26.77	0.30	0	6.62	0	0.21	0	0.19	0	0.00	0	6.51	0	14097306	0	202	0	200.33	0	2.13	0	0.01	0	3.06	0	0.03	0	194.70	0	0.30	0	45162	0	15143442	0	1002398	0	32076	0	28967	0	0	0	985093	0	2394	0	0	0	30956	0	3495495	0	11940	0	3540785	0	86.47	0	13094908	0	170438	3353504	19.675799997653	15143442.0	14097306.0	45162.0	1002398.0	32076.0	28967.0	0.0	985093.0	13094908.0	93.1	0.3	6.6	0.2	0.2	0.0	6.5	86.5	101	101	101.00	38	1529487642	25.0	24.2	24.3	26.5	0.0	37.1	29.0	bulk
933909	SRR1783802	SRP053038	SRS833775	SRX862819	SRA236037	GEO		Purification and transcriptomic analysis of mouse fetal Leydig cells reveals candidate genes for disorders of sex development	To examine the transcriptome of early testicular somatic cells during gonadogenesis at 12.5dpc RNA sequencing (RNA-Seq) was performed on murine primary testicular cell lineages isolated from the Sf1-eGFP line by FACS. The three main somatic cell lineages of the testis were isolated: the Sertoli cells which direct male development; the fetal Leydig cells (FLCs) that produce steroid hormones and virilise the XY individual and a heterogenous population of interstitial cells, some of which give rise to the adult Leydig cells (ALCs). This dataset provides a platform for exploring the biology of FLCs and understanding the role of these cells in testicular development and masculinization of the embryo, and a basis for targeted studies designed to identify causes of idiopathic XY DSD. Overall design: RNA-Seq of 3 enriched cell populations from 12.5dpc mouse gonad (Sertoli cells, Leydig cells and Interstitial cells isolated by FACS-sorting) on an Illumina HiSeq 1500, in triplicate.		GSM1598862: Sertoli repB; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted (Micro RNeasy kit without carrier RNA, Qiagen) from CD31-treated FACS-sorted cells. Each sample represented approximately 10 sorting experiments conducted on different days with 4-10 litters of Sf1-eGFP embryos in each experiment. We prepared sample A, sample B and Sample A+B (a mix of samples A and B), with 100ng of total RNA in each sample. Libraries were prepared using TruSeq Stranded Total RNA Libraries  (Illumina protocol 15031048 Rev C, Sep 2012), with multiplexing, Ribosomal depletion,with all sample run over the 4 rapid lanes	Illumina HiSeq 1500	age;;12.5 dpc|source_name;;Enriched Sertoli cells|strain;;Sf1-eGFP|tissue;;gonad	GEO Accession;;GSM1598862		GSM1598862	Sertoli repB	3020413686	14952543	2015-05-21 16:54:12	1817659054	3020413686	14952543	2	14952543	index:0,count:14952543,average:101,stdev:0|index:1,count:14952543,average:101,stdev:0	GSM1598862_r1	GEO			in_mesa	25855264	9.95	3.24	0.18	2415676034	2349361104	2278992972	2228874473	97.25	97.8	14209575	13850578	180.199	367.881	139	169883	62.6	66.41	15624732	8895094	15624732	8895094	63.47	63.5	15624732	9019453	15624732	8504617	728196315	30.14	0.27	0	5.46	0	0.21	0	0.22	0	0.00	0	4.54	0	14209575	0	202	0	200.45	0	2.18	0	0.01	0	2.80	0	0.02	0	171.43	0	0.28	0	39939	0	14952543	0	816202	0	30751	0	33245	0	0	0	678972	0	2417	0	0	0	28713	0	3413264	0	12973	0	3457367	0	89.57	0	13393373	0	170302	3271429	19.209574755434	14952543.0	14209575.0	39939.0	816202.0	30751.0	33245.0	0.0	678972.0	13393373.0	95.0	0.3	5.5	0.2	0.2	0.0	4.5	89.6	101	101	101.00	38	1510206843	25.7	23.9	23.6	26.8	0.0	37.2	28.7	bulk
933917	SRR1783803	SRP053038	SRS833775	SRX862819	SRA236037	GEO		Purification and transcriptomic analysis of mouse fetal Leydig cells reveals candidate genes for disorders of sex development	To examine the transcriptome of early testicular somatic cells during gonadogenesis at 12.5dpc RNA sequencing (RNA-Seq) was performed on murine primary testicular cell lineages isolated from the Sf1-eGFP line by FACS. The three main somatic cell lineages of the testis were isolated: the Sertoli cells which direct male development; the fetal Leydig cells (FLCs) that produce steroid hormones and virilise the XY individual and a heterogenous population of interstitial cells, some of which give rise to the adult Leydig cells (ALCs). This dataset provides a platform for exploring the biology of FLCs and understanding the role of these cells in testicular development and masculinization of the embryo, and a basis for targeted studies designed to identify causes of idiopathic XY DSD. Overall design: RNA-Seq of 3 enriched cell populations from 12.5dpc mouse gonad (Sertoli cells, Leydig cells and Interstitial cells isolated by FACS-sorting) on an Illumina HiSeq 1500, in triplicate.		GSM1598862: Sertoli repB; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted (Micro RNeasy kit without carrier RNA, Qiagen) from CD31-treated FACS-sorted cells. Each sample represented approximately 10 sorting experiments conducted on different days with 4-10 litters of Sf1-eGFP embryos in each experiment. We prepared sample A, sample B and Sample A+B (a mix of samples A and B), with 100ng of total RNA in each sample. Libraries were prepared using TruSeq Stranded Total RNA Libraries  (Illumina protocol 15031048 Rev C, Sep 2012), with multiplexing, Ribosomal depletion,with all sample run over the 4 rapid lanes	Illumina HiSeq 1500	age;;12.5 dpc|source_name;;Enriched Sertoli cells|strain;;Sf1-eGFP|tissue;;gonad	GEO Accession;;GSM1598862		GSM1598862	Sertoli repB	3010589416	14903908	2015-05-21 16:54:12	1816240079	3010589416	14903908	2	14903908	index:0,count:14903908,average:101,stdev:0|index:1,count:14903908,average:101,stdev:0	GSM1598862_r2	GEO			in_mesa	25855264	9.94	3.23	0.18	2408435092	2342063670	2271829859	2221624329	97.24	97.79	14162304	13805057	180.276	366.578	139	167806	62.58	66.41	15579142	8862991	15579142	8862991	63.47	63.5	15579142	8988328	15579142	8474594	726155504	30.15	0.26	0	5.47	0	0.21	0	0.22	0	0.00	0	4.55	0	14162304	0	202	0	200.47	0	2.18	0	0.01	0	2.83	0	0.02	0	291.60	0	0.28	0	39285	0	14903908	0	815694	0	30914	0	32809	0	0	0	677881	0	2405	0	0	0	28860	0	3403114	0	12960	0	3447339	0	89.55	0	13346610	0	170297	3256807	19.124276998420	14903908.0	14162304.0	39285.0	815694.0	30914.0	32809.0	0.0	677881.0	13346610.0	95.0	0.3	5.5	0.2	0.2	0.0	4.5	89.6	101	101	101.00	38	1505294708	25.7	23.9	23.6	26.8	0.0	37.2	28.8	bulk
933926	SRR1783804	SRP053038	SRS833775	SRX862819	SRA236037	GEO		Purification and transcriptomic analysis of mouse fetal Leydig cells reveals candidate genes for disorders of sex development	To examine the transcriptome of early testicular somatic cells during gonadogenesis at 12.5dpc RNA sequencing (RNA-Seq) was performed on murine primary testicular cell lineages isolated from the Sf1-eGFP line by FACS. The three main somatic cell lineages of the testis were isolated: the Sertoli cells which direct male development; the fetal Leydig cells (FLCs) that produce steroid hormones and virilise the XY individual and a heterogenous population of interstitial cells, some of which give rise to the adult Leydig cells (ALCs). This dataset provides a platform for exploring the biology of FLCs and understanding the role of these cells in testicular development and masculinization of the embryo, and a basis for targeted studies designed to identify causes of idiopathic XY DSD. Overall design: RNA-Seq of 3 enriched cell populations from 12.5dpc mouse gonad (Sertoli cells, Leydig cells and Interstitial cells isolated by FACS-sorting) on an Illumina HiSeq 1500, in triplicate.		GSM1598862: Sertoli repB; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted (Micro RNeasy kit without carrier RNA, Qiagen) from CD31-treated FACS-sorted cells. Each sample represented approximately 10 sorting experiments conducted on different days with 4-10 litters of Sf1-eGFP embryos in each experiment. We prepared sample A, sample B and Sample A+B (a mix of samples A and B), with 100ng of total RNA in each sample. Libraries were prepared using TruSeq Stranded Total RNA Libraries  (Illumina protocol 15031048 Rev C, Sep 2012), with multiplexing, Ribosomal depletion,with all sample run over the 4 rapid lanes	Illumina HiSeq 1500	age;;12.5 dpc|source_name;;Enriched Sertoli cells|strain;;Sf1-eGFP|tissue;;gonad	GEO Accession;;GSM1598862		GSM1598862	Sertoli repB	2948965478	14598839	2015-05-21 16:54:12	1761802716	2948965478	14598839	2	14598839	index:0,count:14598839,average:101,stdev:0|index:1,count:14598839,average:101,stdev:0	GSM1598862_r3	GEO			in_mesa	25855264	9.94	3.25	0.18	2369400479	2304395930	2235261882	2186149558	97.26	97.8	13929474	13578461	180.250	367.513	139	165520	62.58	66.4	15322389	8717180	15322389	8717180	63.46	63.49	15322389	8839077	15322389	8335176	714758255	30.17	0.27	0	5.49	0	0.21	0	0.22	0	0.00	0	4.16	0	13929474	0	202	0	200.53	0	2.17	0	0.01	0	2.81	0	0.02	0	255.13	0	0.28	0	38983	0	14598839	0	800872	0	30303	0	32417	0	0	0	606645	0	2459	0	0	0	27807	0	3342490	0	12829	0	3385585	0	89.93	0	13128602	0	169154	3202459	18.932209702401	14598839.0	13929474.0	38983.0	800872.0	30303.0	32417.0	0.0	606645.0	13128602.0	95.4	0.3	5.5	0.2	0.2	0.0	4.2	89.9	101	101	101.00	38	1474482739	25.7	23.9	23.6	26.8	0.0	37.2	29.2	bulk
933932	SRR1783805	SRP053038	SRS833775	SRX862819	SRA236037	GEO		Purification and transcriptomic analysis of mouse fetal Leydig cells reveals candidate genes for disorders of sex development	To examine the transcriptome of early testicular somatic cells during gonadogenesis at 12.5dpc RNA sequencing (RNA-Seq) was performed on murine primary testicular cell lineages isolated from the Sf1-eGFP line by FACS. The three main somatic cell lineages of the testis were isolated: the Sertoli cells which direct male development; the fetal Leydig cells (FLCs) that produce steroid hormones and virilise the XY individual and a heterogenous population of interstitial cells, some of which give rise to the adult Leydig cells (ALCs). This dataset provides a platform for exploring the biology of FLCs and understanding the role of these cells in testicular development and masculinization of the embryo, and a basis for targeted studies designed to identify causes of idiopathic XY DSD. Overall design: RNA-Seq of 3 enriched cell populations from 12.5dpc mouse gonad (Sertoli cells, Leydig cells and Interstitial cells isolated by FACS-sorting) on an Illumina HiSeq 1500, in triplicate.		GSM1598862: Sertoli repB; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted (Micro RNeasy kit without carrier RNA, Qiagen) from CD31-treated FACS-sorted cells. Each sample represented approximately 10 sorting experiments conducted on different days with 4-10 litters of Sf1-eGFP embryos in each experiment. We prepared sample A, sample B and Sample A+B (a mix of samples A and B), with 100ng of total RNA in each sample. Libraries were prepared using TruSeq Stranded Total RNA Libraries  (Illumina protocol 15031048 Rev C, Sep 2012), with multiplexing, Ribosomal depletion,with all sample run over the 4 rapid lanes	Illumina HiSeq 1500	age;;12.5 dpc|source_name;;Enriched Sertoli cells|strain;;Sf1-eGFP|tissue;;gonad	GEO Accession;;GSM1598862		GSM1598862	Sertoli repB	2942700246	14567823	2015-05-21 16:54:12	1748300623	2942700246	14567823	2	14567823	index:0,count:14567823,average:101,stdev:0|index:1,count:14567823,average:101,stdev:0	GSM1598862_r4	GEO			in_mesa	25855264	9.93	3.23	0.18	2364685084	2299990236	2231138913	2182345312	97.26	97.81	13900501	13551026	180.292	366.077	139	164645	62.61	66.42	15288886	8703265	15288886	8703265	63.47	63.51	15288886	8823178	15288886	8321371	713091439	30.16	0.26	0	5.47	0	0.21	0	0.22	0	0.00	0	4.15	0	13900501	0	202	0	200.53	0	2.17	0	0.01	0	2.80	0	0.02	0	213.19	0	0.27	0	38530	0	14567823	0	797355	0	29951	0	32736	0	0	0	604635	0	2342	0	0	0	27948	0	3344127	0	12732	0	3387149	0	89.95	0	13103146	0	169801	3197712	18.832115240782	14567823.0	13900501.0	38530.0	797355.0	29951.0	32736.0	0.0	604635.0	13103146.0	95.4	0.3	5.5	0.2	0.2	0.0	4.2	89.9	101	101	101.00	38	1471350123	25.7	23.9	23.6	26.8	0.0	37.3	29.3	bulk
934036	SRR1783812	SRP053038	SRS833777	SRX862821	SRA236037	GEO		Purification and transcriptomic analysis of mouse fetal Leydig cells reveals candidate genes for disorders of sex development	To examine the transcriptome of early testicular somatic cells during gonadogenesis at 12.5dpc RNA sequencing (RNA-Seq) was performed on murine primary testicular cell lineages isolated from the Sf1-eGFP line by FACS. The three main somatic cell lineages of the testis were isolated: the Sertoli cells which direct male development; the fetal Leydig cells (FLCs) that produce steroid hormones and virilise the XY individual and a heterogenous population of interstitial cells, some of which give rise to the adult Leydig cells (ALCs). This dataset provides a platform for exploring the biology of FLCs and understanding the role of these cells in testicular development and masculinization of the embryo, and a basis for targeted studies designed to identify causes of idiopathic XY DSD. Overall design: RNA-Seq of 3 enriched cell populations from 12.5dpc mouse gonad (Sertoli cells, Leydig cells and Interstitial cells isolated by FACS-sorting) on an Illumina HiSeq 1500, in triplicate.		GSM1598864: Leydig repA; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted (Micro RNeasy kit without carrier RNA, Qiagen) from CD31-treated FACS-sorted cells. Each sample represented approximately 10 sorting experiments conducted on different days with 4-10 litters of Sf1-eGFP embryos in each experiment. We prepared sample A, sample B and Sample A+B (a mix of samples A and B), with 100ng of total RNA in each sample. Libraries were prepared using TruSeq Stranded Total RNA Libraries  (Illumina protocol 15031048 Rev C, Sep 2012), with multiplexing, Ribosomal depletion,with all sample run over the 4 rapid lanes	Illumina HiSeq 1500	age;;12.5 dpc|source_name;;Enriched Leydig cells|strain;;Sf1-eGFP|tissue;;gonad	GEO Accession;;GSM1598864		GSM1598864	Leydig repA	2662475544	13180572	2015-05-21 16:54:12	1611333653	2662475544	13180572	2	13180572	index:0,count:13180572,average:101,stdev:0|index:1,count:13180572,average:101,stdev:0	GSM1598864_r3	GEO			in_mesa	25855264	10.78	3.26	0.13	2098370919	2056845227	1959800565	1931756372	98.02	98.57	12329288	12007811	180.448	377.618	139	143560	64.82	69.45	13709004	7992033	13709004	7992033	66.38	66.55	13709004	8184081	13709004	7658064	583613759	27.81	0.22	0	6.24	0	0.22	0	0.22	0	0.00	0	6.02	0	12329288	0	202	0	200.74	0	2.16	0	0.01	0	2.39	0	0.02	0	172.55	0	0.25	0	28978	0	13180572	0	822349	0	28997	0	28789	0	0	0	793498	0	2170	0	0	0	26631	0	3095932	0	10643	0	3135376	0	87.30	0	11506939	0	168008	2965018	17.648076282082	13180572.0	12329288.0	28978.0	822349.0	28997.0	28789.0	0.0	793498.0	11506939.0	93.5	0.2	6.2	0.2	0.2	0.0	6.0	87.3	101	101	101.00	38	1331237772	25.4	24.0	23.5	27.1	0.0	37.2	29.1	bulk
934044	SRR1783813	SRP053038	SRS833777	SRX862821	SRA236037	GEO		Purification and transcriptomic analysis of mouse fetal Leydig cells reveals candidate genes for disorders of sex development	To examine the transcriptome of early testicular somatic cells during gonadogenesis at 12.5dpc RNA sequencing (RNA-Seq) was performed on murine primary testicular cell lineages isolated from the Sf1-eGFP line by FACS. The three main somatic cell lineages of the testis were isolated: the Sertoli cells which direct male development; the fetal Leydig cells (FLCs) that produce steroid hormones and virilise the XY individual and a heterogenous population of interstitial cells, some of which give rise to the adult Leydig cells (ALCs). This dataset provides a platform for exploring the biology of FLCs and understanding the role of these cells in testicular development and masculinization of the embryo, and a basis for targeted studies designed to identify causes of idiopathic XY DSD. Overall design: RNA-Seq of 3 enriched cell populations from 12.5dpc mouse gonad (Sertoli cells, Leydig cells and Interstitial cells isolated by FACS-sorting) on an Illumina HiSeq 1500, in triplicate.		GSM1598864: Leydig repA; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted (Micro RNeasy kit without carrier RNA, Qiagen) from CD31-treated FACS-sorted cells. Each sample represented approximately 10 sorting experiments conducted on different days with 4-10 litters of Sf1-eGFP embryos in each experiment. We prepared sample A, sample B and Sample A+B (a mix of samples A and B), with 100ng of total RNA in each sample. Libraries were prepared using TruSeq Stranded Total RNA Libraries  (Illumina protocol 15031048 Rev C, Sep 2012), with multiplexing, Ribosomal depletion,with all sample run over the 4 rapid lanes	Illumina HiSeq 1500	age;;12.5 dpc|source_name;;Enriched Leydig cells|strain;;Sf1-eGFP|tissue;;gonad	GEO Accession;;GSM1598864		GSM1598864	Leydig repA	2660217790	13169395	2015-05-21 16:54:12	1601843399	2660217790	13169395	2	13169395	index:0,count:13169395,average:101,stdev:0|index:1,count:13169395,average:101,stdev:0	GSM1598864_r4	GEO			in_mesa	25855264	10.77	3.26	0.12	2096603608	2055410994	1958500202	1930767756	98.04	98.58	12318457	11997387	180.417	378.738	139	142970	64.86	69.49	13694739	7990114	13694739	7990114	66.4	66.57	13694739	8178868	13694739	7655140	582574715	27.79	0.22	0	6.23	0	0.22	0	0.22	0	0.00	0	6.03	0	12318457	0	202	0	200.74	0	2.16	0	0.01	0	2.40	0	0.02	0	207.03	0	0.24	0	28711	0	13169395	0	819861	0	28826	0	28538	0	0	0	793574	0	2195	0	0	0	27055	0	3098608	0	10622	0	3138480	0	87.31	0	11498596	0	167843	2972078	17.707488545843	13169395.0	12318457.0	28711.0	819861.0	28826.0	28538.0	0.0	793574.0	11498596.0	93.5	0.2	6.2	0.2	0.2	0.0	6.0	87.3	101	101	101.00	38	1330108895	25.4	24.0	23.5	27.1	0.0	37.3	29.3	bulk
934052	SRR1783814	SRP053038	SRS833779	SRX862822	SRA236037	GEO		Purification and transcriptomic analysis of mouse fetal Leydig cells reveals candidate genes for disorders of sex development	To examine the transcriptome of early testicular somatic cells during gonadogenesis at 12.5dpc RNA sequencing (RNA-Seq) was performed on murine primary testicular cell lineages isolated from the Sf1-eGFP line by FACS. The three main somatic cell lineages of the testis were isolated: the Sertoli cells which direct male development; the fetal Leydig cells (FLCs) that produce steroid hormones and virilise the XY individual and a heterogenous population of interstitial cells, some of which give rise to the adult Leydig cells (ALCs). This dataset provides a platform for exploring the biology of FLCs and understanding the role of these cells in testicular development and masculinization of the embryo, and a basis for targeted studies designed to identify causes of idiopathic XY DSD. Overall design: RNA-Seq of 3 enriched cell populations from 12.5dpc mouse gonad (Sertoli cells, Leydig cells and Interstitial cells isolated by FACS-sorting) on an Illumina HiSeq 1500, in triplicate.		GSM1598865: Leydig repB; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted (Micro RNeasy kit without carrier RNA, Qiagen) from CD31-treated FACS-sorted cells. Each sample represented approximately 10 sorting experiments conducted on different days with 4-10 litters of Sf1-eGFP embryos in each experiment. We prepared sample A, sample B and Sample A+B (a mix of samples A and B), with 100ng of total RNA in each sample. Libraries were prepared using TruSeq Stranded Total RNA Libraries  (Illumina protocol 15031048 Rev C, Sep 2012), with multiplexing, Ribosomal depletion,with all sample run over the 4 rapid lanes	Illumina HiSeq 1500	age;;12.5 dpc|source_name;;Enriched Leydig cells|strain;;Sf1-eGFP|tissue;;gonad	GEO Accession;;GSM1598865		GSM1598865	Leydig repB	3108535782	15388791	2015-05-21 16:54:12	1878033201	3108535782	15388791	2	15388791	index:0,count:15388791,average:101,stdev:0|index:1,count:15388791,average:101,stdev:0	GSM1598865_r1	GEO			in_mesa	25855264	10.02	3.17	0.14	2451089156	2379782475	2306899053	2253098745	97.09	97.67	14521480	14181694	178.235	358.260	139	175489	60.46	64.31	16058229	8779505	16058229	8779505	61.1	61.1	16058229	8872110	16058229	8340440	779681103	31.81	0.29	0	5.65	0	0.22	0	0.25	0	0.00	0	5.17	0	14521480	0	202	0	200.33	0	2.24	0	0.01	0	2.95	0	0.03	0	215.56	0	0.30	0	43963	0	15388791	0	870176	0	33471	0	37724	0	0	0	796116	0	2398	0	0	0	28404	0	3229302	0	12471	0	3272575	0	88.71	0	13651304	0	172358	3089331	17.923919980506	15388791.0	14521480.0	43963.0	870176.0	33471.0	37724.0	0.0	796116.0	13651304.0	94.4	0.3	5.7	0.2	0.2	0.0	5.2	88.7	101	101	101.00	38	1554267891	25.7	23.9	23.5	26.9	0.0	37.1	28.5	bulk
934060	SRR1783815	SRP053038	SRS833779	SRX862822	SRA236037	GEO		Purification and transcriptomic analysis of mouse fetal Leydig cells reveals candidate genes for disorders of sex development	To examine the transcriptome of early testicular somatic cells during gonadogenesis at 12.5dpc RNA sequencing (RNA-Seq) was performed on murine primary testicular cell lineages isolated from the Sf1-eGFP line by FACS. The three main somatic cell lineages of the testis were isolated: the Sertoli cells which direct male development; the fetal Leydig cells (FLCs) that produce steroid hormones and virilise the XY individual and a heterogenous population of interstitial cells, some of which give rise to the adult Leydig cells (ALCs). This dataset provides a platform for exploring the biology of FLCs and understanding the role of these cells in testicular development and masculinization of the embryo, and a basis for targeted studies designed to identify causes of idiopathic XY DSD. Overall design: RNA-Seq of 3 enriched cell populations from 12.5dpc mouse gonad (Sertoli cells, Leydig cells and Interstitial cells isolated by FACS-sorting) on an Illumina HiSeq 1500, in triplicate.		GSM1598865: Leydig repB; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted (Micro RNeasy kit without carrier RNA, Qiagen) from CD31-treated FACS-sorted cells. Each sample represented approximately 10 sorting experiments conducted on different days with 4-10 litters of Sf1-eGFP embryos in each experiment. We prepared sample A, sample B and Sample A+B (a mix of samples A and B), with 100ng of total RNA in each sample. Libraries were prepared using TruSeq Stranded Total RNA Libraries  (Illumina protocol 15031048 Rev C, Sep 2012), with multiplexing, Ribosomal depletion,with all sample run over the 4 rapid lanes	Illumina HiSeq 1500	age;;12.5 dpc|source_name;;Enriched Leydig cells|strain;;Sf1-eGFP|tissue;;gonad	GEO Accession;;GSM1598865		GSM1598865	Leydig repB	3098220450	15337725	2015-05-21 16:54:12	1877012294	3098220450	15337725	2	15337725	index:0,count:15337725,average:101,stdev:0|index:1,count:15337725,average:101,stdev:0	GSM1598865_r2	GEO			in_mesa	25855264	10.02	3.18	0.14	2443257234	2372361449	2299605062	2246082886	97.1	97.67	14470380	14131270	178.298	358.841	139	173678	60.48	64.33	15997019	8751524	15997019	8751524	61.12	61.12	15997019	8844149	15997019	8314285	777038527	31.80	0.29	0	5.65	0	0.22	0	0.25	0	0.00	0	5.19	0	14470380	0	202	0	200.33	0	2.25	0	0.01	0	2.94	0	0.03	0	231.03	0	0.30	0	43749	0	15337725	0	866156	0	33002	0	37629	0	0	0	796714	0	2388	0	0	0	28093	0	3222939	0	12473	0	3265893	0	88.70	0	13604224	0	172178	3074956	17.859168999524	15337725.0	14470380.0	43749.0	866156.0	33002.0	37629.0	0.0	796714.0	13604224.0	94.3	0.3	5.6	0.2	0.2	0.0	5.2	88.7	101	101	101.00	38	1549110225	25.8	23.9	23.5	26.9	0.0	37.1	28.6	bulk
934068	SRR1783816	SRP053038	SRS833779	SRX862822	SRA236037	GEO		Purification and transcriptomic analysis of mouse fetal Leydig cells reveals candidate genes for disorders of sex development	To examine the transcriptome of early testicular somatic cells during gonadogenesis at 12.5dpc RNA sequencing (RNA-Seq) was performed on murine primary testicular cell lineages isolated from the Sf1-eGFP line by FACS. The three main somatic cell lineages of the testis were isolated: the Sertoli cells which direct male development; the fetal Leydig cells (FLCs) that produce steroid hormones and virilise the XY individual and a heterogenous population of interstitial cells, some of which give rise to the adult Leydig cells (ALCs). This dataset provides a platform for exploring the biology of FLCs and understanding the role of these cells in testicular development and masculinization of the embryo, and a basis for targeted studies designed to identify causes of idiopathic XY DSD. Overall design: RNA-Seq of 3 enriched cell populations from 12.5dpc mouse gonad (Sertoli cells, Leydig cells and Interstitial cells isolated by FACS-sorting) on an Illumina HiSeq 1500, in triplicate.		GSM1598865: Leydig repB; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted (Micro RNeasy kit without carrier RNA, Qiagen) from CD31-treated FACS-sorted cells. Each sample represented approximately 10 sorting experiments conducted on different days with 4-10 litters of Sf1-eGFP embryos in each experiment. We prepared sample A, sample B and Sample A+B (a mix of samples A and B), with 100ng of total RNA in each sample. Libraries were prepared using TruSeq Stranded Total RNA Libraries  (Illumina protocol 15031048 Rev C, Sep 2012), with multiplexing, Ribosomal depletion,with all sample run over the 4 rapid lanes	Illumina HiSeq 1500	age;;12.5 dpc|source_name;;Enriched Leydig cells|strain;;Sf1-eGFP|tissue;;gonad	GEO Accession;;GSM1598865		GSM1598865	Leydig repB	3041584700	15057350	2015-05-21 16:54:12	1825111583	3041584700	15057350	2	15057350	index:0,count:15057350,average:101,stdev:0|index:1,count:15057350,average:101,stdev:0	GSM1598865_r3	GEO			in_mesa	25855264	10.01	3.17	0.14	2408938359	2338713790	2267603074	2214524480	97.08	97.66	14265652	13932970	178.319	356.541	139	172071	60.48	64.33	15774784	8628071	15774784	8628071	61.12	61.11	15774784	8718608	15774784	8196968	765726028	31.79	0.29	0	5.66	0	0.22	0	0.25	0	0.00	0	4.80	0	14265652	0	202	0	200.39	0	2.25	0	0.01	0	2.92	0	0.03	0	194.99	0	0.30	0	43279	0	15057350	0	852669	0	32542	0	36998	0	0	0	722158	0	2309	0	0	0	27476	0	3174926	0	12188	0	3216899	0	89.08	0	13412983	0	171890	3034782	17.655372622026	15057350.0	14265652.0	43279.0	852669.0	32542.0	36998.0	0.0	722158.0	13412983.0	94.7	0.3	5.7	0.2	0.2	0.0	4.8	89.1	101	101	101.00	38	1520792350	25.8	23.8	23.5	26.9	0.0	37.2	29.0	bulk
934076	SRR1783817	SRP053038	SRS833779	SRX862822	SRA236037	GEO		Purification and transcriptomic analysis of mouse fetal Leydig cells reveals candidate genes for disorders of sex development	To examine the transcriptome of early testicular somatic cells during gonadogenesis at 12.5dpc RNA sequencing (RNA-Seq) was performed on murine primary testicular cell lineages isolated from the Sf1-eGFP line by FACS. The three main somatic cell lineages of the testis were isolated: the Sertoli cells which direct male development; the fetal Leydig cells (FLCs) that produce steroid hormones and virilise the XY individual and a heterogenous population of interstitial cells, some of which give rise to the adult Leydig cells (ALCs). This dataset provides a platform for exploring the biology of FLCs and understanding the role of these cells in testicular development and masculinization of the embryo, and a basis for targeted studies designed to identify causes of idiopathic XY DSD. Overall design: RNA-Seq of 3 enriched cell populations from 12.5dpc mouse gonad (Sertoli cells, Leydig cells and Interstitial cells isolated by FACS-sorting) on an Illumina HiSeq 1500, in triplicate.		GSM1598865: Leydig repB; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted (Micro RNeasy kit without carrier RNA, Qiagen) from CD31-treated FACS-sorted cells. Each sample represented approximately 10 sorting experiments conducted on different days with 4-10 litters of Sf1-eGFP embryos in each experiment. We prepared sample A, sample B and Sample A+B (a mix of samples A and B), with 100ng of total RNA in each sample. Libraries were prepared using TruSeq Stranded Total RNA Libraries  (Illumina protocol 15031048 Rev C, Sep 2012), with multiplexing, Ribosomal depletion,with all sample run over the 4 rapid lanes	Illumina HiSeq 1500	age;;12.5 dpc|source_name;;Enriched Leydig cells|strain;;Sf1-eGFP|tissue;;gonad	GEO Accession;;GSM1598865		GSM1598865	Leydig repB	3027809714	14989157	2015-05-21 16:54:12	1806750136	3027809714	14989157	2	14989157	index:0,count:14989157,average:101,stdev:0|index:1,count:14989157,average:101,stdev:0	GSM1598865_r4	GEO			in_mesa	25855264	10.01	3.17	0.14	2398163107	2327946390	2257590955	2204381082	97.07	97.64	14201518	13869154	178.284	355.918	139	171209	60.45	64.29	15702831	8584675	15702831	8584675	61.1	61.09	15702831	8676531	15702831	8157543	763213956	31.82	0.29	0	5.66	0	0.22	0	0.25	0	0.00	0	4.79	0	14201518	0	202	0	200.39	0	2.24	0	0.01	0	2.93	0	0.03	0	201.35	0	0.29	0	43157	0	14989157	0	848274	0	32411	0	37216	0	0	0	718012	0	2357	0	0	0	27575	0	3160871	0	12136	0	3202939	0	89.09	0	13353244	0	171904	3014317	17.534885750186	14989157.0	14201518.0	43157.0	848274.0	32411.0	37216.0	0.0	718012.0	13353244.0	94.7	0.3	5.7	0.2	0.2	0.0	4.8	89.1	101	101	101.00	38	1513904857	25.8	23.8	23.5	26.9	0.0	37.2	29.1	bulk
934084	SRR1783818	SRP053038	SRS833781	SRX862823	SRA236037	GEO		Purification and transcriptomic analysis of mouse fetal Leydig cells reveals candidate genes for disorders of sex development	To examine the transcriptome of early testicular somatic cells during gonadogenesis at 12.5dpc RNA sequencing (RNA-Seq) was performed on murine primary testicular cell lineages isolated from the Sf1-eGFP line by FACS. The three main somatic cell lineages of the testis were isolated: the Sertoli cells which direct male development; the fetal Leydig cells (FLCs) that produce steroid hormones and virilise the XY individual and a heterogenous population of interstitial cells, some of which give rise to the adult Leydig cells (ALCs). This dataset provides a platform for exploring the biology of FLCs and understanding the role of these cells in testicular development and masculinization of the embryo, and a basis for targeted studies designed to identify causes of idiopathic XY DSD. Overall design: RNA-Seq of 3 enriched cell populations from 12.5dpc mouse gonad (Sertoli cells, Leydig cells and Interstitial cells isolated by FACS-sorting) on an Illumina HiSeq 1500, in triplicate.		GSM1598866: Leydig repC; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted (Micro RNeasy kit without carrier RNA, Qiagen) from CD31-treated FACS-sorted cells. Each sample represented approximately 10 sorting experiments conducted on different days with 4-10 litters of Sf1-eGFP embryos in each experiment. We prepared sample A, sample B and Sample A+B (a mix of samples A and B), with 100ng of total RNA in each sample. Libraries were prepared using TruSeq Stranded Total RNA Libraries  (Illumina protocol 15031048 Rev C, Sep 2012), with multiplexing, Ribosomal depletion,with all sample run over the 4 rapid lanes	Illumina HiSeq 1500	age;;12.5 dpc|source_name;;Enriched Leydig cells|strain;;Sf1-eGFP|tissue;;gonad	GEO Accession;;GSM1598866		GSM1598866	Leydig repC	3049356650	15095825	2015-05-21 16:54:12	1840124215	3049356650	15095825	2	15095825	index:0,count:15095825,average:101,stdev:0|index:1,count:15095825,average:101,stdev:0	GSM1598866_r1	GEO			in_mesa	25855264	10.88	3.32	0.13	2475039530	2427895432	2322442307	2290848203	98.1	98.64	14388992	14024687	182.432	374.579	151	157641	64.26	68.52	15899996	9246366	15899996	9246366	65.77	65.76	15899996	9463796	15899996	8873526	717470168	28.99	0.17	0	5.93	0	0.22	0	0.23	0	0.00	0	4.23	0	14388992	0	202	0	200.81	0	2.20	0	0.01	0	2.20	0	0.02	0	215.65	0	0.22	0	26164	0	15095825	0	894659	0	32695	0	35007	0	0	0	639131	0	2663	0	0	0	30393	0	3538755	0	12525	0	3584336	0	89.39	0	13494333	0	173943	3416656	19.642388598564	15095825.0	14388992.0	26164.0	894659.0	32695.0	35007.0	0.0	639131.0	13494333.0	95.3	0.2	5.9	0.2	0.2	0.0	4.2	89.4	101	101	101.00	38	1524678325	25.7	23.8	23.0	27.4	0.0	37.2	28.8	bulk
934204	SRR1783827	SRP053038	SRS833783	SRX862825	SRA236037	GEO		Purification and transcriptomic analysis of mouse fetal Leydig cells reveals candidate genes for disorders of sex development	To examine the transcriptome of early testicular somatic cells during gonadogenesis at 12.5dpc RNA sequencing (RNA-Seq) was performed on murine primary testicular cell lineages isolated from the Sf1-eGFP line by FACS. The three main somatic cell lineages of the testis were isolated: the Sertoli cells which direct male development; the fetal Leydig cells (FLCs) that produce steroid hormones and virilise the XY individual and a heterogenous population of interstitial cells, some of which give rise to the adult Leydig cells (ALCs). This dataset provides a platform for exploring the biology of FLCs and understanding the role of these cells in testicular development and masculinization of the embryo, and a basis for targeted studies designed to identify causes of idiopathic XY DSD. Overall design: RNA-Seq of 3 enriched cell populations from 12.5dpc mouse gonad (Sertoli cells, Leydig cells and Interstitial cells isolated by FACS-sorting) on an Illumina HiSeq 1500, in triplicate.		GSM1598868: Interstitial repB; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted (Micro RNeasy kit without carrier RNA, Qiagen) from CD31-treated FACS-sorted cells. Each sample represented approximately 10 sorting experiments conducted on different days with 4-10 litters of Sf1-eGFP embryos in each experiment. We prepared sample A, sample B and Sample A+B (a mix of samples A and B), with 100ng of total RNA in each sample. Libraries were prepared using TruSeq Stranded Total RNA Libraries  (Illumina protocol 15031048 Rev C, Sep 2012), with multiplexing, Ribosomal depletion,with all sample run over the 4 rapid lanes	Illumina HiSeq 1500	age;;12.5 dpc|source_name;;Enriched Interstitial cells|strain;;Sf1-eGFP|tissue;;gonad	GEO Accession;;GSM1598868		GSM1598868	Interstitial repB	2874173160	14228580	2015-05-21 16:54:12	1758285122	2874173160	14228580	2	14228580	index:0,count:14228580,average:101,stdev:0|index:1,count:14228580,average:101,stdev:0	GSM1598868_r2	GEO			in_mesa	25855264	10.01	2.94	0.14	2160256708	2104428047	2018907659	1977054917	97.42	97.93	12829873	12484486	178.761	375.196	139	154615	64.77	69.37	14367411	8309523	14367411	8309523	66.52	66.35	14367411	8535072	14367411	7947594	588680338	27.25	0.27	0	5.99	0	0.27	0	0.22	0	0.00	0	9.34	0	12829873	0	202	0	200.42	0	2.39	0	0.01	0	2.99	0	0.02	0	107.16	0	0.29	0	38782	0	14228580	0	851954	0	38427	0	31894	0	0	0	1328386	0	2569	0	0	0	29427	0	3342221	0	11938	0	3386155	0	84.18	0	11977919	0	177653	3292609	18.533934130018	14228580.0	12829873.0	38782.0	851954.0	38427.0	31894.0	0.0	1328386.0	11977919.0	90.2	0.3	6.0	0.3	0.2	0.0	9.3	84.2	101	101	101.00	38	1437086580	24.3	25.0	24.7	26.0	0.0	36.9	28.2	bulk
934212	SRR1783828	SRP053038	SRS833783	SRX862825	SRA236037	GEO		Purification and transcriptomic analysis of mouse fetal Leydig cells reveals candidate genes for disorders of sex development	To examine the transcriptome of early testicular somatic cells during gonadogenesis at 12.5dpc RNA sequencing (RNA-Seq) was performed on murine primary testicular cell lineages isolated from the Sf1-eGFP line by FACS. The three main somatic cell lineages of the testis were isolated: the Sertoli cells which direct male development; the fetal Leydig cells (FLCs) that produce steroid hormones and virilise the XY individual and a heterogenous population of interstitial cells, some of which give rise to the adult Leydig cells (ALCs). This dataset provides a platform for exploring the biology of FLCs and understanding the role of these cells in testicular development and masculinization of the embryo, and a basis for targeted studies designed to identify causes of idiopathic XY DSD. Overall design: RNA-Seq of 3 enriched cell populations from 12.5dpc mouse gonad (Sertoli cells, Leydig cells and Interstitial cells isolated by FACS-sorting) on an Illumina HiSeq 1500, in triplicate.		GSM1598868: Interstitial repB; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted (Micro RNeasy kit without carrier RNA, Qiagen) from CD31-treated FACS-sorted cells. Each sample represented approximately 10 sorting experiments conducted on different days with 4-10 litters of Sf1-eGFP embryos in each experiment. We prepared sample A, sample B and Sample A+B (a mix of samples A and B), with 100ng of total RNA in each sample. Libraries were prepared using TruSeq Stranded Total RNA Libraries  (Illumina protocol 15031048 Rev C, Sep 2012), with multiplexing, Ribosomal depletion,with all sample run over the 4 rapid lanes	Illumina HiSeq 1500	age;;12.5 dpc|source_name;;Enriched Interstitial cells|strain;;Sf1-eGFP|tissue;;gonad	GEO Accession;;GSM1598868		GSM1598868	Interstitial repB	2809688498	13909349	2015-05-21 16:54:12	1704322043	2809688498	13909349	2	13909349	index:0,count:13909349,average:101,stdev:0|index:1,count:13909349,average:101,stdev:0	GSM1598868_r3	GEO			in_mesa	25855264	9.98	2.94	0.14	2119052910	2064031620	1980315853	1939041725	97.4	97.92	12584662	12246336	178.686	377.443	139	152229	64.72	69.32	14095589	8144372	14095589	8144372	66.49	66.31	14095589	8367587	14095589	7790126	578328799	27.29	0.27	0	6.01	0	0.27	0	0.22	0	0.00	0	9.03	0	12584662	0	202	0	200.48	0	2.39	0	0.02	0	2.97	0	0.02	0	175.08	0	0.29	0	38038	0	13909349	0	836498	0	37449	0	30667	0	0	0	1256571	0	2410	0	0	0	29045	0	3275242	0	11597	0	3318294	0	84.46	0	11748164	0	176957	3232835	18.269042761801	13909349.0	12584662.0	38038.0	836498.0	37449.0	30667.0	0.0	1256571.0	11748164.0	90.5	0.3	6.0	0.3	0.2	0.0	9.0	84.5	101	101	101.00	38	1404844249	24.3	25.0	24.7	26.0	0.0	37.0	28.6	bulk
934220	SRR1783829	SRP053038	SRS833783	SRX862825	SRA236037	GEO		Purification and transcriptomic analysis of mouse fetal Leydig cells reveals candidate genes for disorders of sex development	To examine the transcriptome of early testicular somatic cells during gonadogenesis at 12.5dpc RNA sequencing (RNA-Seq) was performed on murine primary testicular cell lineages isolated from the Sf1-eGFP line by FACS. The three main somatic cell lineages of the testis were isolated: the Sertoli cells which direct male development; the fetal Leydig cells (FLCs) that produce steroid hormones and virilise the XY individual and a heterogenous population of interstitial cells, some of which give rise to the adult Leydig cells (ALCs). This dataset provides a platform for exploring the biology of FLCs and understanding the role of these cells in testicular development and masculinization of the embryo, and a basis for targeted studies designed to identify causes of idiopathic XY DSD. Overall design: RNA-Seq of 3 enriched cell populations from 12.5dpc mouse gonad (Sertoli cells, Leydig cells and Interstitial cells isolated by FACS-sorting) on an Illumina HiSeq 1500, in triplicate.		GSM1598868: Interstitial repB; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted (Micro RNeasy kit without carrier RNA, Qiagen) from CD31-treated FACS-sorted cells. Each sample represented approximately 10 sorting experiments conducted on different days with 4-10 litters of Sf1-eGFP embryos in each experiment. We prepared sample A, sample B and Sample A+B (a mix of samples A and B), with 100ng of total RNA in each sample. Libraries were prepared using TruSeq Stranded Total RNA Libraries  (Illumina protocol 15031048 Rev C, Sep 2012), with multiplexing, Ribosomal depletion,with all sample run over the 4 rapid lanes	Illumina HiSeq 1500	age;;12.5 dpc|source_name;;Enriched Interstitial cells|strain;;Sf1-eGFP|tissue;;gonad	GEO Accession;;GSM1598868		GSM1598868	Interstitial repB	2802649202	13874501	2015-05-21 16:54:12	1690349186	2802649202	13874501	2	13874501	index:0,count:13874501,average:101,stdev:0|index:1,count:13874501,average:101,stdev:0	GSM1598868_r4	GEO			in_mesa	25855264	9.98	2.93	0.14	2114642920	2059721663	1976596067	1935320543	97.4	97.91	12556646	12219193	178.759	373.529	139	151036	64.75	69.34	14060744	8130117	14060744	8130117	66.5	66.32	14060744	8349817	14060744	7775772	576748595	27.27	0.27	0	6.00	0	0.27	0	0.22	0	0.00	0	9.00	0	12556646	0	202	0	200.48	0	2.40	0	0.02	0	2.98	0	0.02	0	174.64	0	0.28	0	37787	0	13874501	0	832248	0	37740	0	31217	0	0	0	1248898	0	2464	0	0	0	28672	0	3273730	0	11963	0	3316829	0	84.50	0	11724398	0	176776	3229666	18.269821695253	13874501.0	12556646.0	37787.0	832248.0	37740.0	31217.0	0.0	1248898.0	11724398.0	90.5	0.3	6.0	0.3	0.2	0.0	9.0	84.5	101	101	101.00	38	1401324601	24.3	25.0	24.7	26.0	0.0	37.1	28.8	bulk
934277	SRR1783830	SRP053038	SRS833782	SRX862826	SRA236037	GEO		Purification and transcriptomic analysis of mouse fetal Leydig cells reveals candidate genes for disorders of sex development	To examine the transcriptome of early testicular somatic cells during gonadogenesis at 12.5dpc RNA sequencing (RNA-Seq) was performed on murine primary testicular cell lineages isolated from the Sf1-eGFP line by FACS. The three main somatic cell lineages of the testis were isolated: the Sertoli cells which direct male development; the fetal Leydig cells (FLCs) that produce steroid hormones and virilise the XY individual and a heterogenous population of interstitial cells, some of which give rise to the adult Leydig cells (ALCs). This dataset provides a platform for exploring the biology of FLCs and understanding the role of these cells in testicular development and masculinization of the embryo, and a basis for targeted studies designed to identify causes of idiopathic XY DSD. Overall design: RNA-Seq of 3 enriched cell populations from 12.5dpc mouse gonad (Sertoli cells, Leydig cells and Interstitial cells isolated by FACS-sorting) on an Illumina HiSeq 1500, in triplicate.		GSM1598869: Interstitial repC; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted (Micro RNeasy kit without carrier RNA, Qiagen) from CD31-treated FACS-sorted cells. Each sample represented approximately 10 sorting experiments conducted on different days with 4-10 litters of Sf1-eGFP embryos in each experiment. We prepared sample A, sample B and Sample A+B (a mix of samples A and B), with 100ng of total RNA in each sample. Libraries were prepared using TruSeq Stranded Total RNA Libraries  (Illumina protocol 15031048 Rev C, Sep 2012), with multiplexing, Ribosomal depletion,with all sample run over the 4 rapid lanes	Illumina HiSeq 1500	age;;12.5 dpc|source_name;;Enriched Interstitial cells|strain;;Sf1-eGFP|tissue;;gonad	GEO Accession;;GSM1598869		GSM1598869	Interstitial repC	3143031322	15559561	2015-05-21 16:54:12	1883869300	3143031322	15559561	2	15559561	index:0,count:15559561,average:101,stdev:0|index:1,count:15559561,average:101,stdev:0	GSM1598869_r1	GEO			in_mesa	25855264	10.3	3.15	0.14	2535037340	2492422355	2358170548	2331191378	98.32	98.86	14933556	14542005	180.036	377.687	139	170863	64.45	69.32	16768338	9624329	16768338	9624329	66.76	66.51	16768338	9969207	16768338	9234229	715801781	28.24	0.19	0	6.75	0	0.29	0	0.25	0	0.00	0	3.48	0	14933556	0	202	0	200.85	0	2.26	0	0.01	0	1.95	0	0.01	0	231.46	0	0.21	0	29612	0	15559561	0	1049653	0	45875	0	39403	0	0	0	540727	0	2938	0	0	0	34955	0	3804656	0	13317	0	3855866	0	89.23	0	13883903	0	182644	3782311	20.708651803508	15559561.0	14933556.0	29612.0	1049653.0	45875.0	39403.0	0.0	540727.0	13883903.0	96.0	0.2	6.7	0.3	0.3	0.0	3.5	89.2	101	101	101.00	38	1571515661	25.9	23.7	22.8	27.5	0.0	37.3	28.9	bulk
934285	SRR1783831	SRP053038	SRS833782	SRX862826	SRA236037	GEO		Purification and transcriptomic analysis of mouse fetal Leydig cells reveals candidate genes for disorders of sex development	To examine the transcriptome of early testicular somatic cells during gonadogenesis at 12.5dpc RNA sequencing (RNA-Seq) was performed on murine primary testicular cell lineages isolated from the Sf1-eGFP line by FACS. The three main somatic cell lineages of the testis were isolated: the Sertoli cells which direct male development; the fetal Leydig cells (FLCs) that produce steroid hormones and virilise the XY individual and a heterogenous population of interstitial cells, some of which give rise to the adult Leydig cells (ALCs). This dataset provides a platform for exploring the biology of FLCs and understanding the role of these cells in testicular development and masculinization of the embryo, and a basis for targeted studies designed to identify causes of idiopathic XY DSD. Overall design: RNA-Seq of 3 enriched cell populations from 12.5dpc mouse gonad (Sertoli cells, Leydig cells and Interstitial cells isolated by FACS-sorting) on an Illumina HiSeq 1500, in triplicate.		GSM1598869: Interstitial repC; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted (Micro RNeasy kit without carrier RNA, Qiagen) from CD31-treated FACS-sorted cells. Each sample represented approximately 10 sorting experiments conducted on different days with 4-10 litters of Sf1-eGFP embryos in each experiment. We prepared sample A, sample B and Sample A+B (a mix of samples A and B), with 100ng of total RNA in each sample. Libraries were prepared using TruSeq Stranded Total RNA Libraries  (Illumina protocol 15031048 Rev C, Sep 2012), with multiplexing, Ribosomal depletion,with all sample run over the 4 rapid lanes	Illumina HiSeq 1500	age;;12.5 dpc|source_name;;Enriched Interstitial cells|strain;;Sf1-eGFP|tissue;;gonad	GEO Accession;;GSM1598869		GSM1598869	Interstitial repC	3129879910	15494455	2015-05-21 16:54:12	1881033768	3129879910	15494455	2	15494455	index:0,count:15494455,average:101,stdev:0|index:1,count:15494455,average:101,stdev:0	GSM1598869_r2	GEO			in_mesa	25855264	10.26	3.15	0.14	2524803279	2482531522	2348674105	2321986626	98.33	98.86	14868468	14478630	180.136	376.943	139	170683	64.43	69.3	16696696	9579019	16696696	9579019	66.73	66.48	16696696	9922144	16696696	9189536	713714045	28.27	0.19	0	6.74	0	0.29	0	0.25	0	0.00	0	3.50	0	14868468	0	202	0	200.86	0	2.26	0	0.01	0	1.96	0	0.01	0	193.01	0	0.21	0	29472	0	15494455	0	1045097	0	45372	0	38800	0	0	0	541815	0	2840	0	0	0	34413	0	3787492	0	13231	0	3837976	0	89.21	0	13823371	0	182379	3771720	20.680670471929	15494455.0	14868468.0	29472.0	1045097.0	45372.0	38800.0	0.0	541815.0	13823371.0	96.0	0.2	6.7	0.3	0.3	0.0	3.5	89.2	101	101	101.00	38	1564939955	25.9	23.7	22.8	27.5	0.0	37.3	29.0	bulk
934292	SRR1783832	SRP053038	SRS833782	SRX862826	SRA236037	GEO		Purification and transcriptomic analysis of mouse fetal Leydig cells reveals candidate genes for disorders of sex development	To examine the transcriptome of early testicular somatic cells during gonadogenesis at 12.5dpc RNA sequencing (RNA-Seq) was performed on murine primary testicular cell lineages isolated from the Sf1-eGFP line by FACS. The three main somatic cell lineages of the testis were isolated: the Sertoli cells which direct male development; the fetal Leydig cells (FLCs) that produce steroid hormones and virilise the XY individual and a heterogenous population of interstitial cells, some of which give rise to the adult Leydig cells (ALCs). This dataset provides a platform for exploring the biology of FLCs and understanding the role of these cells in testicular development and masculinization of the embryo, and a basis for targeted studies designed to identify causes of idiopathic XY DSD. Overall design: RNA-Seq of 3 enriched cell populations from 12.5dpc mouse gonad (Sertoli cells, Leydig cells and Interstitial cells isolated by FACS-sorting) on an Illumina HiSeq 1500, in triplicate.		GSM1598869: Interstitial repC; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted (Micro RNeasy kit without carrier RNA, Qiagen) from CD31-treated FACS-sorted cells. Each sample represented approximately 10 sorting experiments conducted on different days with 4-10 litters of Sf1-eGFP embryos in each experiment. We prepared sample A, sample B and Sample A+B (a mix of samples A and B), with 100ng of total RNA in each sample. Libraries were prepared using TruSeq Stranded Total RNA Libraries  (Illumina protocol 15031048 Rev C, Sep 2012), with multiplexing, Ribosomal depletion,with all sample run over the 4 rapid lanes	Illumina HiSeq 1500	age;;12.5 dpc|source_name;;Enriched Interstitial cells|strain;;Sf1-eGFP|tissue;;gonad	GEO Accession;;GSM1598869		GSM1598869	Interstitial repC	3081962682	15257241	2015-05-21 16:54:12	1836704695	3081962682	15257241	2	15257241	index:0,count:15257241,average:101,stdev:0|index:1,count:15257241,average:101,stdev:0	GSM1598869_r3	GEO			in_mesa	25855264	10.25	3.14	0.15	2496558770	2454421031	2322253613	2295567578	98.31	98.85	14698833	14312934	180.139	376.699	139	167910	64.38	69.25	16507869	9463075	16507869	9463075	66.7	66.45	16507869	9804256	16507869	9079944	706793414	28.31	0.19	0	6.78	0	0.29	0	0.25	0	0.00	0	3.11	0	14698833	0	202	0	200.92	0	2.24	0	0.01	0	1.95	0	0.01	0	203.43	0	0.21	0	29409	0	15257241	0	1034035	0	44949	0	38305	0	0	0	475154	0	2822	0	0	0	33504	0	3746729	0	13261	0	3796316	0	89.56	0	13664798	0	181843	3730202	20.513310933058	15257241.0	14698833.0	29409.0	1034035.0	44949.0	38305.0	0.0	475154.0	13664798.0	96.3	0.2	6.8	0.3	0.3	0.0	3.1	89.6	101	101	101.00	38	1540981341	25.9	23.7	22.8	27.5	0.0	37.3	29.3	bulk
1909594	SRR1787235	SRP053189	SRS836616	SRX865245	SRA236340	GEO		RNA-seq analysis of neonatal mouse cochlear hair cells	This study examined transcripts that are enriched in neonatal mouse cochlear hair cells. Hair cells were purified by FACS sorting for GFP fluorescence from the cochleas of transgenic mice in which the endogenous Atoh1 gene was fused with GFP Overall design: Two replicates of GFP+ hair cells were compared with all other cochlear cell types that were GFP-		GSM1602228: Purified Atoh1-GFP+ cells from mouse cochlea_1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted from FACS-purified cells using an RNeasy Plus Micro kit (Qiagen). RNA-seq libraries of FACS purified cells were generated as previously described: Lott SE, Villalta JE, Schroth GP, Luo S, Tonkin LA, Eisen MB (2011) Noncanonical compensation of zygotic X transcription in early Drosophila melanogaster development revealed through single-embryo RNA-seq. PLoS Biol 9:e1000590.	Illumina HiSeq 2000	background strain;;outbred (ICR)|genotype;;Atoh1-GFP Knock-in Mouse (Atoh1tm4.1Hzo)|source_name;;Cochlea GFP+ rep 1|tissue;;P0 Mouse cochlea	GEO Accession;;GSM1602228		GSM1602228	Purified Atoh1-GFP+ cells from mouse cochlea_1	20498923640	101479820	2015-03-05 17:37:14	13623798942	20498923640	101479820	2	101479820	index:0,count:101479820,average:101,stdev:0|index:1,count:101479820,average:101,stdev:0	GSM1602228_r1	GEO			in_mesa	25855195	2.61	3.17	0.14	13805623756	13779849239	12827715081	12857258550	99.81	100.23	95558040	90156103	165.129	553.645	128	1222439	82.1	88.48	107295993	78457445	107295993	78457445	84.68	84.68	107295993	80921068	107295993	75088889	1483398482	10.74	1.00	0	6.79	0	0.25	0	0.10	0	0.00	0	5.48	0	95558040	0	202	0	199.82	0	1.95	0	0.01	0	1.61	0	0.01	0	129.00	0	0.43	0	1018977	0	101479820	0	6885956	0	251636	0	105788	0	0	0	5564356	0	26950	0	0	0	247249	0	40199243	0	74580	0	40548022	0	87.38	0	88672084	0	295411	33277072	112.646692235563	101479820.0	95558040.0	1018977.0	6885956.0	251636.0	105788.0	0.0	5564356.0	88672084.0	94.2	1.0	6.8	0.2	0.1	0.0	5.5	87.4	101	101	101.00	37	10249461820	24.5	25.7	25.1	24.6	0.1	35.0	18.0	bulk
1909610	SRR1787236	SRP053189	SRS836615	SRX865246	SRA236340	GEO		RNA-seq analysis of neonatal mouse cochlear hair cells	This study examined transcripts that are enriched in neonatal mouse cochlear hair cells. Hair cells were purified by FACS sorting for GFP fluorescence from the cochleas of transgenic mice in which the endogenous Atoh1 gene was fused with GFP Overall design: Two replicates of GFP+ hair cells were compared with all other cochlear cell types that were GFP-		GSM1602229: Purified Atoh1-GFP+ cells from mouse cochlea_2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted from FACS-purified cells using an RNeasy Plus Micro kit (Qiagen). RNA-seq libraries of FACS purified cells were generated as previously described: Lott SE, Villalta JE, Schroth GP, Luo S, Tonkin LA, Eisen MB (2011) Noncanonical compensation of zygotic X transcription in early Drosophila melanogaster development revealed through single-embryo RNA-seq. PLoS Biol 9:e1000590.	Illumina HiSeq 2000	background strain;;outbred (ICR)|genotype;;Atoh1-GFP Knock-in Mouse (Atoh1tm4.1Hzo)|source_name;;Cochlea GFP+ rep 2|tissue;;P0 Mouse cochlea	GEO Accession;;GSM1602229		GSM1602229	Purified Atoh1-GFP+ cells from mouse cochlea_2	37936648178	187805189	2015-03-05 17:37:14	26764489627	37936648178	187805189	2	187805189	index:0,count:187805189,average:101,stdev:0|index:1,count:187805189,average:101,stdev:0	GSM1602229_r1	GEO			in_mesa	25855195	2.44	3.3	0.13	24865235379	24948247880	22416041150	22589458769	100.33	100.77	175866366	166268704	162.086	566.885	124	2463539	84.25	93.62	206667410	148172578	206667410	148172578	89.04	89.26	206667410	156593307	206667410	141277142	1419076911	5.71	1.65	0	9.37	0	0.29	0	0.06	0	0.00	0	6.01	0	175866366	0	202	0	199.60	0	1.95	0	0.01	0	1.61	0	0.00	0	223.36	0	0.45	0	3102490	0	187805189	0	17594280	0	544778	0	112381	0	0	0	11281664	0	55765	0	0	0	443651	0	75622328	0	123690	0	76245434	0	84.27	0	158272086	0	310228	63163809	203.604474773392	187805189.0	175866366.0	3102490.0	17594280.0	544778.0	112381.0	0.0	11281664.0	158272086.0	93.6	1.7	9.4	0.3	0.1	0.0	6.0	84.3	101	101	101.00	37	18968324089	24.0	25.9	25.6	24.3	0.2	34.4	18.7	bulk
1909627	SRR1787237	SRP053189	SRS836617	SRX865247	SRA236340	GEO		RNA-seq analysis of neonatal mouse cochlear hair cells	This study examined transcripts that are enriched in neonatal mouse cochlear hair cells. Hair cells were purified by FACS sorting for GFP fluorescence from the cochleas of transgenic mice in which the endogenous Atoh1 gene was fused with GFP Overall design: Two replicates of GFP+ hair cells were compared with all other cochlear cell types that were GFP-		GSM1602230: Purified Atoh1-GFP- cells from mouse cochlea_1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted from FACS-purified cells using an RNeasy Plus Micro kit (Qiagen). RNA-seq libraries of FACS purified cells were generated as previously described: Lott SE, Villalta JE, Schroth GP, Luo S, Tonkin LA, Eisen MB (2011) Noncanonical compensation of zygotic X transcription in early Drosophila melanogaster development revealed through single-embryo RNA-seq. PLoS Biol 9:e1000590.	Illumina HiSeq 2000	background strain;;outbred (ICR)|genotype;;Atoh1-GFP Knock-in Mouse (Atoh1tm4.1Hzo)|source_name;;Cochlea GFP- rep 1|tissue;;P0 Mouse cochlea	GEO Accession;;GSM1602230		GSM1602230	Purified Atoh1-GFP- cells from mouse cochlea_1	23177072970	114737985	2015-03-05 17:37:14	15837678652	23177072970	114737985	2	114737985	index:0,count:114737985,average:101,stdev:0|index:1,count:114737985,average:101,stdev:0	GSM1602230_r1	GEO			in_mesa	25855195	4.18	2.56	0.04	15782641235	15700579179	14594342489	14582096125	99.48	99.92	107954133	100934088	166.997	585.254	128	1290753	87.24	94.45	120678809	94183666	120678809	94183666	90.31	90.63	120678809	97496025	120678809	90371068	642244592	4.07	0.97	0	7.18	0	0.25	0	0.07	0	0.00	0	5.59	0	107954133	0	202	0	199.69	0	1.95	0	0.01	0	1.65	0	0.01	0	141.12	0	0.48	0	1107367	0	114737985	0	8234766	0	291763	0	79488	0	0	0	6412601	0	39136	0	0	0	321461	0	48990469	0	87247	0	49438313	0	86.91	0	99719367	0	295573	40251358	136.180767526127	114737985.0	107954133.0	1107367.0	8234766.0	291763.0	79488.0	0.0	6412601.0	99719367.0	94.1	1.0	7.2	0.3	0.1	0.0	5.6	86.9	101	101	101.00	37	11588536485	24.5	25.7	25.1	24.7	0.1	34.5	17.4	bulk
1909642	SRR1787238	SRP053189	SRS836614	SRX865248	SRA236340	GEO		RNA-seq analysis of neonatal mouse cochlear hair cells	This study examined transcripts that are enriched in neonatal mouse cochlear hair cells. Hair cells were purified by FACS sorting for GFP fluorescence from the cochleas of transgenic mice in which the endogenous Atoh1 gene was fused with GFP Overall design: Two replicates of GFP+ hair cells were compared with all other cochlear cell types that were GFP-		GSM1602231: Purified Atoh1-GFP- cells from mouse cochlea_2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted from FACS-purified cells using an RNeasy Plus Micro kit (Qiagen). RNA-seq libraries of FACS purified cells were generated as previously described: Lott SE, Villalta JE, Schroth GP, Luo S, Tonkin LA, Eisen MB (2011) Noncanonical compensation of zygotic X transcription in early Drosophila melanogaster development revealed through single-embryo RNA-seq. PLoS Biol 9:e1000590.	Illumina HiSeq 2000	background strain;;outbred (ICR)|genotype;;Atoh1-GFP Knock-in Mouse (Atoh1tm4.1Hzo)|source_name;;Cochlea GFP- rep 2|tissue;;P0 Mouse cochlea	GEO Accession;;GSM1602231		GSM1602231	Purified Atoh1-GFP- cells from mouse cochlea_2	19979331362	98907581	2015-03-05 17:37:14	13306184980	19979331362	98907581	2	98907581	index:0,count:98907581,average:101,stdev:0|index:1,count:98907581,average:101,stdev:0	GSM1602231_r1	GEO			in_mesa	25855195	3.14	2.54	0.03	13025785928	12997204235	12075222843	12092915287	99.78	100.15	93785822	86671708	161.617	679.705	122	1224333	88.04	95.08	104962626	82570918	104962626	82570918	90.79	91.14	104962626	85151194	104962626	79155131	473814893	3.64	1.29	0	7.02	0	0.28	0	0.07	0	0.00	0	4.83	0	93785822	0	202	0	199.52	0	1.92	0	0.01	0	1.68	0	0.00	0	121.52	0	0.42	0	1279502	0	98907581	0	6938895	0	281547	0	67507	0	0	0	4772705	0	36001	0	0	0	304514	0	46491548	0	76227	0	46908290	0	87.81	0	86846927	0	276067	36330151	131.599035741324	98907581.0	93785822.0	1279502.0	6938895.0	281547.0	67507.0	0.0	4772705.0	86846927.0	94.8	1.3	7.0	0.3	0.1	0.0	4.8	87.8	101	101	101.00	37	9989665681	23.9	26.1	25.7	24.2	0.1	35.0	17.9	bulk
1639294	SRR1810037	SRP055125	SRS849135	SRX882877	SRA243151	GEO		Functional characterization of DNA methylation in the oligodendrocyte lineage [RNASeq_development]	Myelination in the CNS is modulated by interplay between transcription factors and recruitment of chromatin modifying enzymes. Using a network built from genome-wide DNA methylation and transcriptomic profiling of sorted oligodendrocyte lineage cells that integrates oligodendrocyte-specific ChIP-Seq data, we defined a crucial role of DNA methylation in coordinating the transition between progenitor cell cycle arrest and oligodendrocyte differentiation. We further identified DNA methyltransferase 1 (DNMT1) as key regulator of oligodendrocyte survival at this transition point, as we detected severe and extensive developmental hypomyelination only in Olig1cre/+;Dnmt1flox/flox but not in Olig1cre/+;Dnmt3aflox/flox mice  or in Cnpcre/+;Dnmt1flox/flox. This phenotype was characterized by decreased expression of genes regulating myelination and lipid metabolism – despite the hypomethylation observed at these genetic loci  – and upregulation of cell cycle and DNA-damage pathways. Therefore DNMT1 is a nodal point regulating proliferation, survival, and differentiation in the oligodendrocyte lineage, and is critical for cell number regulation in the developing brain. Overall design: mRNA profiles of FAC-sorted P2 Pdgfra::GFP and P18 Plp1-GFP purified cell samples from mouse brains were generated by RNA-sequencing, in triplicate, using Illumina HiSeq 2000.		GSM1613116: P2 brain oligodendrocyte progenitor cells_RNASeq_n1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNAs were obtained from FAC-sorted P2 oligodendrocyte progenitor cells or P18 oligodendrocytes, isolated from mouse brains. We used AllPrep DNA/RNA Mini Kit (Qiagen), with on-column DNase treatment during the RNA isolation, in accordance with the manufacturer’s protocol, to isolate DNA and RNA simultaneously from the same cell pellet. RNA purity was assessed by measuring the A260/A280 ratio using a NanoDrop, and RNA quality checked using an Agilent 2100 Bioanalyzer (Agilent Technologies). RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2000	cell type;;Primary FAC-sorted Pdgfra::GFP+ cells|development stage;;Post-natal day 2|source_name;;Brain|strain;;C57BL/6|tissue;;brain	GEO Accession;;GSM1613116		GSM1613116	P2 brain oligodendrocyte progenitor cells_RNASeq_n1	7282074576	71392888	2016-04-14 16:08:06	4724891521	7282074576	71392888	2	71392888	index:0,count:71392888,average:51,stdev:0|index:1,count:71392888,average:51,stdev:0	GSM1613116_r1	GEO					4.55	3.66	0.04	6926036151	6897621373	6166153006	6202323658	99.59	100.59	68641621	59720800	204.250	1055.275	136	642441	85.08	95.52	81465882	58403605	81465882	58403605	91.2	92.08	81465882	62597856	81465882	56295485	241975120	3.49	0.85	0	10.51	0	0.33	0	0.08	0	0.00	0	3.44	0	68641621	0	102	0	100.96	0	1.92	0	0.00	0	1.23	0	0.01	0	353.04	0	0.27	0	609719	0	71392888	0	7501690	0	236512	0	58551	0	0	0	2456204	0	9115	0	0	0	58598	0	10040859	0	19684	0	10128256	0	85.64	0	61139931	0	157037	10457766	66.594280328840	71392888.0	68641621.0	609719.0	7501690.0	236512.0	58551.0	0.0	2456204.0	61139931.0	96.1	0.9	10.5	0.3	0.1	0.0	3.4	85.6	51	51	51.00	38	3641037288	24.8	25.1	25.2	24.8	0.0	36.7	18.1	bulk
1639309	SRR1810038	SRP055125	SRS849134	SRX882878	SRA243151	GEO		Functional characterization of DNA methylation in the oligodendrocyte lineage [RNASeq_development]	Myelination in the CNS is modulated by interplay between transcription factors and recruitment of chromatin modifying enzymes. Using a network built from genome-wide DNA methylation and transcriptomic profiling of sorted oligodendrocyte lineage cells that integrates oligodendrocyte-specific ChIP-Seq data, we defined a crucial role of DNA methylation in coordinating the transition between progenitor cell cycle arrest and oligodendrocyte differentiation. We further identified DNA methyltransferase 1 (DNMT1) as key regulator of oligodendrocyte survival at this transition point, as we detected severe and extensive developmental hypomyelination only in Olig1cre/+;Dnmt1flox/flox but not in Olig1cre/+;Dnmt3aflox/flox mice  or in Cnpcre/+;Dnmt1flox/flox. This phenotype was characterized by decreased expression of genes regulating myelination and lipid metabolism – despite the hypomethylation observed at these genetic loci  – and upregulation of cell cycle and DNA-damage pathways. Therefore DNMT1 is a nodal point regulating proliferation, survival, and differentiation in the oligodendrocyte lineage, and is critical for cell number regulation in the developing brain. Overall design: mRNA profiles of FAC-sorted P2 Pdgfra::GFP and P18 Plp1-GFP purified cell samples from mouse brains were generated by RNA-sequencing, in triplicate, using Illumina HiSeq 2000.		GSM1613117: P2 brain oligodendrocyte progenitor cells_RNASeq_n2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNAs were obtained from FAC-sorted P2 oligodendrocyte progenitor cells or P18 oligodendrocytes, isolated from mouse brains. We used AllPrep DNA/RNA Mini Kit (Qiagen), with on-column DNase treatment during the RNA isolation, in accordance with the manufacturer’s protocol, to isolate DNA and RNA simultaneously from the same cell pellet. RNA purity was assessed by measuring the A260/A280 ratio using a NanoDrop, and RNA quality checked using an Agilent 2100 Bioanalyzer (Agilent Technologies). RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2000	cell type;;Primary FAC-sorted Pdgfra::GFP+ cells|development stage;;Post-natal day 2|source_name;;Brain|strain;;C57BL/6|tissue;;brain	GEO Accession;;GSM1613117		GSM1613117	P2 brain oligodendrocyte progenitor cells_RNASeq_n2	7472452170	73259335	2016-04-14 16:08:06	4845113130	7472452170	73259335	2	73259335	index:0,count:73259335,average:51,stdev:0|index:1,count:73259335,average:51,stdev:0	GSM1613117_r1	GEO					2.98	3.73	0.05	7108010133	7098230024	6447335095	6494485571	99.86	100.73	70473154	59700549	212.073	1296.120	136	605372	87.17	96.07	81983984	61432997	81983984	61432997	91.77	92.68	81983984	64676578	81983984	59265428	216558892	3.05	0.91	0	8.91	0	0.32	0	0.09	0	0.00	0	3.40	0	70473154	0	102	0	100.93	0	1.98	0	0.00	0	1.21	0	0.01	0	364.78	0	0.26	0	665318	0	73259335	0	6524571	0	233461	0	63894	0	0	0	2488826	0	9755	0	0	0	68519	0	11197476	0	21117	0	11296867	0	87.29	0	63948583	0	181599	11610044	63.932312402601	73259335.0	70473154.0	665318.0	6524571.0	233461.0	63894.0	0.0	2488826.0	63948583.0	96.2	0.9	8.9	0.3	0.1	0.0	3.4	87.3	51	51	51.00	38	3736226085	24.7	25.3	25.3	24.8	0.0	36.7	18.3	bulk
1639326	SRR1810039	SRP055125	SRS849133	SRX882879	SRA243151	GEO		Functional characterization of DNA methylation in the oligodendrocyte lineage [RNASeq_development]	Myelination in the CNS is modulated by interplay between transcription factors and recruitment of chromatin modifying enzymes. Using a network built from genome-wide DNA methylation and transcriptomic profiling of sorted oligodendrocyte lineage cells that integrates oligodendrocyte-specific ChIP-Seq data, we defined a crucial role of DNA methylation in coordinating the transition between progenitor cell cycle arrest and oligodendrocyte differentiation. We further identified DNA methyltransferase 1 (DNMT1) as key regulator of oligodendrocyte survival at this transition point, as we detected severe and extensive developmental hypomyelination only in Olig1cre/+;Dnmt1flox/flox but not in Olig1cre/+;Dnmt3aflox/flox mice  or in Cnpcre/+;Dnmt1flox/flox. This phenotype was characterized by decreased expression of genes regulating myelination and lipid metabolism – despite the hypomethylation observed at these genetic loci  – and upregulation of cell cycle and DNA-damage pathways. Therefore DNMT1 is a nodal point regulating proliferation, survival, and differentiation in the oligodendrocyte lineage, and is critical for cell number regulation in the developing brain. Overall design: mRNA profiles of FAC-sorted P2 Pdgfra::GFP and P18 Plp1-GFP purified cell samples from mouse brains were generated by RNA-sequencing, in triplicate, using Illumina HiSeq 2000.		GSM1613118: P2 brain oligodendrocyte progenitor cells_RNASeq_n3; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNAs were obtained from FAC-sorted P2 oligodendrocyte progenitor cells or P18 oligodendrocytes, isolated from mouse brains. We used AllPrep DNA/RNA Mini Kit (Qiagen), with on-column DNase treatment during the RNA isolation, in accordance with the manufacturer’s protocol, to isolate DNA and RNA simultaneously from the same cell pellet. RNA purity was assessed by measuring the A260/A280 ratio using a NanoDrop, and RNA quality checked using an Agilent 2100 Bioanalyzer (Agilent Technologies). RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2000	cell type;;Primary FAC-sorted Pdgfra::GFP+ cells|development stage;;Post-natal day 2|source_name;;Brain|strain;;C57BL/6|tissue;;brain	GEO Accession;;GSM1613118		GSM1613118	P2 brain oligodendrocyte progenitor cells_RNASeq_n3	7508823024	73615912	2016-04-14 16:08:06	4880756641	7508823024	73615912	2	73615912	index:0,count:73615912,average:51,stdev:0|index:1,count:73615912,average:51,stdev:0	GSM1613118_r1	GEO					3.75	3.76	0.04	7180387520	7161578703	6510427508	6549196421	99.74	100.6	71176169	60468673	209.186	1249.210	146	625400	85.93	94.73	82533318	61158462	82533318	61158462	90.63	91.39	82533318	64509864	82533318	59002751	314438985	4.38	0.73	0	8.99	0	0.30	0	0.09	0	0.00	0	2.92	0	71176169	0	102	0	100.94	0	1.96	0	0.00	0	1.21	0	0.01	0	473.25	0	0.27	0	538219	0	73615912	0	6614426	0	220641	0	67948	0	0	0	2151154	0	9382	0	0	0	68902	0	11374122	0	20659	0	11473065	0	87.70	0	64561743	0	179600	11794900	65.673162583519	73615912.0	71176169.0	538219.0	6614426.0	220641.0	67948.0	0.0	2151154.0	64561743.0	96.7	0.7	9.0	0.3	0.1	0.0	2.9	87.7	51	51	51.00	38	3754411512	25.0	25.0	25.0	25.0	0.0	36.7	18.4	bulk
1639437	SRR1810040	SRP055125	SRS849132	SRX882880	SRA243151	GEO		Functional characterization of DNA methylation in the oligodendrocyte lineage [RNASeq_development]	Myelination in the CNS is modulated by interplay between transcription factors and recruitment of chromatin modifying enzymes. Using a network built from genome-wide DNA methylation and transcriptomic profiling of sorted oligodendrocyte lineage cells that integrates oligodendrocyte-specific ChIP-Seq data, we defined a crucial role of DNA methylation in coordinating the transition between progenitor cell cycle arrest and oligodendrocyte differentiation. We further identified DNA methyltransferase 1 (DNMT1) as key regulator of oligodendrocyte survival at this transition point, as we detected severe and extensive developmental hypomyelination only in Olig1cre/+;Dnmt1flox/flox but not in Olig1cre/+;Dnmt3aflox/flox mice  or in Cnpcre/+;Dnmt1flox/flox. This phenotype was characterized by decreased expression of genes regulating myelination and lipid metabolism – despite the hypomethylation observed at these genetic loci  – and upregulation of cell cycle and DNA-damage pathways. Therefore DNMT1 is a nodal point regulating proliferation, survival, and differentiation in the oligodendrocyte lineage, and is critical for cell number regulation in the developing brain. Overall design: mRNA profiles of FAC-sorted P2 Pdgfra::GFP and P18 Plp1-GFP purified cell samples from mouse brains were generated by RNA-sequencing, in triplicate, using Illumina HiSeq 2000.		GSM1613119: P18 brain oligodendrocytes_RNASeq_n1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNAs were obtained from FAC-sorted P2 oligodendrocyte progenitor cells or P18 oligodendrocytes, isolated from mouse brains. We used AllPrep DNA/RNA Mini Kit (Qiagen), with on-column DNase treatment during the RNA isolation, in accordance with the manufacturer’s protocol, to isolate DNA and RNA simultaneously from the same cell pellet. RNA purity was assessed by measuring the A260/A280 ratio using a NanoDrop, and RNA quality checked using an Agilent 2100 Bioanalyzer (Agilent Technologies). RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2000	cell type;;Primary FAC-sorted Plp1-GFP+ cells|development stage;;Post-natal day 18|source_name;;Brain|strain;;C57BL/6|tissue;;brain	GEO Accession;;GSM1613119		GSM1613119	P18 brain oligodendrocytes_RNASeq_n1	9326751276	91438738	2016-04-14 16:08:06	6040493701	9326751276	91438738	2	91438738	index:0,count:91438738,average:51,stdev:0|index:1,count:91438738,average:51,stdev:0	GSM1613119_r1	GEO					2.64	11.97	0.02	8806852135	8778774318	8320888320	8351973967	99.68	100.37	87363743	72903257	211.000	1291.696	136	742690	90.45	95.71	95158364	79017614	95158364	79017614	92.28	93.15	95158364	80621158	95158364	76903030	297650948	3.38	0.94	0	5.26	0	0.25	0	0.17	0	0.00	0	4.04	0	87363743	0	102	0	100.93	0	1.92	0	0.00	0	1.38	0	0.01	0	552.31	0	0.29	0	860704	0	91438738	0	4805794	0	227236	0	152625	0	0	0	3695134	0	8915	0	0	0	78402	0	14285809	0	24315	0	14397441	0	90.29	0	82557949	0	171284	14640655	85.475905513650	91438738.0	87363743.0	860704.0	4805794.0	227236.0	152625.0	0.0	3695134.0	82557949.0	95.5	0.9	5.3	0.2	0.2	0.0	4.0	90.3	51	51	51.00	38	4663375638	24.9	25.0	25.0	25.0	0.0	36.7	18.3	bulk
1639452	SRR1810041	SRP055125	SRS849144	SRX882881	SRA243151	GEO		Functional characterization of DNA methylation in the oligodendrocyte lineage [RNASeq_development]	Myelination in the CNS is modulated by interplay between transcription factors and recruitment of chromatin modifying enzymes. Using a network built from genome-wide DNA methylation and transcriptomic profiling of sorted oligodendrocyte lineage cells that integrates oligodendrocyte-specific ChIP-Seq data, we defined a crucial role of DNA methylation in coordinating the transition between progenitor cell cycle arrest and oligodendrocyte differentiation. We further identified DNA methyltransferase 1 (DNMT1) as key regulator of oligodendrocyte survival at this transition point, as we detected severe and extensive developmental hypomyelination only in Olig1cre/+;Dnmt1flox/flox but not in Olig1cre/+;Dnmt3aflox/flox mice  or in Cnpcre/+;Dnmt1flox/flox. This phenotype was characterized by decreased expression of genes regulating myelination and lipid metabolism – despite the hypomethylation observed at these genetic loci  – and upregulation of cell cycle and DNA-damage pathways. Therefore DNMT1 is a nodal point regulating proliferation, survival, and differentiation in the oligodendrocyte lineage, and is critical for cell number regulation in the developing brain. Overall design: mRNA profiles of FAC-sorted P2 Pdgfra::GFP and P18 Plp1-GFP purified cell samples from mouse brains were generated by RNA-sequencing, in triplicate, using Illumina HiSeq 2000.		GSM1613120: P18 brain oligodendrocytes_RNASeq_n2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNAs were obtained from FAC-sorted P2 oligodendrocyte progenitor cells or P18 oligodendrocytes, isolated from mouse brains. We used AllPrep DNA/RNA Mini Kit (Qiagen), with on-column DNase treatment during the RNA isolation, in accordance with the manufacturer’s protocol, to isolate DNA and RNA simultaneously from the same cell pellet. RNA purity was assessed by measuring the A260/A280 ratio using a NanoDrop, and RNA quality checked using an Agilent 2100 Bioanalyzer (Agilent Technologies). RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2000	cell type;;Primary FAC-sorted Plp1-GFP+ cells|development stage;;Post-natal day 18|source_name;;Brain|strain;;C57BL/6|tissue;;brain	GEO Accession;;GSM1613120		GSM1613120	P18 brain oligodendrocytes_RNASeq_n2	7276211106	71335403	2016-04-14 16:08:06	4710155288	7276211106	71335403	2	71335403	index:0,count:71335403,average:51,stdev:0|index:1,count:71335403,average:51,stdev:0	GSM1613120_r1	GEO					9.56	6.03	0.01	6823663787	6713026185	5889251066	5871658017	98.38	99.7	67689975	58212573	204.964	1017.705	136	619371	82.97	96.06	81281892	56162035	81281892	56162035	91.96	93.3	81281892	62249676	81281892	54544545	177722303	2.60	0.98	0	12.93	0	0.22	0	0.13	0	0.00	0	4.76	0	67689975	0	102	0	100.84	0	1.83	0	0.00	0	1.62	0	0.01	0	393.27	0	0.34	0	697344	0	71335403	0	9225737	0	158543	0	91361	0	0	0	3395524	0	7586	0	0	0	44255	0	9836978	0	17689	0	9906508	0	81.96	0	58464238	0	120076	10242299	85.298469302775	71335403.0	67689975.0	697344.0	9225737.0	158543.0	91361.0	0.0	3395524.0	58464238.0	94.9	1.0	12.9	0.2	0.1	0.0	4.8	82.0	51	51	51.00	38	3638105553	25.0	24.8	25.0	25.2	0.0	36.8	18.3	bulk
1639468	SRR1810042	SRP055125	SRS849145	SRX882882	SRA243151	GEO		Functional characterization of DNA methylation in the oligodendrocyte lineage [RNASeq_development]	Myelination in the CNS is modulated by interplay between transcription factors and recruitment of chromatin modifying enzymes. Using a network built from genome-wide DNA methylation and transcriptomic profiling of sorted oligodendrocyte lineage cells that integrates oligodendrocyte-specific ChIP-Seq data, we defined a crucial role of DNA methylation in coordinating the transition between progenitor cell cycle arrest and oligodendrocyte differentiation. We further identified DNA methyltransferase 1 (DNMT1) as key regulator of oligodendrocyte survival at this transition point, as we detected severe and extensive developmental hypomyelination only in Olig1cre/+;Dnmt1flox/flox but not in Olig1cre/+;Dnmt3aflox/flox mice  or in Cnpcre/+;Dnmt1flox/flox. This phenotype was characterized by decreased expression of genes regulating myelination and lipid metabolism – despite the hypomethylation observed at these genetic loci  – and upregulation of cell cycle and DNA-damage pathways. Therefore DNMT1 is a nodal point regulating proliferation, survival, and differentiation in the oligodendrocyte lineage, and is critical for cell number regulation in the developing brain. Overall design: mRNA profiles of FAC-sorted P2 Pdgfra::GFP and P18 Plp1-GFP purified cell samples from mouse brains were generated by RNA-sequencing, in triplicate, using Illumina HiSeq 2000.		GSM1613121: P18 brain oligodendrocytes_RNASeq_n3; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNAs were obtained from FAC-sorted P2 oligodendrocyte progenitor cells or P18 oligodendrocytes, isolated from mouse brains. We used AllPrep DNA/RNA Mini Kit (Qiagen), with on-column DNase treatment during the RNA isolation, in accordance with the manufacturer’s protocol, to isolate DNA and RNA simultaneously from the same cell pellet. RNA purity was assessed by measuring the A260/A280 ratio using a NanoDrop, and RNA quality checked using an Agilent 2100 Bioanalyzer (Agilent Technologies). RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2000	cell type;;Primary FAC-sorted Plp1-GFP+ cells|development stage;;Post-natal day 18|source_name;;Brain|strain;;C57BL/6|tissue;;brain	GEO Accession;;GSM1613121		GSM1613121	P18 brain oligodendrocytes_RNASeq_n3	8128395504	79690152	2016-04-14 16:08:06	5280354308	8128395504	79690152	2	79690152	index:0,count:79690152,average:51,stdev:0|index:1,count:79690152,average:51,stdev:0	GSM1613121_r1	GEO					9.34	6.76	0.01	7641352544	7569640616	6695860806	6712149476	99.06	100.24	75788309	63963094	211.558	1149.072	145	652501	84.87	96.79	89249239	64322413	89249239	64322413	93.0	94.05	89249239	70486463	89249239	62502498	166569161	2.18	0.92	0	11.71	0	0.27	0	0.13	0	0.00	0	4.50	0	75788309	0	102	0	100.85	0	1.93	0	0.00	0	1.54	0	0.01	0	387.16	0	0.33	0	733940	0	79690152	0	9331196	0	213386	0	105634	0	0	0	3582823	0	8291	0	0	0	55817	0	11762024	0	19841	0	11845973	0	83.39	0	66457113	0	133380	12199448	91.463847653321	79690152.0	75788309.0	733940.0	9331196.0	213386.0	105634.0	0.0	3582823.0	66457113.0	95.1	0.9	11.7	0.3	0.1	0.0	4.5	83.4	51	51	51.00	38	4064197752	25.0	24.9	25.1	25.1	0.0	36.7	18.2	bulk
1399167	SRR1811597	SRP055201	SRS851170	SRX884159	SRA243458	GEO		The Calcium Channel Subunit Alpha2delta2 Suppresses Axon Regeneration in the Adult CNS	Purpose: Injuries to the adult central nervous system (CNS) often result in permanent disabilities because neurons lose the ability to regenerate their axon during development. Although the developmental transition from a growing to a transmitting phase may represent one of the first steps in the gradual loss of axon growth and regeneration ability, the molecular mechanisms regulating this process has yet to be identified. The main goal of this study was to dissect the molecular mechanisms mediating the decline in axon growth ability and its relationship with regeneration failure in the adult CNS. To this end, we sequenced the whole transcriptome of dorsal root ganglia (DRG) neurons in both growth competent and incompetent states at different developmental stages, in diverse culture and in vivo experimental conditions. Overall design: mRNA profiles of mouse embryonic E12.5 and E17.5 lumbar DRGs, conditioned and sham operated adult L4-5DRGs, and cultured adult lumbar DRG (6, 12, 24 and 36 hr after plating) neurons were generated by deep sequencing, in triplicate, using the Illumina TruSeq RNA Sample Prep Kits V2.		GSM1614845: 24h [347]; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Cells were isolated by cell sorting, lyzed in Qiazol and RNA isolated. Illumina TruSeq RNA Sample Prep Kits V2 was used with 10 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 1500	developmental stage;;adult|source_name;;DRG neuron|time after plating;;24 hrs	GEO Accession;;GSM1614845		GSM1614845	24h [347]	5492145096	34760412	2016-09-18 20:49:05	3895751526	5492145096	34760412	2	34760412	index:0,count:34760412,average:79,stdev:0|index:1,count:34760412,average:79,stdev:0	GSM1614845_r1	GEO			in_mesa	27720483	4.27	3.54	0.04	4186336197	4099284442	3916851836	3861427668	97.92	98.58	31745180	30198825	152.904	499.184	115	417614	82.8	88.57	35003291	26286223	35003291	26286223	85.17	85.6	35003291	27036206	35003291	25404737	375407114	8.97	0.79	0	5.95	0	0.28	0	0.20	0	0.00	0	8.19	0	31745180	0	158	0	156.30	0	1.54	0	0.00	0	1.21	0	0.01	0	199.90	0	0.74	0	276055	0	34760412	0	2068304	0	98523	0	69435	0	0	0	2847274	0	6681	0	0	0	65187	0	9130954	0	16735	0	9219557	0	85.38	0	29676876	0	216465	8512404	39.324620608412	34760412.0	31745180.0	276055.0	2068304.0	98523.0	69435.0	0.0	2847274.0	29676876.0	91.3	0.8	6.0	0.3	0.2	0.0	8.2	85.4	79	79	79.00	38	2746072548	26.8	23.1	22.9	27.0	0.2	30.6	11.6	bulk
1399183	SRR1811598	SRP055201	SRS851168	SRX884160	SRA243458	GEO		The Calcium Channel Subunit Alpha2delta2 Suppresses Axon Regeneration in the Adult CNS	Purpose: Injuries to the adult central nervous system (CNS) often result in permanent disabilities because neurons lose the ability to regenerate their axon during development. Although the developmental transition from a growing to a transmitting phase may represent one of the first steps in the gradual loss of axon growth and regeneration ability, the molecular mechanisms regulating this process has yet to be identified. The main goal of this study was to dissect the molecular mechanisms mediating the decline in axon growth ability and its relationship with regeneration failure in the adult CNS. To this end, we sequenced the whole transcriptome of dorsal root ganglia (DRG) neurons in both growth competent and incompetent states at different developmental stages, in diverse culture and in vivo experimental conditions. Overall design: mRNA profiles of mouse embryonic E12.5 and E17.5 lumbar DRGs, conditioned and sham operated adult L4-5DRGs, and cultured adult lumbar DRG (6, 12, 24 and 36 hr after plating) neurons were generated by deep sequencing, in triplicate, using the Illumina TruSeq RNA Sample Prep Kits V2.		GSM1614846: 36h [348]; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Cells were isolated by cell sorting, lyzed in Qiazol and RNA isolated. Illumina TruSeq RNA Sample Prep Kits V2 was used with 10 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 1500	developmental stage;;adult|source_name;;DRG neuron|time after plating;;36 hrs	GEO Accession;;GSM1614846		GSM1614846	36h [348]	3926217366	24849477	2016-09-18 20:49:05	2821188933	3926217366	24849477	2	24849477	index:0,count:24849477,average:79,stdev:0|index:1,count:24849477,average:79,stdev:0	GSM1614846_r1	GEO			in_mesa	27720483	4.7	3.43	0.04	3152147706	3106396384	2940098879	2914744275	98.55	99.14	23172643	21580339	172.352	614.475	115	243926	83.09	89.18	25643557	19255155	25643557	19255155	85.96	86.24	25643557	19918943	25643557	18621522	283576984	9.00	0.92	0	6.36	0	0.29	0	0.18	0	0.00	0	6.28	0	23172643	0	158	0	156.37	0	1.46	0	0.00	0	1.19	0	0.01	0	229.97	0	0.68	0	227975	0	24849477	0	1580191	0	71711	0	44311	0	0	0	1560812	0	4797	0	0	0	46501	0	6792449	0	12250	0	6855997	0	86.89	0	21592452	0	193508	6454270	33.354021539161	24849477.0	23172643.0	227975.0	1580191.0	71711.0	44311.0	0.0	1560812.0	21592452.0	93.3	0.9	6.4	0.3	0.2	0.0	6.3	86.9	79	79	79.00	38	1963108683	26.3	23.7	23.5	26.3	0.2	31.7	12.6	bulk
1400847	SRR1811600	SRP055201	SRS851166	SRX884162	SRA243458	GEO		The Calcium Channel Subunit Alpha2delta2 Suppresses Axon Regeneration in the Adult CNS	Purpose: Injuries to the adult central nervous system (CNS) often result in permanent disabilities because neurons lose the ability to regenerate their axon during development. Although the developmental transition from a growing to a transmitting phase may represent one of the first steps in the gradual loss of axon growth and regeneration ability, the molecular mechanisms regulating this process has yet to be identified. The main goal of this study was to dissect the molecular mechanisms mediating the decline in axon growth ability and its relationship with regeneration failure in the adult CNS. To this end, we sequenced the whole transcriptome of dorsal root ganglia (DRG) neurons in both growth competent and incompetent states at different developmental stages, in diverse culture and in vivo experimental conditions. Overall design: mRNA profiles of mouse embryonic E12.5 and E17.5 lumbar DRGs, conditioned and sham operated adult L4-5DRGs, and cultured adult lumbar DRG (6, 12, 24 and 36 hr after plating) neurons were generated by deep sequencing, in triplicate, using the Illumina TruSeq RNA Sample Prep Kits V2.		GSM1614848: 36h [350]; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Cells were isolated by cell sorting, lyzed in Qiazol and RNA isolated. Illumina TruSeq RNA Sample Prep Kits V2 was used with 10 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 1500	developmental stage;;adult|source_name;;DRG neuron|time after plating;;36 hrs	GEO Accession;;GSM1614848		GSM1614848	36h [350]	4729573738	29934011	2016-09-18 20:49:05	3373915292	4729573738	29934011	2	29934011	index:0,count:29934011,average:79,stdev:0|index:1,count:29934011,average:79,stdev:0	GSM1614848_r1	GEO			in_mesa	27720483	3.39	3.31	0.05	3635044735	3587749775	3414513445	3388948690	98.7	99.25	27075767	25054604	171.986	688.291	116	276827	84.01	89.54	29796303	22745390	29796303	22745390	85.92	86.31	29796303	23264561	29796303	21925972	308321267	8.48	1.39	0	5.59	0	0.32	0	0.16	0	0.00	0	9.07	0	27075767	0	158	0	156.17	0	1.58	0	0.00	0	1.30	0	0.01	0	226.87	0	0.74	0	414984	0	29934011	0	1673374	0	94772	0	49329	0	0	0	2714143	0	5537	0	0	0	56590	0	8308451	0	15187	0	8385765	0	84.86	0	25402393	0	190753	7806640	40.925385183981	29934011.0	27075767.0	414984.0	1673374.0	94772.0	49329.0	0.0	2714143.0	25402393.0	90.5	1.4	5.6	0.3	0.2	0.0	9.1	84.9	79	79	79.00	38	2364786869	25.6	24.4	24.2	25.6	0.2	30.6	11.6	bulk
1400863	SRR1811601	SRP055201	SRS851165	SRX884163	SRA243458	GEO		The Calcium Channel Subunit Alpha2delta2 Suppresses Axon Regeneration in the Adult CNS	Purpose: Injuries to the adult central nervous system (CNS) often result in permanent disabilities because neurons lose the ability to regenerate their axon during development. Although the developmental transition from a growing to a transmitting phase may represent one of the first steps in the gradual loss of axon growth and regeneration ability, the molecular mechanisms regulating this process has yet to be identified. The main goal of this study was to dissect the molecular mechanisms mediating the decline in axon growth ability and its relationship with regeneration failure in the adult CNS. To this end, we sequenced the whole transcriptome of dorsal root ganglia (DRG) neurons in both growth competent and incompetent states at different developmental stages, in diverse culture and in vivo experimental conditions. Overall design: mRNA profiles of mouse embryonic E12.5 and E17.5 lumbar DRGs, conditioned and sham operated adult L4-5DRGs, and cultured adult lumbar DRG (6, 12, 24 and 36 hr after plating) neurons were generated by deep sequencing, in triplicate, using the Illumina TruSeq RNA Sample Prep Kits V2.		GSM1614849: Peripheral lesion [74]; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Cells were isolated by cell sorting, lyzed in Qiazol and RNA isolated. Illumina TruSeq RNA Sample Prep Kits V2 was used with 10 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 1500	developmental stage;;adult|source_name;;DRG neuron|time after plating;;none	GEO Accession;;GSM1614849		GSM1614849	Peripheral lesion [74]	7622633400	38113167	2016-09-18 20:49:05	5043477437	7622633400	38113167	2	38113167	index:0,count:38113167,average:100,stdev:0|index:1,count:38113167,average:100,stdev:0	GSM1614849_r1	GEO			in_mesa	27720483	3.15	3.29	0.02	5912526156	5884560520	5580099613	5579660402	99.53	99.99	35722735	32754656	200.112	774.503	145	301342	88.11	93.44	38853744	31474642	38853744	31474642	89.74	90.09	38853744	32056484	38853744	30348075	315071197	5.33	0.91	0	5.35	0	0.26	0	0.08	0	0.00	0	5.93	0	35722735	0	200	0	196.31	0	1.56	0	0.00	0	1.29	0	0.01	0	191.63	0	0.78	0	345685	0	38113167	0	2038159	0	97708	0	31622	0	0	0	2261102	0	11440	0	0	0	111951	0	15469934	0	23957	0	15617282	0	88.38	0	33684576	0	235192	14334784	60.949283989251	38113167.0	35722735.0	345685.0	2038159.0	97708.0	31622.0	0.0	2261102.0	33684576.0	93.7	0.9	5.3	0.3	0.1	0.0	5.9	88.4	100	100	100.00	38	3811316700	25.1	24.8	24.8	25.0	0.3	30.7	11.5	bulk
1400879	SRR1811602	SRP055201	SRS851164	SRX884164	SRA243458	GEO		The Calcium Channel Subunit Alpha2delta2 Suppresses Axon Regeneration in the Adult CNS	Purpose: Injuries to the adult central nervous system (CNS) often result in permanent disabilities because neurons lose the ability to regenerate their axon during development. Although the developmental transition from a growing to a transmitting phase may represent one of the first steps in the gradual loss of axon growth and regeneration ability, the molecular mechanisms regulating this process has yet to be identified. The main goal of this study was to dissect the molecular mechanisms mediating the decline in axon growth ability and its relationship with regeneration failure in the adult CNS. To this end, we sequenced the whole transcriptome of dorsal root ganglia (DRG) neurons in both growth competent and incompetent states at different developmental stages, in diverse culture and in vivo experimental conditions. Overall design: mRNA profiles of mouse embryonic E12.5 and E17.5 lumbar DRGs, conditioned and sham operated adult L4-5DRGs, and cultured adult lumbar DRG (6, 12, 24 and 36 hr after plating) neurons were generated by deep sequencing, in triplicate, using the Illumina TruSeq RNA Sample Prep Kits V2.		GSM1614850: Peripheral lesion [75]; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Cells were isolated by cell sorting, lyzed in Qiazol and RNA isolated. Illumina TruSeq RNA Sample Prep Kits V2 was used with 10 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 1500	developmental stage;;adult|source_name;;DRG neuron|time after plating;;none	GEO Accession;;GSM1614850		GSM1614850	Peripheral lesion [75]	7707899200	38539496	2016-09-18 20:49:05	5088634919	7707899200	38539496	2	38539496	index:0,count:38539496,average:100,stdev:0|index:1,count:38539496,average:100,stdev:0	GSM1614850_r1	GEO			in_mesa	27720483	2.94	3.33	0.02	5900902117	5863343400	5586511388	5576935532	99.36	99.83	35497691	32605297	200.513	779.008	155	272076	87.98	93.01	38452917	31231820	38452917	31231820	89.43	89.79	38452917	31747258	38452917	30147540	334555039	5.67	1.59	0	4.98	0	0.24	0	0.09	0	0.00	0	7.56	0	35497691	0	200	0	196.09	0	1.55	0	0.00	0	1.29	0	0.01	0	187.74	0	0.78	0	611967	0	38539496	0	1920355	0	93420	0	33577	0	0	0	2914808	0	11695	0	0	0	110310	0	15146639	0	26483	0	15295127	0	87.12	0	33577336	0	236599	14074789	59.487947962586	38539496.0	35497691.0	611967.0	1920355.0	93420.0	33577.0	0.0	2914808.0	33577336.0	92.1	1.6	5.0	0.2	0.1	0.0	7.6	87.1	100	100	100.00	38	3853949600	25.3	24.7	24.7	25.1	0.3	30.6	11.4	bulk
1400895	SRR1811603	SRP055201	SRS851163	SRX884165	SRA243458	GEO		The Calcium Channel Subunit Alpha2delta2 Suppresses Axon Regeneration in the Adult CNS	Purpose: Injuries to the adult central nervous system (CNS) often result in permanent disabilities because neurons lose the ability to regenerate their axon during development. Although the developmental transition from a growing to a transmitting phase may represent one of the first steps in the gradual loss of axon growth and regeneration ability, the molecular mechanisms regulating this process has yet to be identified. The main goal of this study was to dissect the molecular mechanisms mediating the decline in axon growth ability and its relationship with regeneration failure in the adult CNS. To this end, we sequenced the whole transcriptome of dorsal root ganglia (DRG) neurons in both growth competent and incompetent states at different developmental stages, in diverse culture and in vivo experimental conditions. Overall design: mRNA profiles of mouse embryonic E12.5 and E17.5 lumbar DRGs, conditioned and sham operated adult L4-5DRGs, and cultured adult lumbar DRG (6, 12, 24 and 36 hr after plating) neurons were generated by deep sequencing, in triplicate, using the Illumina TruSeq RNA Sample Prep Kits V2.		GSM1614851: Peripheral lesion [124]; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Cells were isolated by cell sorting, lyzed in Qiazol and RNA isolated. Illumina TruSeq RNA Sample Prep Kits V2 was used with 10 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 1500	developmental stage;;adult|source_name;;DRG neuron|time after plating;;none	GEO Accession;;GSM1614851		GSM1614851	Peripheral lesion [124]	9847717200	49238586	2016-09-18 20:49:05	6488089468	9847717200	49238586	2	49238586	index:0,count:49238586,average:100,stdev:0|index:1,count:49238586,average:100,stdev:0	GSM1614851_r1	GEO			in_mesa	27720483	2.71	3.31	0.02	6899176450	6865807184	6518081222	6517051253	99.52	99.98	44763676	41381168	180.280	734.356	136	408578	88.27	93.54	48786986	39511275	48786986	39511275	89.7	90.11	48786986	40150946	48786986	38060575	361911767	5.25	1.31	0	5.13	0	0.27	0	0.09	0	0.00	0	8.73	0	44763676	0	200	0	195.84	0	1.45	0	0.00	0	1.24	0	0.01	0	189.99	0	0.77	0	643739	0	49238586	0	2523675	0	134419	0	42122	0	0	0	4298369	0	14257	0	0	0	142915	0	19791019	0	32295	0	19980486	0	85.79	0	42240001	0	231655	17340317	74.854058837495	49238586.0	44763676.0	643739.0	2523675.0	134419.0	42122.0	0.0	4298369.0	42240001.0	90.9	1.3	5.1	0.3	0.1	0.0	8.7	85.8	100	100	100.00	38	4923858600	25.1	25.0	24.8	24.8	0.3	30.4	11.2	bulk
1400943	SRR1811606	SRP055201	SRS851169	SRX884168	SRA243458	GEO		The Calcium Channel Subunit Alpha2delta2 Suppresses Axon Regeneration in the Adult CNS	Purpose: Injuries to the adult central nervous system (CNS) often result in permanent disabilities because neurons lose the ability to regenerate their axon during development. Although the developmental transition from a growing to a transmitting phase may represent one of the first steps in the gradual loss of axon growth and regeneration ability, the molecular mechanisms regulating this process has yet to be identified. The main goal of this study was to dissect the molecular mechanisms mediating the decline in axon growth ability and its relationship with regeneration failure in the adult CNS. To this end, we sequenced the whole transcriptome of dorsal root ganglia (DRG) neurons in both growth competent and incompetent states at different developmental stages, in diverse culture and in vivo experimental conditions. Overall design: mRNA profiles of mouse embryonic E12.5 and E17.5 lumbar DRGs, conditioned and sham operated adult L4-5DRGs, and cultured adult lumbar DRG (6, 12, 24 and 36 hr after plating) neurons were generated by deep sequencing, in triplicate, using the Illumina TruSeq RNA Sample Prep Kits V2.		GSM1614854: Sham operated [123]; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Cells were isolated by cell sorting, lyzed in Qiazol and RNA isolated. Illumina TruSeq RNA Sample Prep Kits V2 was used with 10 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 1500	developmental stage;;adult|source_name;;DRG neuron|time after plating;;none	GEO Accession;;GSM1614854		GSM1614854	Sham operated [123]	10222090200	51110451	2016-09-18 20:49:05	6751215777	10222090200	51110451	2	51110451	index:0,count:51110451,average:100,stdev:0|index:1,count:51110451,average:100,stdev:0	GSM1614854_r1	GEO			in_mesa	27720483	3.86	3.4	0.02	7512155947	7476690532	7077988640	7078784252	99.53	100.01	47100604	43458899	187.478	765.019	146	389964	88.71	94.24	51291292	41780608	51291292	41780608	90.53	90.89	51291292	42638661	51291292	40295396	335490267	4.47	1.32	0	5.42	0	0.26	0	0.09	0	0.00	0	7.50	0	47100604	0	200	0	195.93	0	1.46	0	0.00	0	1.23	0	0.01	0	188.33	0	0.76	0	674841	0	51110451	0	2767742	0	131036	0	44487	0	0	0	3834324	0	16261	0	0	0	149087	0	20545794	0	35612	0	20746754	0	86.74	0	44332862	0	242362	18492847	76.302584563587	51110451.0	47100604.0	674841.0	2767742.0	131036.0	44487.0	0.0	3834324.0	44332862.0	92.2	1.3	5.4	0.3	0.1	0.0	7.5	86.7	100	100	100.00	38	5111045100	25.4	24.6	24.6	25.2	0.3	30.7	11.4	bulk
2797873	SRR1811589	SRP055201	SRS851178	SRX884151	SRA243458	GEO		The Calcium Channel Subunit Alpha2delta2 Suppresses Axon Regeneration in the Adult CNS	Purpose: Injuries to the adult central nervous system (CNS) often result in permanent disabilities because neurons lose the ability to regenerate their axon during development. Although the developmental transition from a growing to a transmitting phase may represent one of the first steps in the gradual loss of axon growth and regeneration ability, the molecular mechanisms regulating this process has yet to be identified. The main goal of this study was to dissect the molecular mechanisms mediating the decline in axon growth ability and its relationship with regeneration failure in the adult CNS. To this end, we sequenced the whole transcriptome of dorsal root ganglia (DRG) neurons in both growth competent and incompetent states at different developmental stages, in diverse culture and in vivo experimental conditions. Overall design: mRNA profiles of mouse embryonic E12.5 and E17.5 lumbar DRGs, conditioned and sham operated adult L4-5DRGs, and cultured adult lumbar DRG (6, 12, 24 and 36 hr after plating) neurons were generated by deep sequencing, in triplicate, using the Illumina TruSeq RNA Sample Prep Kits V2.		GSM1614837: 06h [339]; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Cells were isolated by cell sorting, lyzed in Qiazol and RNA isolated. Illumina TruSeq RNA Sample Prep Kits V2 was used with 10 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 1500	developmental stage;;adult|source_name;;DRG neuron|time after plating;;6 hrs	GEO Accession;;GSM1614837		GSM1614837	06h [339]	8048056548	41061513	2016-09-18 20:49:05	5039823527	8048056548	41061513	2	41061513	index:0,count:41061513,average:98,stdev:0|index:1,count:41061513,average:98,stdev:0	GSM1614837_r1	GEO			in_mesa	27720483	4.11	3.42	0.02	6218305382	6090353331	5857078241	5770467373	97.94	98.52	39817660	36917528	183.633	675.176	135	379649	86.01	91.41	43407217	34247183	43407217	34247183	87.74	88.23	43407217	34935324	43407217	33055501	373357083	6.00	1.03	0	5.73	0	0.27	0	0.13	0	0.00	0	2.63	0	39817660	0	196	0	194.25	0	1.62	0	0.01	0	1.25	0	0.01	0	282.10	0	0.26	0	422986	0	41061513	0	2353174	0	110084	0	55402	0	0	0	1078367	0	14317	0	0	0	127060	0	17019255	0	31468	0	17192100	0	91.24	0	37464486	0	233329	14648407	62.780053058128	41061513.0	39817660.0	422986.0	2353174.0	110084.0	55402.0	0.0	1078367.0	37464486.0	97.0	1.0	5.7	0.3	0.1	0.0	2.6	91.2	98	98	98.00	38	4024028274	26.5	23.5	23.2	26.7	0.0	36.0	18.0	bulk
2798096	SRR1811590	SRP055201	SRS851177	SRX884152	SRA243458	GEO		The Calcium Channel Subunit Alpha2delta2 Suppresses Axon Regeneration in the Adult CNS	Purpose: Injuries to the adult central nervous system (CNS) often result in permanent disabilities because neurons lose the ability to regenerate their axon during development. Although the developmental transition from a growing to a transmitting phase may represent one of the first steps in the gradual loss of axon growth and regeneration ability, the molecular mechanisms regulating this process has yet to be identified. The main goal of this study was to dissect the molecular mechanisms mediating the decline in axon growth ability and its relationship with regeneration failure in the adult CNS. To this end, we sequenced the whole transcriptome of dorsal root ganglia (DRG) neurons in both growth competent and incompetent states at different developmental stages, in diverse culture and in vivo experimental conditions. Overall design: mRNA profiles of mouse embryonic E12.5 and E17.5 lumbar DRGs, conditioned and sham operated adult L4-5DRGs, and cultured adult lumbar DRG (6, 12, 24 and 36 hr after plating) neurons were generated by deep sequencing, in triplicate, using the Illumina TruSeq RNA Sample Prep Kits V2.		GSM1614838: 06h [340]; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Cells were isolated by cell sorting, lyzed in Qiazol and RNA isolated. Illumina TruSeq RNA Sample Prep Kits V2 was used with 10 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 1500	developmental stage;;adult|source_name;;DRG neuron|time after plating;;6 hrs	GEO Accession;;GSM1614838		GSM1614838	06h [340]	8289319110	52464045	2016-09-18 20:49:05	5888163701	8289319110	52464045	2	52464045	index:0,count:52464045,average:79,stdev:0|index:1,count:52464045,average:79,stdev:0	GSM1614838_r1	GEO			in_mesa	27720483	3.71	3.32	0.03	6405867861	6267243016	6018326912	5924430711	97.84	98.44	47762539	44562007	164.999	655.690	115	540502	85.44	91.02	52362497	40806868	52362497	40806868	87.52	88.04	52362497	41801518	52362497	39472217	402785550	6.29	0.98	0	5.58	0	0.29	0	0.14	0	0.00	0	8.53	0	47762539	0	158	0	156.22	0	1.57	0	0.00	0	1.21	0	0.01	0	261.23	0	0.76	0	514458	0	52464045	0	2929191	0	150597	0	74649	0	0	0	4476260	0	11585	0	0	0	102978	0	14588625	0	27950	0	14731138	0	85.46	0	44833348	0	237562	13704991	57.690165093744	52464045.0	47762539.0	514458.0	2929191.0	150597.0	74649.0	0.0	4476260.0	44833348.0	91.0	1.0	5.6	0.3	0.1	0.0	8.5	85.5	79	79	79.00	38	4144659555	26.3	23.7	23.5	26.3	0.2	30.5	11.5	bulk
2798128	SRR1811591	SRP055201	SRS851176	SRX884153	SRA243458	GEO		The Calcium Channel Subunit Alpha2delta2 Suppresses Axon Regeneration in the Adult CNS	Purpose: Injuries to the adult central nervous system (CNS) often result in permanent disabilities because neurons lose the ability to regenerate their axon during development. Although the developmental transition from a growing to a transmitting phase may represent one of the first steps in the gradual loss of axon growth and regeneration ability, the molecular mechanisms regulating this process has yet to be identified. The main goal of this study was to dissect the molecular mechanisms mediating the decline in axon growth ability and its relationship with regeneration failure in the adult CNS. To this end, we sequenced the whole transcriptome of dorsal root ganglia (DRG) neurons in both growth competent and incompetent states at different developmental stages, in diverse culture and in vivo experimental conditions. Overall design: mRNA profiles of mouse embryonic E12.5 and E17.5 lumbar DRGs, conditioned and sham operated adult L4-5DRGs, and cultured adult lumbar DRG (6, 12, 24 and 36 hr after plating) neurons were generated by deep sequencing, in triplicate, using the Illumina TruSeq RNA Sample Prep Kits V2.		GSM1614839: 06h [341]; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Cells were isolated by cell sorting, lyzed in Qiazol and RNA isolated. Illumina TruSeq RNA Sample Prep Kits V2 was used with 10 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 1500	developmental stage;;adult|source_name;;DRG neuron|time after plating;;6 hrs	GEO Accession;;GSM1614839		GSM1614839	06h [341]	1267792000	8024000	2016-09-18 20:49:05	914685685	1267792000	8024000	2	8024000	index:0,count:8024000,average:79,stdev:0|index:1,count:8024000,average:79,stdev:0	GSM1614839_r1	GEO			in_mesa	27720483	4.42	3.6	0.03	973320440	949392015	909110271	893049478	97.54	98.23	7498402	7133535	148.665	525.210	116	95826	85.17	91.25	8268743	6386086	8268743	6386086	87.86	88.43	8268743	6588303	8268743	6188939	58412697	6.00	1.10	0	6.23	0	0.28	0	0.16	0	0.00	0	6.11	0	7498402	0	158	0	156.33	0	1.47	0	0.00	0	1.18	0	0.01	0	209.32	0	0.68	0	88645	0	8024000	0	499969	0	22426	0	12580	0	0	0	490592	0	1938	0	0	0	15530	0	2186508	0	4553	0	2208529	0	87.22	0	6998433	0	147503	2008587	13.617262021789	8024000.0	7498402.0	88645.0	499969.0	22426.0	12580.0	0.0	490592.0	6998433.0	93.4	1.1	6.2	0.3	0.2	0.0	6.1	87.2	79	79	79.00	38	633896000	27.1	22.7	22.6	27.4	0.2	31.6	12.5	bulk
2798160	SRR1811592	SRP055201	SRS851175	SRX884154	SRA243458	GEO		The Calcium Channel Subunit Alpha2delta2 Suppresses Axon Regeneration in the Adult CNS	Purpose: Injuries to the adult central nervous system (CNS) often result in permanent disabilities because neurons lose the ability to regenerate their axon during development. Although the developmental transition from a growing to a transmitting phase may represent one of the first steps in the gradual loss of axon growth and regeneration ability, the molecular mechanisms regulating this process has yet to be identified. The main goal of this study was to dissect the molecular mechanisms mediating the decline in axon growth ability and its relationship with regeneration failure in the adult CNS. To this end, we sequenced the whole transcriptome of dorsal root ganglia (DRG) neurons in both growth competent and incompetent states at different developmental stages, in diverse culture and in vivo experimental conditions. Overall design: mRNA profiles of mouse embryonic E12.5 and E17.5 lumbar DRGs, conditioned and sham operated adult L4-5DRGs, and cultured adult lumbar DRG (6, 12, 24 and 36 hr after plating) neurons were generated by deep sequencing, in triplicate, using the Illumina TruSeq RNA Sample Prep Kits V2.		GSM1614840: 12h [342]; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Cells were isolated by cell sorting, lyzed in Qiazol and RNA isolated. Illumina TruSeq RNA Sample Prep Kits V2 was used with 10 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 1500	developmental stage;;adult|source_name;;DRG neuron|time after plating;;12 hrs	GEO Accession;;GSM1614840		GSM1614840	12h [342]	1142785244	7232818	2016-09-18 20:49:05	824877598	1142785244	7232818	2	7232818	index:0,count:7232818,average:79,stdev:0|index:1,count:7232818,average:79,stdev:0	GSM1614840_r1	GEO			in_mesa	27720483	5.25	3.54	0.03	862373014	835896804	798985405	781088999	96.93	97.76	6802960	6550886	140.104	426.359	115	107305	81.26	87.77	7580367	5528137	7580367	5528137	84.13	84.69	7580367	5723093	7580367	5334055	76133098	8.83	0.95	0	6.98	0	0.26	0	0.20	0	0.00	0	5.48	0	6802960	0	158	0	156.41	0	1.58	0	0.01	0	1.28	0	0.01	0	205.02	0	0.67	0	68826	0	7232818	0	504667	0	19072	0	14355	0	0	0	396431	0	1535	0	0	0	13161	0	1815160	0	3682	0	1833538	0	87.08	0	6298293	0	140694	1641758	11.668997967220	7232818.0	6802960.0	68826.0	504667.0	19072.0	14355.0	0.0	396431.0	6298293.0	94.1	1.0	7.0	0.3	0.2	0.0	5.5	87.1	79	79	79.00	38	571392622	27.4	22.4	22.3	27.7	0.2	31.8	12.8	bulk
2798193	SRR1811593	SRP055201	SRS851174	SRX884155	SRA243458	GEO		The Calcium Channel Subunit Alpha2delta2 Suppresses Axon Regeneration in the Adult CNS	Purpose: Injuries to the adult central nervous system (CNS) often result in permanent disabilities because neurons lose the ability to regenerate their axon during development. Although the developmental transition from a growing to a transmitting phase may represent one of the first steps in the gradual loss of axon growth and regeneration ability, the molecular mechanisms regulating this process has yet to be identified. The main goal of this study was to dissect the molecular mechanisms mediating the decline in axon growth ability and its relationship with regeneration failure in the adult CNS. To this end, we sequenced the whole transcriptome of dorsal root ganglia (DRG) neurons in both growth competent and incompetent states at different developmental stages, in diverse culture and in vivo experimental conditions. Overall design: mRNA profiles of mouse embryonic E12.5 and E17.5 lumbar DRGs, conditioned and sham operated adult L4-5DRGs, and cultured adult lumbar DRG (6, 12, 24 and 36 hr after plating) neurons were generated by deep sequencing, in triplicate, using the Illumina TruSeq RNA Sample Prep Kits V2.		GSM1614841: 12h [343]; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Cells were isolated by cell sorting, lyzed in Qiazol and RNA isolated. Illumina TruSeq RNA Sample Prep Kits V2 was used with 10 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 1500	developmental stage;;adult|source_name;;DRG neuron|time after plating;;12 hrs	GEO Accession;;GSM1614841		GSM1614841	12h [343]	9230580884	58421398	2016-09-18 20:49:05	6533922472	9230580884	58421398	2	58421398	index:0,count:58421398,average:79,stdev:0|index:1,count:58421398,average:79,stdev:0	GSM1614841_r1	GEO			in_mesa	27720483	3.26	3.25	0.04	7044976640	6919914385	6630963096	6551570704	98.22	98.8	52217925	48084697	173.638	758.102	115	526038	85.03	90.44	57242039	44401870	57242039	44401870	86.64	87.14	57242039	45243678	57242039	42781823	494959386	7.03	1.18	0	5.34	0	0.32	0	0.16	0	0.00	0	10.14	0	52217925	0	158	0	156.10	0	1.67	0	0.00	0	1.31	0	0.01	0	189.82	0	0.78	0	687116	0	58421398	0	3121190	0	185884	0	92742	0	0	0	5924847	0	11587	0	0	0	116111	0	16227964	0	30829	0	16386491	0	84.04	0	49096735	0	263701	15277888	57.936405246852	58421398.0	52217925.0	687116.0	3121190.0	185884.0	92742.0	0.0	5924847.0	49096735.0	89.4	1.2	5.3	0.3	0.2	0.0	10.1	84.0	79	79	79.00	38	4615290442	25.6	24.3	24.2	25.6	0.2	30.1	11.2	bulk
2798225	SRR1811594	SRP055201	SRS851172	SRX884156	SRA243458	GEO		The Calcium Channel Subunit Alpha2delta2 Suppresses Axon Regeneration in the Adult CNS	Purpose: Injuries to the adult central nervous system (CNS) often result in permanent disabilities because neurons lose the ability to regenerate their axon during development. Although the developmental transition from a growing to a transmitting phase may represent one of the first steps in the gradual loss of axon growth and regeneration ability, the molecular mechanisms regulating this process has yet to be identified. The main goal of this study was to dissect the molecular mechanisms mediating the decline in axon growth ability and its relationship with regeneration failure in the adult CNS. To this end, we sequenced the whole transcriptome of dorsal root ganglia (DRG) neurons in both growth competent and incompetent states at different developmental stages, in diverse culture and in vivo experimental conditions. Overall design: mRNA profiles of mouse embryonic E12.5 and E17.5 lumbar DRGs, conditioned and sham operated adult L4-5DRGs, and cultured adult lumbar DRG (6, 12, 24 and 36 hr after plating) neurons were generated by deep sequencing, in triplicate, using the Illumina TruSeq RNA Sample Prep Kits V2.		GSM1614842: 12h [344]; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Cells were isolated by cell sorting, lyzed in Qiazol and RNA isolated. Illumina TruSeq RNA Sample Prep Kits V2 was used with 10 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 1500	developmental stage;;adult|source_name;;DRG neuron|time after plating;;12 hrs	GEO Accession;;GSM1614842		GSM1614842	12h [344]	8943803988	45631653	2016-09-18 20:49:05	5635774673	8943803988	45631653	2	45631653	index:0,count:45631653,average:98,stdev:0|index:1,count:45631653,average:98,stdev:0	GSM1614842_r1	GEO			in_mesa	27720483	3.18	3.28	0.03	7116093800	6967076293	6769976835	6660053083	97.91	98.38	43849915	40089120	199.198	782.759	136	359675	85.81	90.29	47279161	37626329	47279161	37626329	86.87	87.25	47279161	38091157	47279161	36357001	509015386	7.15	1.44	0	4.78	0	0.29	0	0.16	0	0.00	0	3.45	0	43849915	0	196	0	194.21	0	1.57	0	0.01	0	1.27	0	0.01	0	275.63	0	0.27	0	659062	0	45631653	0	2179256	0	131753	0	74222	0	0	0	1575763	0	14939	0	0	0	149376	0	19327772	0	35086	0	19527173	0	91.32	0	41670659	0	281431	17268246	61.358720254698	45631653.0	43849915.0	659062.0	2179256.0	131753.0	74222.0	0.0	1575763.0	41670659.0	96.1	1.4	4.8	0.3	0.2	0.0	3.5	91.3	98	98	98.00	38	4471901994	25.7	24.2	24.0	26.0	0.0	35.7	17.4	bulk
2798257	SRR1811595	SRP055201	SRS851173	SRX884157	SRA243458	GEO		The Calcium Channel Subunit Alpha2delta2 Suppresses Axon Regeneration in the Adult CNS	Purpose: Injuries to the adult central nervous system (CNS) often result in permanent disabilities because neurons lose the ability to regenerate their axon during development. Although the developmental transition from a growing to a transmitting phase may represent one of the first steps in the gradual loss of axon growth and regeneration ability, the molecular mechanisms regulating this process has yet to be identified. The main goal of this study was to dissect the molecular mechanisms mediating the decline in axon growth ability and its relationship with regeneration failure in the adult CNS. To this end, we sequenced the whole transcriptome of dorsal root ganglia (DRG) neurons in both growth competent and incompetent states at different developmental stages, in diverse culture and in vivo experimental conditions. Overall design: mRNA profiles of mouse embryonic E12.5 and E17.5 lumbar DRGs, conditioned and sham operated adult L4-5DRGs, and cultured adult lumbar DRG (6, 12, 24 and 36 hr after plating) neurons were generated by deep sequencing, in triplicate, using the Illumina TruSeq RNA Sample Prep Kits V2.		GSM1614843: 24h [345]; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Cells were isolated by cell sorting, lyzed in Qiazol and RNA isolated. Illumina TruSeq RNA Sample Prep Kits V2 was used with 10 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 1500	developmental stage;;adult|source_name;;DRG neuron|time after plating;;24 hrs	GEO Accession;;GSM1614843		GSM1614843	24h [345]	1816038412	11493914	2016-09-18 20:49:05	1305700325	1816038412	11493914	2	11493914	index:0,count:11493914,average:79,stdev:0|index:1,count:11493914,average:79,stdev:0	GSM1614843_r1	GEO			in_mesa	27720483	4.14	3.3	0.04	1450683148	1418978395	1354164716	1334460949	97.81	98.54	10665721	9972901	170.205	606.600	125	110940	80.68	86.54	11820317	8605348	11820317	8605348	82.41	82.94	11820317	8789380	11820317	8247304	150314257	10.36	0.94	0	6.28	0	0.28	0	0.19	0	0.00	0	6.73	0	10665721	0	158	0	156.26	0	1.92	0	0.01	0	1.49	0	0.01	0	220.10	0	0.71	0	107558	0	11493914	0	721820	0	32517	0	21904	0	0	0	773772	0	2158	0	0	0	21105	0	2987066	0	5636	0	3015965	0	86.51	0	9943901	0	165069	2841131	17.211778104914	11493914.0	10665721.0	107558.0	721820.0	32517.0	21904.0	0.0	773772.0	9943901.0	92.8	0.9	6.3	0.3	0.2	0.0	6.7	86.5	79	79	79.00	38	908019206	26.2	23.7	23.6	26.3	0.2	31.6	12.5	bulk
2798288	SRR1811596	SRP055201	SRS851171	SRX884158	SRA243458	GEO		The Calcium Channel Subunit Alpha2delta2 Suppresses Axon Regeneration in the Adult CNS	Purpose: Injuries to the adult central nervous system (CNS) often result in permanent disabilities because neurons lose the ability to regenerate their axon during development. Although the developmental transition from a growing to a transmitting phase may represent one of the first steps in the gradual loss of axon growth and regeneration ability, the molecular mechanisms regulating this process has yet to be identified. The main goal of this study was to dissect the molecular mechanisms mediating the decline in axon growth ability and its relationship with regeneration failure in the adult CNS. To this end, we sequenced the whole transcriptome of dorsal root ganglia (DRG) neurons in both growth competent and incompetent states at different developmental stages, in diverse culture and in vivo experimental conditions. Overall design: mRNA profiles of mouse embryonic E12.5 and E17.5 lumbar DRGs, conditioned and sham operated adult L4-5DRGs, and cultured adult lumbar DRG (6, 12, 24 and 36 hr after plating) neurons were generated by deep sequencing, in triplicate, using the Illumina TruSeq RNA Sample Prep Kits V2.		GSM1614844: 24h [346]; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Cells were isolated by cell sorting, lyzed in Qiazol and RNA isolated. Illumina TruSeq RNA Sample Prep Kits V2 was used with 10 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 1500	developmental stage;;adult|source_name;;DRG neuron|time after plating;;24 hrs	GEO Accession;;GSM1614844		GSM1614844	24h [346]	10344455288	65471236	2016-09-18 20:49:05	7314822917	10344455288	65471236	2	65471236	index:0,count:65471236,average:79,stdev:0|index:1,count:65471236,average:79,stdev:0	GSM1614844_r1	GEO			in_mesa	27720483	3.98	3.3	0.05	8120496854	7966046817	7611751518	7515294396	98.1	98.73	58982543	54485716	178.067	696.851	125	577411	82.56	88.16	64945050	48693406	64945050	48693406	84.4	84.86	64945050	49782740	64945050	46871055	750302304	9.24	0.91	0	5.73	0	0.28	0	0.19	0	0.00	0	9.44	0	58982543	0	158	0	156.14	0	1.75	0	0.01	0	1.42	0	0.01	0	200.25	0	0.78	0	592910	0	65471236	0	3752247	0	185788	0	124462	0	0	0	6178443	0	12294	0	0	0	123161	0	17249614	0	33034	0	17418103	0	84.36	0	55230296	0	254513	16530968	64.951369871087	65471236.0	58982543.0	592910.0	3752247.0	185788.0	124462.0	0.0	6178443.0	55230296.0	90.1	0.9	5.7	0.3	0.2	0.0	9.4	84.4	79	79	79.00	38	5172227644	26.0	24.0	23.8	26.0	0.2	30.3	11.3	bulk
2798384	SRR1811599	SRP055201	SRS851167	SRX884161	SRA243458	GEO		The Calcium Channel Subunit Alpha2delta2 Suppresses Axon Regeneration in the Adult CNS	Purpose: Injuries to the adult central nervous system (CNS) often result in permanent disabilities because neurons lose the ability to regenerate their axon during development. Although the developmental transition from a growing to a transmitting phase may represent one of the first steps in the gradual loss of axon growth and regeneration ability, the molecular mechanisms regulating this process has yet to be identified. The main goal of this study was to dissect the molecular mechanisms mediating the decline in axon growth ability and its relationship with regeneration failure in the adult CNS. To this end, we sequenced the whole transcriptome of dorsal root ganglia (DRG) neurons in both growth competent and incompetent states at different developmental stages, in diverse culture and in vivo experimental conditions. Overall design: mRNA profiles of mouse embryonic E12.5 and E17.5 lumbar DRGs, conditioned and sham operated adult L4-5DRGs, and cultured adult lumbar DRG (6, 12, 24 and 36 hr after plating) neurons were generated by deep sequencing, in triplicate, using the Illumina TruSeq RNA Sample Prep Kits V2.		GSM1614847: 36h [349]; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Cells were isolated by cell sorting, lyzed in Qiazol and RNA isolated. Illumina TruSeq RNA Sample Prep Kits V2 was used with 10 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 1500	developmental stage;;adult|source_name;;DRG neuron|time after plating;;36 hrs	GEO Accession;;GSM1614847		GSM1614847	36h [349]	2834443844	17939518	2016-09-18 20:49:05	2010233767	2834443844	17939518	2	17939518	index:0,count:17939518,average:79,stdev:0|index:1,count:17939518,average:79,stdev:0	GSM1614847_r1	GEO			in_mesa	27720483	3.92	3.24	0.05	2154823213	2124877091	2017117791	2000428786	98.61	99.17	15990050	14865479	170.859	657.916	115	177450	83.26	89.05	17666830	13313581	17666830	13313581	85.35	85.73	17666830	13647339	17666830	12816590	190859201	8.86	1.08	0	5.79	0	0.31	0	0.18	0	0.00	0	10.38	0	15990050	0	158	0	156.15	0	1.63	0	0.00	0	1.36	0	0.01	0	179.40	0	0.77	0	194004	0	17939518	0	1039493	0	56226	0	31639	0	0	0	1861603	0	3125	0	0	0	33077	0	4816220	0	8557	0	4860979	0	83.34	0	14950557	0	143061	4552920	31.825025688343	17939518.0	15990050.0	194004.0	1039493.0	56226.0	31639.0	0.0	1861603.0	14950557.0	89.1	1.1	5.8	0.3	0.2	0.0	10.4	83.3	79	79	79.00	38	1417221922	25.5	24.5	24.4	25.4	0.2	30.0	11.2	bulk
2801809	SRR1811604	SRP055201	SRS851161	SRX884166	SRA243458	GEO		The Calcium Channel Subunit Alpha2delta2 Suppresses Axon Regeneration in the Adult CNS	Purpose: Injuries to the adult central nervous system (CNS) often result in permanent disabilities because neurons lose the ability to regenerate their axon during development. Although the developmental transition from a growing to a transmitting phase may represent one of the first steps in the gradual loss of axon growth and regeneration ability, the molecular mechanisms regulating this process has yet to be identified. The main goal of this study was to dissect the molecular mechanisms mediating the decline in axon growth ability and its relationship with regeneration failure in the adult CNS. To this end, we sequenced the whole transcriptome of dorsal root ganglia (DRG) neurons in both growth competent and incompetent states at different developmental stages, in diverse culture and in vivo experimental conditions. Overall design: mRNA profiles of mouse embryonic E12.5 and E17.5 lumbar DRGs, conditioned and sham operated adult L4-5DRGs, and cultured adult lumbar DRG (6, 12, 24 and 36 hr after plating) neurons were generated by deep sequencing, in triplicate, using the Illumina TruSeq RNA Sample Prep Kits V2.		GSM1614852: Sham operated [69]; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Cells were isolated by cell sorting, lyzed in Qiazol and RNA isolated. Illumina TruSeq RNA Sample Prep Kits V2 was used with 10 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 1500	developmental stage;;adult|source_name;;DRG neuron|time after plating;;none	GEO Accession;;GSM1614852		GSM1614852	Sham operated [69]	6359348600	31796743	2016-09-18 20:49:05	4212910100	6359348600	31796743	2	31796743	index:0,count:31796743,average:100,stdev:0|index:1,count:31796743,average:100,stdev:0	GSM1614852_r1	GEO			in_mesa	27720483	4.43	3.22	0.02	4575644617	4566999509	4266063680	4283748525	99.81	100.41	29250277	27303700	178.624	665.029	145	303674	86.66	93.07	32302203	25347092	32302203	25347092	87.74	88.26	32302203	25665301	32302203	24037346	212201038	4.64	1.53	0	6.34	0	0.26	0	0.08	0	0.00	0	7.67	0	29250277	0	200	0	195.83	0	2.29	0	0.01	0	1.57	0	0.01	0	219.29	0	0.81	0	484936	0	31796743	0	2015588	0	81749	0	25363	0	0	0	2439354	0	9373	0	0	0	86532	0	12258342	0	23048	0	12377295	0	85.65	0	27234689	0	213758	10956666	51.257337737067	31796743.0	29250277.0	484936.0	2015588.0	81749.0	25363.0	0.0	2439354.0	27234689.0	92.0	1.5	6.3	0.3	0.1	0.0	7.7	85.7	100	100	100.00	38	3179674300	25.1	24.8	25.0	24.8	0.3	30.6	11.4	bulk
2801840	SRR1811605	SRP055201	SRS851160	SRX884167	SRA243458	GEO		The Calcium Channel Subunit Alpha2delta2 Suppresses Axon Regeneration in the Adult CNS	Purpose: Injuries to the adult central nervous system (CNS) often result in permanent disabilities because neurons lose the ability to regenerate their axon during development. Although the developmental transition from a growing to a transmitting phase may represent one of the first steps in the gradual loss of axon growth and regeneration ability, the molecular mechanisms regulating this process has yet to be identified. The main goal of this study was to dissect the molecular mechanisms mediating the decline in axon growth ability and its relationship with regeneration failure in the adult CNS. To this end, we sequenced the whole transcriptome of dorsal root ganglia (DRG) neurons in both growth competent and incompetent states at different developmental stages, in diverse culture and in vivo experimental conditions. Overall design: mRNA profiles of mouse embryonic E12.5 and E17.5 lumbar DRGs, conditioned and sham operated adult L4-5DRGs, and cultured adult lumbar DRG (6, 12, 24 and 36 hr after plating) neurons were generated by deep sequencing, in triplicate, using the Illumina TruSeq RNA Sample Prep Kits V2.		GSM1614853: Sham operated [70]; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Cells were isolated by cell sorting, lyzed in Qiazol and RNA isolated. Illumina TruSeq RNA Sample Prep Kits V2 was used with 10 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 1500	developmental stage;;adult|source_name;;DRG neuron|time after plating;;none	GEO Accession;;GSM1614853		GSM1614853	Sham operated [70]	8068413400	40342067	2016-09-18 20:49:05	5361169862	8068413400	40342067	2	40342067	index:0,count:40342067,average:100,stdev:0|index:1,count:40342067,average:100,stdev:0	GSM1614853_r1	GEO			in_mesa	27720483	4.28	3.36	0.02	5989242191	5968595300	5606748462	5616929591	99.66	100.18	37775830	34500351	190.539	829.615	136	330206	88.02	94.16	41530490	33250983	41530490	33250983	90.06	90.46	41530490	34022432	41530490	31945713	263486627	4.40	0.86	0	6.10	0	0.27	0	0.10	0	0.00	0	5.99	0	37775830	0	200	0	196.30	0	1.66	0	0.00	0	1.27	0	0.01	0	189.60	0	0.78	0	348060	0	40342067	0	2461829	0	109208	0	39221	0	0	0	2417808	0	12399	0	0	0	119378	0	16636239	0	23503	0	16791519	0	87.54	0	35314001	0	232133	14888667	64.138519727915	40342067.0	37775830.0	348060.0	2461829.0	109208.0	39221.0	0.0	2417808.0	35314001.0	93.6	0.9	6.1	0.3	0.1	0.0	6.0	87.5	100	100	100.00	38	4034206700	25.1	24.8	24.9	24.9	0.3	30.8	11.5	bulk
2801904	SRR1811607	SRP055201	SRS851162	SRX884169	SRA243458	GEO		The Calcium Channel Subunit Alpha2delta2 Suppresses Axon Regeneration in the Adult CNS	Purpose: Injuries to the adult central nervous system (CNS) often result in permanent disabilities because neurons lose the ability to regenerate their axon during development. Although the developmental transition from a growing to a transmitting phase may represent one of the first steps in the gradual loss of axon growth and regeneration ability, the molecular mechanisms regulating this process has yet to be identified. The main goal of this study was to dissect the molecular mechanisms mediating the decline in axon growth ability and its relationship with regeneration failure in the adult CNS. To this end, we sequenced the whole transcriptome of dorsal root ganglia (DRG) neurons in both growth competent and incompetent states at different developmental stages, in diverse culture and in vivo experimental conditions. Overall design: mRNA profiles of mouse embryonic E12.5 and E17.5 lumbar DRGs, conditioned and sham operated adult L4-5DRGs, and cultured adult lumbar DRG (6, 12, 24 and 36 hr after plating) neurons were generated by deep sequencing, in triplicate, using the Illumina TruSeq RNA Sample Prep Kits V2.		GSM1614855: E12.5 [84]; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Cells were isolated by cell sorting, lyzed in Qiazol and RNA isolated. Illumina TruSeq RNA Sample Prep Kits V2 was used with 10 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 1500	developmental stage;;embryonic 12.5|source_name;;DRG neuron|time after plating;;none	GEO Accession;;GSM1614855		GSM1614855	E12.5 [84]	9825233600	49126168	2016-09-18 20:49:05	6497522492	9825233600	49126168	2	49126168	index:0,count:49126168,average:100,stdev:0|index:1,count:49126168,average:100,stdev:0	GSM1614855_r1	GEO			in_mesa	27720483	2.91	3.7	0.06	6998162455	6974851334	6466607968	6481332723	99.67	100.23	44674049	41660949	182.964	598.729	136	450639	83.85	90.89	50522803	37460083	50522803	37460083	86.82	87.1	50522803	38783999	50522803	35897101	569997942	8.14	0.68	0	7.04	0	0.27	0	0.08	0	0.00	0	8.71	0	44674049	0	200	0	196.31	0	1.58	0	0.00	0	1.29	0	0.01	0	158.76	0	0.80	0	336034	0	49126168	0	3458698	0	130989	0	40322	0	0	0	4280808	0	14939	0	0	0	125368	0	18620271	0	31614	0	18792192	0	83.90	0	41215351	0	238429	16843336	70.642983865218	49126168.0	44674049.0	336034.0	3458698.0	130989.0	40322.0	0.0	4280808.0	41215351.0	90.9	0.7	7.0	0.3	0.1	0.0	8.7	83.9	100	100	100.00	38	4912616800	25.3	24.8	24.7	24.9	0.3	30.3	11.1	bulk
2801937	SRR1811608	SRP055201	SRS851159	SRX884170	SRA243458	GEO		The Calcium Channel Subunit Alpha2delta2 Suppresses Axon Regeneration in the Adult CNS	Purpose: Injuries to the adult central nervous system (CNS) often result in permanent disabilities because neurons lose the ability to regenerate their axon during development. Although the developmental transition from a growing to a transmitting phase may represent one of the first steps in the gradual loss of axon growth and regeneration ability, the molecular mechanisms regulating this process has yet to be identified. The main goal of this study was to dissect the molecular mechanisms mediating the decline in axon growth ability and its relationship with regeneration failure in the adult CNS. To this end, we sequenced the whole transcriptome of dorsal root ganglia (DRG) neurons in both growth competent and incompetent states at different developmental stages, in diverse culture and in vivo experimental conditions. Overall design: mRNA profiles of mouse embryonic E12.5 and E17.5 lumbar DRGs, conditioned and sham operated adult L4-5DRGs, and cultured adult lumbar DRG (6, 12, 24 and 36 hr after plating) neurons were generated by deep sequencing, in triplicate, using the Illumina TruSeq RNA Sample Prep Kits V2.		GSM1614856: E12.5 [86]; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Cells were isolated by cell sorting, lyzed in Qiazol and RNA isolated. Illumina TruSeq RNA Sample Prep Kits V2 was used with 10 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 1500	developmental stage;;embryonic 12.5|source_name;;DRG neuron|time after plating;;none	GEO Accession;;GSM1614856		GSM1614856	E12.5 [86]	8390834200	41954171	2016-09-18 20:49:05	5549052519	8390834200	41954171	2	41954171	index:0,count:41954171,average:100,stdev:0|index:1,count:41954171,average:100,stdev:0	GSM1614856_r1	GEO			in_mesa	27720483	2.78	3.7	0.05	6025797251	5998689387	5584168076	5590705318	99.55	100.12	38455604	35654345	186.762	670.386	134	319818	83.2	89.95	43357977	31995956	43357977	31995956	86.01	86.25	43357977	33074961	43357977	30678685	544745011	9.04	1.43	0	6.88	0	0.27	0	0.10	0	0.00	0	7.97	0	38455604	0	200	0	195.88	0	1.61	0	0.01	0	1.27	0	0.01	0	191.18	0	0.79	0	598437	0	41954171	0	2885348	0	112835	0	40047	0	0	0	3345685	0	12613	0	0	0	107378	0	15763182	0	30208	0	15913381	0	84.78	0	35570256	0	234591	14227062	60.646239625561	41954171.0	38455604.0	598437.0	2885348.0	112835.0	40047.0	0.0	3345685.0	35570256.0	91.7	1.4	6.9	0.3	0.1	0.0	8.0	84.8	100	100	100.00	38	4195417100	25.4	24.5	24.8	25.0	0.3	30.7	11.5	bulk
2801970	SRR1811609	SRP055201	SRS851158	SRX884171	SRA243458	GEO		The Calcium Channel Subunit Alpha2delta2 Suppresses Axon Regeneration in the Adult CNS	Purpose: Injuries to the adult central nervous system (CNS) often result in permanent disabilities because neurons lose the ability to regenerate their axon during development. Although the developmental transition from a growing to a transmitting phase may represent one of the first steps in the gradual loss of axon growth and regeneration ability, the molecular mechanisms regulating this process has yet to be identified. The main goal of this study was to dissect the molecular mechanisms mediating the decline in axon growth ability and its relationship with regeneration failure in the adult CNS. To this end, we sequenced the whole transcriptome of dorsal root ganglia (DRG) neurons in both growth competent and incompetent states at different developmental stages, in diverse culture and in vivo experimental conditions. Overall design: mRNA profiles of mouse embryonic E12.5 and E17.5 lumbar DRGs, conditioned and sham operated adult L4-5DRGs, and cultured adult lumbar DRG (6, 12, 24 and 36 hr after plating) neurons were generated by deep sequencing, in triplicate, using the Illumina TruSeq RNA Sample Prep Kits V2.		GSM1614857: E12.5 [87]; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Cells were isolated by cell sorting, lyzed in Qiazol and RNA isolated. Illumina TruSeq RNA Sample Prep Kits V2 was used with 10 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 1500	developmental stage;;embryonic 12.5|source_name;;DRG neuron|time after plating;;none	GEO Accession;;GSM1614857		GSM1614857	E12.5 [87]	7307078400	36535392	2016-09-18 20:49:05	4815337757	7307078400	36535392	2	36535392	index:0,count:36535392,average:100,stdev:0|index:1,count:36535392,average:100,stdev:0	GSM1614857_r1	GEO			in_mesa	27720483	3.21	3.85	0.05	5255044379	5237088724	4851460818	4863916233	99.66	100.26	33430382	31148447	184.652	627.277	134	295691	83.98	91.12	37804444	28074349	37804444	28074349	87.01	87.27	37804444	29087030	37804444	26890075	422830553	8.05	1.27	0	7.17	0	0.27	0	0.09	0	0.00	0	8.14	0	33430382	0	200	0	195.88	0	1.51	0	0.00	0	1.24	0	0.01	0	204.55	0	0.78	0	465662	0	36535392	0	2618688	0	98954	0	32061	0	0	0	2973995	0	11369	0	0	0	92367	0	13952383	0	27062	0	14083181	0	84.33	0	30811694	0	226431	12638085	55.814287796282	36535392.0	33430382.0	465662.0	2618688.0	98954.0	32061.0	0.0	2973995.0	30811694.0	91.5	1.3	7.2	0.3	0.1	0.0	8.1	84.3	100	100	100.00	38	3653539200	25.5	24.5	24.5	25.2	0.3	30.6	11.3	bulk
2802193	SRR1811610	SRP055201	SRS851157	SRX884172	SRA243458	GEO		The Calcium Channel Subunit Alpha2delta2 Suppresses Axon Regeneration in the Adult CNS	Purpose: Injuries to the adult central nervous system (CNS) often result in permanent disabilities because neurons lose the ability to regenerate their axon during development. Although the developmental transition from a growing to a transmitting phase may represent one of the first steps in the gradual loss of axon growth and regeneration ability, the molecular mechanisms regulating this process has yet to be identified. The main goal of this study was to dissect the molecular mechanisms mediating the decline in axon growth ability and its relationship with regeneration failure in the adult CNS. To this end, we sequenced the whole transcriptome of dorsal root ganglia (DRG) neurons in both growth competent and incompetent states at different developmental stages, in diverse culture and in vivo experimental conditions. Overall design: mRNA profiles of mouse embryonic E12.5 and E17.5 lumbar DRGs, conditioned and sham operated adult L4-5DRGs, and cultured adult lumbar DRG (6, 12, 24 and 36 hr after plating) neurons were generated by deep sequencing, in triplicate, using the Illumina TruSeq RNA Sample Prep Kits V2.		GSM1614858: E17.5 [336]; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Cells were isolated by cell sorting, lyzed in Qiazol and RNA isolated. Illumina TruSeq RNA Sample Prep Kits V2 was used with 10 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 1500	developmental stage;;embryonic 17.5|source_name;;DRG neuron|time after plating;;none	GEO Accession;;GSM1614858		GSM1614858	E17.5 [336]	9104614752	57624144	2016-09-18 20:49:05	6456852056	9104614752	57624144	2	57624144	index:0,count:57624144,average:79,stdev:0|index:1,count:57624144,average:79,stdev:0	GSM1614858_r1	GEO			in_mesa	27720483	4.46	3.63	0.04	6675059546	6618726939	6162331073	6145578177	99.16	99.73	51821058	48949273	152.141	573.943	114	610901	85.42	92.66	58433851	44267791	58433851	44267791	88.94	89.34	58433851	46091553	58433851	42683462	394542588	5.91	1.53	0	7.02	0	0.26	0	0.10	0	0.00	0	9.71	0	51821058	0	158	0	156.06	0	1.42	0	0.00	0	1.20	0	0.00	0	200.63	0	0.76	0	884418	0	57624144	0	4047062	0	149969	0	56262	0	0	0	5596855	0	14396	0	0	0	102573	0	16000989	0	29260	0	16147218	0	82.91	0	47773996	0	231375	14845646	64.162705564560	57624144.0	51821058.0	884418.0	4047062.0	149969.0	56262.0	0.0	5596855.0	47773996.0	89.9	1.5	7.0	0.3	0.1	0.0	9.7	82.9	79	79	79.00	38	4552307376	26.1	23.8	23.8	26.1	0.2	30.2	11.3	bulk
2802226	SRR1811611	SRP055201	SRS851156	SRX884173	SRA243458	GEO		The Calcium Channel Subunit Alpha2delta2 Suppresses Axon Regeneration in the Adult CNS	Purpose: Injuries to the adult central nervous system (CNS) often result in permanent disabilities because neurons lose the ability to regenerate their axon during development. Although the developmental transition from a growing to a transmitting phase may represent one of the first steps in the gradual loss of axon growth and regeneration ability, the molecular mechanisms regulating this process has yet to be identified. The main goal of this study was to dissect the molecular mechanisms mediating the decline in axon growth ability and its relationship with regeneration failure in the adult CNS. To this end, we sequenced the whole transcriptome of dorsal root ganglia (DRG) neurons in both growth competent and incompetent states at different developmental stages, in diverse culture and in vivo experimental conditions. Overall design: mRNA profiles of mouse embryonic E12.5 and E17.5 lumbar DRGs, conditioned and sham operated adult L4-5DRGs, and cultured adult lumbar DRG (6, 12, 24 and 36 hr after plating) neurons were generated by deep sequencing, in triplicate, using the Illumina TruSeq RNA Sample Prep Kits V2.		GSM1614859: E17.5 [337]; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Cells were isolated by cell sorting, lyzed in Qiazol and RNA isolated. Illumina TruSeq RNA Sample Prep Kits V2 was used with 10 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 1500	developmental stage;;embryonic 17.5|source_name;;DRG neuron|time after plating;;none	GEO Accession;;GSM1614859		GSM1614859	E17.5 [337]	1110819790	7030505	2016-09-18 20:49:05	801271785	1110819790	7030505	2	7030505	index:0,count:7030505,average:79,stdev:0|index:1,count:7030505,average:79,stdev:0	GSM1614859_r1	GEO			in_mesa	27720483	4.93	3.94	0.04	880398197	869137356	812937867	807985191	98.72	99.39	6584107	6216664	160.857	558.284	115	74359	84.01	91.08	7398460	5531568	7398460	5531568	87.75	88.08	7398460	5777430	7398460	5348860	64559713	7.33	1.03	0	7.27	0	0.22	0	0.12	0	0.00	0	6.02	0	6584107	0	158	0	156.37	0	1.36	0	0.00	0	1.16	0	0.01	0	207.46	0	0.69	0	72299	0	7030505	0	511133	0	15117	0	8346	0	0	0	422935	0	1821	0	0	0	11634	0	1825841	0	3365	0	1842661	0	86.38	0	6072974	0	144953	1761173	12.149958952212	7030505.0	6584107.0	72299.0	511133.0	15117.0	8346.0	0.0	422935.0	6072974.0	93.7	1.0	7.3	0.2	0.1	0.0	6.0	86.4	79	79	79.00	38	555409895	27.0	23.0	22.7	27.0	0.2	31.6	12.5	bulk
2802258	SRR1811612	SRP055201	SRS851155	SRX884174	SRA243458	GEO		The Calcium Channel Subunit Alpha2delta2 Suppresses Axon Regeneration in the Adult CNS	Purpose: Injuries to the adult central nervous system (CNS) often result in permanent disabilities because neurons lose the ability to regenerate their axon during development. Although the developmental transition from a growing to a transmitting phase may represent one of the first steps in the gradual loss of axon growth and regeneration ability, the molecular mechanisms regulating this process has yet to be identified. The main goal of this study was to dissect the molecular mechanisms mediating the decline in axon growth ability and its relationship with regeneration failure in the adult CNS. To this end, we sequenced the whole transcriptome of dorsal root ganglia (DRG) neurons in both growth competent and incompetent states at different developmental stages, in diverse culture and in vivo experimental conditions. Overall design: mRNA profiles of mouse embryonic E12.5 and E17.5 lumbar DRGs, conditioned and sham operated adult L4-5DRGs, and cultured adult lumbar DRG (6, 12, 24 and 36 hr after plating) neurons were generated by deep sequencing, in triplicate, using the Illumina TruSeq RNA Sample Prep Kits V2.		GSM1614860: E17.5 [338]; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Cells were isolated by cell sorting, lyzed in Qiazol and RNA isolated. Illumina TruSeq RNA Sample Prep Kits V2 was used with 10 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 1500	developmental stage;;embryonic 17.5|source_name;;DRG neuron|time after plating;;none	GEO Accession;;GSM1614860		GSM1614860	E17.5 [338]	1719016300	10879850	2016-09-18 20:49:05	1224258792	1719016300	10879850	2	10879850	index:0,count:10879850,average:79,stdev:0|index:1,count:10879850,average:79,stdev:0	GSM1614860_r1	GEO			in_mesa	27720483	3.99	3.57	0.04	1377414670	1371183656	1281219602	1282374658	99.55	100.09	9847232	8995705	187.025	822.584	126	86407	86.21	92.76	10948602	8488989	10948602	8488989	89.07	89.39	10948602	8771413	10948602	8180544	84055507	6.10	1.14	0	6.40	0	0.21	0	0.09	0	0.00	0	9.19	0	9847232	0	158	0	156.12	0	1.41	0	0.00	0	1.19	0	0.01	0	186.51	0	0.78	0	123570	0	10879850	0	696025	0	23298	0	9650	0	0	0	999670	0	2616	0	0	0	18690	0	2945555	0	5465	0	2972326	0	84.11	0	9151207	0	158815	2900889	18.265837609798	10879850.0	9847232.0	123570.0	696025.0	23298.0	9650.0	0.0	999670.0	9151207.0	90.5	1.1	6.4	0.2	0.1	0.0	9.2	84.1	79	79	79.00	38	859508150	25.6	24.4	24.2	25.6	0.2	30.3	11.4	bulk
1386831	SRR1947294	SRP056191	SRS874594	SRX973877	SRA246770	INSERM	U1043 CPTP	Mouse regulatory T cells Transcriptome	Regulatory T-cells (Tregs) differentiate in the thymus. After selection, they migrate to the periphery where they exert their effector functions. In the thymus and in the spleen of Rag2-GFP transgenic mice, two populations of Treg are found: I. a GFP+ population (respectively, developing cells and recent thymic emigrants) II. a GFP- population (mature cells).		Thymus GFP+ Tregs replicate 2	RNA sequencing analysis Rag2-GFP+ and Rag2-GFP- CD4+CD8-Foxp3-Thy1.1+ Tregs from mouse thymus and spleen were sorted by FACS and total RNA was immediately extracted by using the RNeasy® Micro Kit (QIAGEN) (including a DNase I treatment step) and the quality of the RNA was assessed by using an Agilent 2100 BioAnalyzer (Agilent Technologies). Three biological replicates were performed per cell population. Libraries for RNA-sequencing (RNAseq) were prepared according to the TotalScript RNA-seq protocol (Epicentre), starting from 5 ng of high-quality total RNA (i.e. RIN>7) and using the Oligo(dT) primer synthesis strategy. The quality of each library was assessed by using an Agilent 2100 BioAnalyzer. Samples were indexed and sequenced on Illumina HiSeq 2000 (paired-end 2x100bp). Reads were trimmed by using Cutadapt (v1.3), removing low-quality bases (-q < 10) and clipping adapter sequences. High-quality RNAseq reads were aligned to the mouse reference genome mm10 by using TopHat (v2.0.5) (11). Mice Rag2-Gfp transgenic mice (Rag-GFP) (W. Yu et al., Nature 400, 682 (1999)) on a C57BL/6 (B6) genetic background were provided by Dr. Pamela Fink (T. E. Boursalian, J. Golob, D. M. Soper, C. J. Cooper, P. J. Fink, Nature Immunol 5, 418 (2004)), B6 Foxp3-Thy1.1 knock-in mice by Dr. Alexander Rudensky (A. Liston et al., Proc Natl Acad Sci U S A 105, 11903 (2008)), and B6 GK mice by Dr. Andrew Lew (Y. Zhan, A. J. Corbett, J. L. Brady, R. M. Sutherland, A. M. Lew, Xenotransplantation 7, 267 (2000)). 	Treg recently generated from thymus		RNA-Seq	TRANSCRIPTOMIC	PolyA	paired		0.0E0		Illumina HiSeq 2000	age;;8 weeks|BioSampleModel;;Model organism or animal|breed;;C57Bl6 Rag2GFP Foxp3 Thy1 1|sample_type;;ThymusGFPplusTreg|sex;;male|tissue;;Regulatory T cells		200	ThymusGFPplusTreg	ThymusGFPplusTreg	2908430528	14958091	2015-04-15 00:00:00	1394272750	2908430528	14958091	2	14958091	index:0,count:14716667,average:99.30,stdev:3.96|index:1,count:14638057,average:98.86,stdev:5.35	ThymusGFPplusTreg_replicate2	INSERM			in_mesa	25939024	5.63	3.52	0.03	2351656175	2336753423	2087595384	2089742506	99.37	100.1	14265098	13449625	202.017	487.905	130	111776	85.69	96.88	17689560	12223494	17689560	12223494	92.82	93.47	17689560	13240315	17689560	11793598	135147123	5.75	0.41	0.08	11.45	13.86	0.34	0.75	0.11	0.10	0.00	0.00	0.46	0.06	14265098	556340	198	96	197.77	95.10	1.16	1.19	0.00	0.00	1.11	1.12	0.00	0.01	442.97	202.12	0.12	0.26	58707	473	14396633	561458	1647871	77791	48611	4213	16500	547	0	0	66424	358	2273	63	0	0	22944	537	3984979	111722	984	78	4011180	112400	87.64	85.23	12617227	478549	85339	3896734	45.661819332310	14958091.0	14821438.0	59180.0	1725662.0	52824.0	17047.0	0.0	66782.0	13095776.0	99.1	0.4	11.5	0.4	0.1	0.0	0.4	87.5	50	100	96.07	38	53940360	26.5	23.2	22.6	27.7	0.0	35.1	25.3	bulk
1389135	SRR1947324	SRP056191	SRS874613	SRX973874	SRA246770	INSERM	U1043 CPTP	Mouse regulatory T cells Transcriptome	Regulatory T-cells (Tregs) differentiate in the thymus. After selection, they migrate to the periphery where they exert their effector functions. In the thymus and in the spleen of Rag2-GFP transgenic mice, two populations of Treg are found: I. a GFP+ population (respectively, developing cells and recent thymic emigrants) II. a GFP- population (mature cells).		Spleen GFP- Tregs replicate 1	RNA sequencing analysis Rag2-GFP+ and Rag2-GFP- CD4+CD8-Foxp3-Thy1.1+ Tregs from mouse thymus and spleen were sorted by FACS and total RNA was immediately extracted by using the RNeasy® Micro Kit (QIAGEN) (including a DNase I treatment step) and the quality of the RNA was assessed by using an Agilent 2100 BioAnalyzer (Agilent Technologies). Three biological replicates were performed per cell population. Libraries for RNA-sequencing (RNAseq) were prepared according to the TotalScript RNA-seq protocol (Epicentre), starting from 5 ng of high-quality total RNA (i.e. RIN>7) and using the Oligo(dT) primer synthesis strategy. The quality of each library was assessed by using an Agilent 2100 BioAnalyzer. Samples were indexed and sequenced on Illumina HiSeq 2000 (paired-end 2x100bp). Reads were trimmed by using Cutadapt (v1.3), removing low-quality bases (-q < 10) and clipping adapter sequences. High-quality RNAseq reads were aligned to the mouse reference genome mm10 by using TopHat (v2.0.5) (11). Mice Rag2-Gfp transgenic mice (Rag-GFP) (W. Yu et al., Nature 400, 682 (1999)) on a C57BL/6 (B6) genetic background were provided by Dr. Pamela Fink (T. E. Boursalian, J. Golob, D. M. Soper, C. J. Cooper, P. J. Fink, Nature Immunol 5, 418 (2004)), B6 Foxp3-Thy1.1 knock-in mice by Dr. Alexander Rudensky (A. Liston et al., Proc Natl Acad Sci U S A 105, 11903 (2008)), and B6 GK mice by Dr. Andrew Lew (Y. Zhan, A. J. Corbett, J. L. Brady, R. M. Sutherland, A. M. Lew, Xenotransplantation 7, 267 (2000)). 	Treg from spleen		RNA-Seq	TRANSCRIPTOMIC	PolyA	paired		0.0E0		Illumina HiSeq 2000	age;;8 weeks|BioSampleModel;;Model organism or animal|breed;;C57Bl6 Rag2GFP Foxp3 Thy1 1|sample_type;;SpleenGFPminusTreg|sex;;male|tissue;;Regulatory T cells		200	SpleenGFPminusTreg	SpleenGFPminusTreg	2545422427	13309105	2015-04-15 00:00:00	1218093206	2545422427	13309105	2	13309105	index:0,count:12881467,average:99.21,stdev:4.32|index:1,count:12842146,average:98.69,stdev:5.85	SpleenGFPminusTreg	INSERM			in_mesa	25939024	6.03	3.62	0.03	1839963927	1783443415	1613110156	1577624272	96.93	97.8	12235528	11629316	163.505	429.579	109	160246	82.91	94.98	15982527	10144621	15982527	10144621	89.42	91.21	15982527	10941538	15982527	9742365	153397416	8.34	0.73	0.08	12.52	22.45	0.37	0.43	0.16	0.06	0.00	0.00	0.92	0.07	12235528	889542	198	94	197.46	94.17	1.14	1.17	0.00	0.01	1.10	1.14	0.00	0.01	343.79	357.84	0.17	0.57	90685	688	12414508	894597	1554325	200828	46123	3865	19259	553	0	0	113598	637	2399	99	0	0	28020	691	3990892	128161	1484	137	4022795	129088	86.04	76.99	10681203	688714	100454	3542780	35.267684711410	13309105.0	13125070.0	91373.0	1755153.0	49988.0	19812.0	0.0	114235.0	11369917.0	98.6	0.7	13.2	0.4	0.1	0.0	0.9	85.4	50	100	94.83	38	84834267	25.0	24.1	23.9	27.0	0.0	35.1	25.4	bulk
1389150	SRR1947325	SRP056191	SRS874613	SRX973887	SRA246770	INSERM	U1043 CPTP	Mouse regulatory T cells Transcriptome	Regulatory T-cells (Tregs) differentiate in the thymus. After selection, they migrate to the periphery where they exert their effector functions. In the thymus and in the spleen of Rag2-GFP transgenic mice, two populations of Treg are found: I. a GFP+ population (respectively, developing cells and recent thymic emigrants) II. a GFP- population (mature cells).		Spleen GFP- Tregs replicate 2	RNA sequencing analysis Rag2-GFP+ and Rag2-GFP- CD4+CD8-Foxp3-Thy1.1+ Tregs from mouse thymus and spleen were sorted by FACS and total RNA was immediately extracted by using the RNeasy® Micro Kit (QIAGEN) (including a DNase I treatment step) and the quality of the RNA was assessed by using an Agilent 2100 BioAnalyzer (Agilent Technologies). Three biological replicates were performed per cell population. Libraries for RNA-sequencing (RNAseq) were prepared according to the TotalScript RNA-seq protocol (Epicentre), starting from 5 ng of high-quality total RNA (i.e. RIN>7) and using the Oligo(dT) primer synthesis strategy. The quality of each library was assessed by using an Agilent 2100 BioAnalyzer. Samples were indexed and sequenced on Illumina HiSeq 2000 (paired-end 2x100bp). Reads were trimmed by using Cutadapt (v1.3), removing low-quality bases (-q < 10) and clipping adapter sequences. High-quality RNAseq reads were aligned to the mouse reference genome mm10 by using TopHat (v2.0.5) (11). Mice Rag2-Gfp transgenic mice (Rag-GFP) (W. Yu et al., Nature 400, 682 (1999)) on a C57BL/6 (B6) genetic background were provided by Dr. Pamela Fink (T. E. Boursalian, J. Golob, D. M. Soper, C. J. Cooper, P. J. Fink, Nature Immunol 5, 418 (2004)), B6 Foxp3-Thy1.1 knock-in mice by Dr. Alexander Rudensky (A. Liston et al., Proc Natl Acad Sci U S A 105, 11903 (2008)), and B6 GK mice by Dr. Andrew Lew (Y. Zhan, A. J. Corbett, J. L. Brady, R. M. Sutherland, A. M. Lew, Xenotransplantation 7, 267 (2000)). 	Treg from spleen		RNA-Seq	TRANSCRIPTOMIC	PolyA	paired		0.0E0		Illumina HiSeq 2000	age;;8 weeks|BioSampleModel;;Model organism or animal|breed;;C57Bl6 Rag2GFP Foxp3 Thy1 1|sample_type;;SpleenGFPminusTreg|sex;;male|tissue;;Regulatory T cells		200	SpleenGFPminusTreg	SpleenGFPminusTreg	2389746870	12364654	2015-04-15 00:00:00	1147292279	2389746870	12364654	2	12364654	index:0,count:12097406,average:99.20,stdev:4.33|index:1,count:12033895,average:98.86,stdev:5.37	SpleenGFPminusTreg_replicate2	INSERM			in_mesa	25939024	6.43	4.0	0.03	1822601530	1806174783	1603683446	1602659173	99.1	99.94	11617451	11054038	182.944	466.530	108	122209	83.65	95.43	14843188	9718481	14843188	9718481	91.14	91.66	14843188	10587830	14843188	9334235	143951167	7.90	0.64	0.09	12.19	14.80	0.37	0.70	0.16	0.11	0.00	0.00	0.74	0.07	11617451	592737	198	95	197.72	94.01	1.14	1.18	0.00	0.01	1.09	1.14	0.00	0.01	385.09	269.10	0.12	0.28	75842	544	11766647	598007	1434062	88517	43709	4168	18449	656	0	0	87038	446	1865	67	0	0	17875	576	3131249	105921	843	99	3151832	106663	86.54	84.32	10183389	504220	75733	2961397	39.103125453897	12364654.0	12210188.0	76386.0	1522579.0	47877.0	19105.0	0.0	87484.0	10687609.0	98.8	0.6	12.3	0.4	0.2	0.0	0.7	86.4	50	100	95.19	38	56922584	26.6	23.0	22.4	28.0	0.0	35.2	25.4	bulk
1389183	SRR1947327	SRP056191	SRS874613	SRX973888	SRA246770	INSERM	U1043 CPTP	Mouse regulatory T cells Transcriptome	Regulatory T-cells (Tregs) differentiate in the thymus. After selection, they migrate to the periphery where they exert their effector functions. In the thymus and in the spleen of Rag2-GFP transgenic mice, two populations of Treg are found: I. a GFP+ population (respectively, developing cells and recent thymic emigrants) II. a GFP- population (mature cells).		Spleen GFP- Tregs replicate 3	RNA sequencing analysis Rag2-GFP+ and Rag2-GFP- CD4+CD8-Foxp3-Thy1.1+ Tregs from mouse thymus and spleen were sorted by FACS and total RNA was immediately extracted by using the RNeasy® Micro Kit (QIAGEN) (including a DNase I treatment step) and the quality of the RNA was assessed by using an Agilent 2100 BioAnalyzer (Agilent Technologies). Three biological replicates were performed per cell population. Libraries for RNA-sequencing (RNAseq) were prepared according to the TotalScript RNA-seq protocol (Epicentre), starting from 5 ng of high-quality total RNA (i.e. RIN>7) and using the Oligo(dT) primer synthesis strategy. The quality of each library was assessed by using an Agilent 2100 BioAnalyzer. Samples were indexed and sequenced on Illumina HiSeq 2000 (paired-end 2x100bp). Reads were trimmed by using Cutadapt (v1.3), removing low-quality bases (-q < 10) and clipping adapter sequences. High-quality RNAseq reads were aligned to the mouse reference genome mm10 by using TopHat (v2.0.5) (11). Mice Rag2-Gfp transgenic mice (Rag-GFP) (W. Yu et al., Nature 400, 682 (1999)) on a C57BL/6 (B6) genetic background were provided by Dr. Pamela Fink (T. E. Boursalian, J. Golob, D. M. Soper, C. J. Cooper, P. J. Fink, Nature Immunol 5, 418 (2004)), B6 Foxp3-Thy1.1 knock-in mice by Dr. Alexander Rudensky (A. Liston et al., Proc Natl Acad Sci U S A 105, 11903 (2008)), and B6 GK mice by Dr. Andrew Lew (Y. Zhan, A. J. Corbett, J. L. Brady, R. M. Sutherland, A. M. Lew, Xenotransplantation 7, 267 (2000)). 	Treg from spleen		RNA-Seq	TRANSCRIPTOMIC	PolyA	paired		0.0E0		Illumina HiSeq 2000	age;;8 weeks|BioSampleModel;;Model organism or animal|breed;;C57Bl6 Rag2GFP Foxp3 Thy1 1|sample_type;;SpleenGFPminusTreg|sex;;male|tissue;;Regulatory T cells		200	SpleenGFPminusTreg	SpleenGFPminusTreg	2824557087	14571725	2015-04-15 00:00:00	1363076340	2824557087	14571725	2	14571725	index:0,count:14296526,average:99.23,stdev:4.21|index:1,count:14215354,average:98.90,stdev:5.26	SpleenGFPminusTreg_replicate3	INSERM			in_mesa	25939024	8.32	3.87	0.03	2212690101	2193036835	1933721812	1931267151	99.11	99.87	13776604	13150195	189.314	446.971	119	126372	81.52	93.71	17585118	11231057	17585118	11231057	89.77	89.98	17585118	12367483	17585118	10784541	196275345	8.87	0.53	0.08	12.85	15.27	0.36	0.68	0.20	0.13	0.00	0.00	0.61	0.08	13776604	625934	198	95	197.80	94.79	1.16	1.19	0.00	0.01	1.10	1.12	0.00	0.01	332.35	252.63	0.12	0.27	73994	492	13940155	631570	1791338	96468	50359	4299	27573	847	0	0	85619	490	1892	81	0	0	19533	600	3437680	108224	813	91	3459918	108996	85.98	83.83	11985266	529466	83997	3359961	40.000964320154	14571725.0	14402538.0	74486.0	1887806.0	54658.0	28420.0	0.0	86109.0	12514732.0	98.8	0.5	13.0	0.4	0.2	0.0	0.6	85.9	50	100	95.71	38	60447550	26.6	23.0	22.5	27.8	0.0	35.3	25.4	bulk
1389199	SRR1947328	SRP056191	SRS874663	SRX973884	SRA246770	INSERM	U1043 CPTP	Mouse regulatory T cells Transcriptome	Regulatory T-cells (Tregs) differentiate in the thymus. After selection, they migrate to the periphery where they exert their effector functions. In the thymus and in the spleen of Rag2-GFP transgenic mice, two populations of Treg are found: I. a GFP+ population (respectively, developing cells and recent thymic emigrants) II. a GFP- population (mature cells).		Thymus GFP- Tregs replicate 2	RNA sequencing analysis Rag2-GFP+ and Rag2-GFP- CD4+CD8-Foxp3-Thy1.1+ Tregs from mouse thymus and spleen were sorted by FACS and total RNA was immediately extracted by using the RNeasy® Micro Kit (QIAGEN) (including a DNase I treatment step) and the quality of the RNA was assessed by using an Agilent 2100 BioAnalyzer (Agilent Technologies). Three biological replicates were performed per cell population. Libraries for RNA-sequencing (RNAseq) were prepared according to the TotalScript RNA-seq protocol (Epicentre), starting from 5 ng of high-quality total RNA (i.e. RIN>7) and using the Oligo(dT) primer synthesis strategy. The quality of each library was assessed by using an Agilent 2100 BioAnalyzer. Samples were indexed and sequenced on Illumina HiSeq 2000 (paired-end 2x100bp). Reads were trimmed by using Cutadapt (v1.3), removing low-quality bases (-q < 10) and clipping adapter sequences. High-quality RNAseq reads were aligned to the mouse reference genome mm10 by using TopHat (v2.0.5) (11). Mice Rag2-Gfp transgenic mice (Rag-GFP) (W. Yu et al., Nature 400, 682 (1999)) on a C57BL/6 (B6) genetic background were provided by Dr. Pamela Fink (T. E. Boursalian, J. Golob, D. M. Soper, C. J. Cooper, P. J. Fink, Nature Immunol 5, 418 (2004)), B6 Foxp3-Thy1.1 knock-in mice by Dr. Alexander Rudensky (A. Liston et al., Proc Natl Acad Sci U S A 105, 11903 (2008)), and B6 GK mice by Dr. Andrew Lew (Y. Zhan, A. J. Corbett, J. L. Brady, R. M. Sutherland, A. M. Lew, Xenotransplantation 7, 267 (2000)). 	Recirculating Treg		RNA-Seq	TRANSCRIPTOMIC	PolyA	paired		0.0E0		Illumina HiSeq 2000	age;;8 weeks|BioSampleModel;;Model organism or animal|breed;;C57Bl6 Rag2GFP Foxp3 Thy1 1|sample_type;;ThymusGFPminusTreg|sex;;male|tissue;;Regulatory T cells		200	ThymusGFPminusTreg	ThymusGFPminusTreg	2435734382	12580149	2015-04-15 00:00:00	1165234321	2435734382	12580149	2	12580149	index:0,count:12312790,average:99.25,stdev:4.17|index:1,count:12280500,average:98.83,stdev:5.45	ThymusGFPminusTreg_replicate2	INSERM			in_mesa	25939024	5.24	3.84	0.04	1837526371	1827418324	1616854427	1623036871	99.45	100.38	11866366	11275262	179.406	426.306	118	129215	85.11	97.12	15164260	10099972	15164260	10099972	92.56	93.3	15164260	10983194	15164260	9702703	114156009	6.21	0.62	0.10	12.21	15.10	0.38	0.75	0.13	0.09	0.00	0.00	0.72	0.09	11866366	561722	198	95	197.70	93.92	1.15	1.18	0.00	0.01	1.10	1.13	0.00	0.01	327.63	204.12	0.12	0.28	75052	584	12013141	567008	1467266	85614	45072	4266	15266	538	0	0	86437	482	1904	60	0	0	21599	569	3503056	106700	783	118	3527342	107447	86.56	83.97	10399100	476108	76536	3238301	42.310821051531	12580149.0	12428088.0	75636.0	1552880.0	49338.0	15804.0	0.0	86919.0	10875208.0	98.8	0.6	12.3	0.4	0.1	0.0	0.7	86.4	50	100	95.06	38	53899979	26.3	23.2	22.6	27.8	0.0	35.1	25.2	bulk
1389214	SRR1947329	SRP056191	SRS874663	SRX973886	SRA246770	INSERM	U1043 CPTP	Mouse regulatory T cells Transcriptome	Regulatory T-cells (Tregs) differentiate in the thymus. After selection, they migrate to the periphery where they exert their effector functions. In the thymus and in the spleen of Rag2-GFP transgenic mice, two populations of Treg are found: I. a GFP+ population (respectively, developing cells and recent thymic emigrants) II. a GFP- population (mature cells).		Thymus GFP- Tregs replicate 3	RNA sequencing analysis Rag2-GFP+ and Rag2-GFP- CD4+CD8-Foxp3-Thy1.1+ Tregs from mouse thymus and spleen were sorted by FACS and total RNA was immediately extracted by using the RNeasy® Micro Kit (QIAGEN) (including a DNase I treatment step) and the quality of the RNA was assessed by using an Agilent 2100 BioAnalyzer (Agilent Technologies). Three biological replicates were performed per cell population. Libraries for RNA-sequencing (RNAseq) were prepared according to the TotalScript RNA-seq protocol (Epicentre), starting from 5 ng of high-quality total RNA (i.e. RIN>7) and using the Oligo(dT) primer synthesis strategy. The quality of each library was assessed by using an Agilent 2100 BioAnalyzer. Samples were indexed and sequenced on Illumina HiSeq 2000 (paired-end 2x100bp). Reads were trimmed by using Cutadapt (v1.3), removing low-quality bases (-q < 10) and clipping adapter sequences. High-quality RNAseq reads were aligned to the mouse reference genome mm10 by using TopHat (v2.0.5) (11). Mice Rag2-Gfp transgenic mice (Rag-GFP) (W. Yu et al., Nature 400, 682 (1999)) on a C57BL/6 (B6) genetic background were provided by Dr. Pamela Fink (T. E. Boursalian, J. Golob, D. M. Soper, C. J. Cooper, P. J. Fink, Nature Immunol 5, 418 (2004)), B6 Foxp3-Thy1.1 knock-in mice by Dr. Alexander Rudensky (A. Liston et al., Proc Natl Acad Sci U S A 105, 11903 (2008)), and B6 GK mice by Dr. Andrew Lew (Y. Zhan, A. J. Corbett, J. L. Brady, R. M. Sutherland, A. M. Lew, Xenotransplantation 7, 267 (2000)). 	Recirculating Treg		RNA-Seq	TRANSCRIPTOMIC	PolyA	paired		0.0E0		Illumina HiSeq 2000	age;;8 weeks|BioSampleModel;;Model organism or animal|breed;;C57Bl6 Rag2GFP Foxp3 Thy1 1|sample_type;;ThymusGFPminusTreg|sex;;male|tissue;;Regulatory T cells		200	ThymusGFPminusTreg	ThymusGFPminusTreg	2389901684	12370071	2015-04-15 00:00:00	1134321252	2389901684	12370071	2	12370071	index:0,count:12089382,average:99.24,stdev:4.24|index:1,count:12045605,average:98.81,stdev:5.55	ThymusGFPminusTreg_replicate3	INSERM			in_mesa	25939024	6.23	3.54	0.03	1795201879	1780328120	1576149811	1575812248	99.17	99.98	11605708	11089981	179.182	399.067	108	135968	85.04	97.21	14822432	9869573	14822432	9869573	92.8	93.5	14822432	10770508	14822432	9492261	111880892	6.23	0.74	0.09	12.35	15.25	0.37	0.69	0.14	0.11	0.00	0.00	0.85	0.08	11605708	599817	198	94	197.77	93.12	1.14	1.18	0.00	0.01	1.10	1.13	0.00	0.01	325.80	217.86	0.12	0.28	87208	516	11764916	605155	1453337	92301	43347	4184	16348	659	0	0	99513	495	1302	34	0	0	13841	482	2850295	99280	581	55	2866019	99851	86.29	83.87	10152371	507516	63159	2662200	42.150762361659	12370071.0	12205525.0	87724.0	1545638.0	47531.0	17007.0	0.0	100008.0	10659887.0	98.7	0.7	12.5	0.4	0.1	0.0	0.8	86.2	50	100	94.40	38	57126530	26.5	23.0	22.4	28.2	0.0	35.2	25.1	bulk
2772050	SRR1916262	SRP056191	SRS874663	SRX957257	SRA246770	INSERM	U1043 CPTP	Mouse regulatory T cells Transcriptome	Regulatory T-cells (Tregs) differentiate in the thymus. After selection, they migrate to the periphery where they exert their effector functions. In the thymus and in the spleen of Rag2-GFP transgenic mice, two populations of Treg are found: I. a GFP+ population (respectively, developing cells and recent thymic emigrants) II. a GFP- population (mature cells).		Thymus GFP- Tregs replicate 1	RNA sequencing analysis Rag2-GFP+ and Rag2-GFP- CD4+CD8-Foxp3-Thy1.1+ Tregs from mouse thymus and spleen were sorted by FACS and total RNA was immediately extracted by using the RNeasy® Micro Kit (QIAGEN) (including a DNase I treatment step) and the quality of the RNA was assessed by using an Agilent 2100 BioAnalyzer (Agilent Technologies). Three biological replicates were performed per cell population. Libraries for RNA-sequencing (RNAseq) were prepared according to the TotalScript RNA-seq protocol (Epicentre), starting from 5 ng of high-quality total RNA (i.e. RIN>7) and using the Oligo(dT) primer synthesis strategy. The quality of each library was assessed by using an Agilent 2100 BioAnalyzer. Samples were indexed and sequenced on Illumina HiSeq 2000 (paired-end 2x100bp). Reads were trimmed by using Cutadapt (v1.3), removing low-quality bases (-q < 10) and clipping adapter sequences. High-quality RNAseq reads were aligned to the mouse reference genome mm10 by using TopHat (v2.0.5) (11). Mice Rag2-Gfp transgenic mice (Rag-GFP) (W. Yu et al., Nature 400, 682 (1999)) on a C57BL/6 (B6) genetic background were provided by Dr. Pamela Fink (T. E. Boursalian, J. Golob, D. M. Soper, C. J. Cooper, P. J. Fink, Nature Immunol 5, 418 (2004)), B6 Foxp3-Thy1.1 knock-in mice by Dr. Alexander Rudensky (A. Liston et al., Proc Natl Acad Sci U S A 105, 11903 (2008)), and B6 GK mice by Dr. Andrew Lew (Y. Zhan, A. J. Corbett, J. L. Brady, R. M. Sutherland, A. M. Lew, Xenotransplantation 7, 267 (2000)). 	Recirculating Treg		RNA-Seq	TRANSCRIPTOMIC	PolyA	paired		0.0E0		Illumina HiSeq 2000	age;;8 weeks|BioSampleModel;;Model organism or animal|breed;;C57Bl6 Rag2GFP Foxp3 Thy1 1|sample_type;;ThymusGFPminusTreg|sex;;male|tissue;;Regulatory T cells		200	ThymusGFPminusTreg	ThymusGFPminusTreg	2857286094	14832509	2015-04-15 00:00:00	1356531005	2857286094	14832509	2	14832509	index:0,count:14438505,average:99.22,stdev:4.29|index:1,count:14404086,average:98.91,stdev:5.24	RNA-seq regulatory T cells	INSERM			in_mesa	25939024	6.27	3.19	0.03	2142300615	2086961710	1925368676	1891910089	97.42	98.26	13842854	13154952	169.656	411.321	120	148973	83.63	93.43	17204763	11576964	17204763	11576964	88.86	90.11	17204763	12300726	17204763	11164893	193548077	9.03	0.57	0.08	10.37	18.38	0.33	0.50	0.15	0.07	0.00	0.00	0.71	0.06	13842854	817275	198	95	197.66	94.76	1.14	1.17	0.00	0.01	1.09	1.13	0.00	0.01	382.09	370.09	0.15	0.53	80545	654	14010082	822427	1452154	151161	46395	4121	21245	547	0	0	99588	484	2753	69	0	0	28719	640	4427776	125298	1415	120	4460663	126127	88.44	80.99	12390700	666114	101580	3980229	39.183195510927	14832509.0	14660129.0	81199.0	1603315.0	50516.0	21792.0	0.0	100072.0	13056814.0	98.8	0.5	10.8	0.3	0.1	0.0	0.7	88.0	50	100	95.55	38	78582974	25.6	23.5	23.4	27.6	0.0	35.2	25.6	bulk
2777809	SRR1947316	SRP056191	SRS874594	SRX973879	SRA246770	INSERM	U1043 CPTP	Mouse regulatory T cells Transcriptome	Regulatory T-cells (Tregs) differentiate in the thymus. After selection, they migrate to the periphery where they exert their effector functions. In the thymus and in the spleen of Rag2-GFP transgenic mice, two populations of Treg are found: I. a GFP+ population (respectively, developing cells and recent thymic emigrants) II. a GFP- population (mature cells).		Thymus GFP+ Tregs replicate 3	RNA sequencing analysis Rag2-GFP+ and Rag2-GFP- CD4+CD8-Foxp3-Thy1.1+ Tregs from mouse thymus and spleen were sorted by FACS and total RNA was immediately extracted by using the RNeasy® Micro Kit (QIAGEN) (including a DNase I treatment step) and the quality of the RNA was assessed by using an Agilent 2100 BioAnalyzer (Agilent Technologies). Three biological replicates were performed per cell population. Libraries for RNA-sequencing (RNAseq) were prepared according to the TotalScript RNA-seq protocol (Epicentre), starting from 5 ng of high-quality total RNA (i.e. RIN>7) and using the Oligo(dT) primer synthesis strategy. The quality of each library was assessed by using an Agilent 2100 BioAnalyzer. Samples were indexed and sequenced on Illumina HiSeq 2000 (paired-end 2x100bp). Reads were trimmed by using Cutadapt (v1.3), removing low-quality bases (-q < 10) and clipping adapter sequences. High-quality RNAseq reads were aligned to the mouse reference genome mm10 by using TopHat (v2.0.5) (11). Mice Rag2-Gfp transgenic mice (Rag-GFP) (W. Yu et al., Nature 400, 682 (1999)) on a C57BL/6 (B6) genetic background were provided by Dr. Pamela Fink (T. E. Boursalian, J. Golob, D. M. Soper, C. J. Cooper, P. J. Fink, Nature Immunol 5, 418 (2004)), B6 Foxp3-Thy1.1 knock-in mice by Dr. Alexander Rudensky (A. Liston et al., Proc Natl Acad Sci U S A 105, 11903 (2008)), and B6 GK mice by Dr. Andrew Lew (Y. Zhan, A. J. Corbett, J. L. Brady, R. M. Sutherland, A. M. Lew, Xenotransplantation 7, 267 (2000)). 	Treg recently generated from thymus		RNA-Seq	TRANSCRIPTOMIC	PolyA	paired		0.0E0		Illumina HiSeq 2000	age;;8 weeks|BioSampleModel;;Model organism or animal|breed;;C57Bl6 Rag2GFP Foxp3 Thy1 1|sample_type;;ThymusGFPplusTreg|sex;;male|tissue;;Regulatory T cells		200	ThymusGFPplusTreg	ThymusGFPplusTreg	2757560751	14225664	2015-04-15 00:00:00	1329632426	2757560751	14225664	2	14225664	index:0,count:13956006,average:99.27,stdev:4.08|index:1,count:13879018,average:98.87,stdev:5.35	ThymusGFPplusTreg	INSERM			in_mesa	25939024	7.6	3.97	0.03	2109887427	2085076730	1819891081	1815935620	98.82	99.78	13452013	12995639	176.182	343.285	120	142585	79.28	92.38	17499175	10664882	17499175	10664882	88.41	88.6	17499175	11892865	17499175	10228344	202728566	9.61	0.56	0.07	14.02	16.47	0.35	0.70	0.17	0.12	0.00	0.00	0.64	0.07	13452013	610807	198	95	197.86	94.71	1.15	1.18	0.00	0.01	1.11	1.15	0.00	0.01	357.62	246.52	0.12	0.26	76226	413	13609360	616304	1907506	101484	47254	4317	22649	751	0	0	87444	429	1255	58	0	0	12211	414	2894937	93452	670	57	2909073	93981	84.83	82.64	11544507	509323	67054	2836009	42.294404509798	14225664.0	14062820.0	76639.0	2008990.0	51571.0	23400.0	0.0	87873.0	12053830.0	98.9	0.5	14.1	0.4	0.2	0.0	0.6	84.7	50	100	95.59	38	58913314	27.1	22.6	21.9	28.4	0.0	35.2	25.4	bulk
2778192	SRR1947322	SRP056191	SRS874599	SRX973881	SRA246770	INSERM	U1043 CPTP	Mouse regulatory T cells Transcriptome	Regulatory T-cells (Tregs) differentiate in the thymus. After selection, they migrate to the periphery where they exert their effector functions. In the thymus and in the spleen of Rag2-GFP transgenic mice, two populations of Treg are found: I. a GFP+ population (respectively, developing cells and recent thymic emigrants) II. a GFP- population (mature cells).		Spleen GFP+ Tregs replicate 2	RNA sequencing analysis Rag2-GFP+ and Rag2-GFP- CD4+CD8-Foxp3-Thy1.1+ Tregs from mouse thymus and spleen were sorted by FACS and total RNA was immediately extracted by using the RNeasy® Micro Kit (QIAGEN) (including a DNase I treatment step) and the quality of the RNA was assessed by using an Agilent 2100 BioAnalyzer (Agilent Technologies). Three biological replicates were performed per cell population. Libraries for RNA-sequencing (RNAseq) were prepared according to the TotalScript RNA-seq protocol (Epicentre), starting from 5 ng of high-quality total RNA (i.e. RIN>7) and using the Oligo(dT) primer synthesis strategy. The quality of each library was assessed by using an Agilent 2100 BioAnalyzer. Samples were indexed and sequenced on Illumina HiSeq 2000 (paired-end 2x100bp). Reads were trimmed by using Cutadapt (v1.3), removing low-quality bases (-q < 10) and clipping adapter sequences. High-quality RNAseq reads were aligned to the mouse reference genome mm10 by using TopHat (v2.0.5) (11). Mice Rag2-Gfp transgenic mice (Rag-GFP) (W. Yu et al., Nature 400, 682 (1999)) on a C57BL/6 (B6) genetic background were provided by Dr. Pamela Fink (T. E. Boursalian, J. Golob, D. M. Soper, C. J. Cooper, P. J. Fink, Nature Immunol 5, 418 (2004)), B6 Foxp3-Thy1.1 knock-in mice by Dr. Alexander Rudensky (A. Liston et al., Proc Natl Acad Sci U S A 105, 11903 (2008)), and B6 GK mice by Dr. Andrew Lew (Y. Zhan, A. J. Corbett, J. L. Brady, R. M. Sutherland, A. M. Lew, Xenotransplantation 7, 267 (2000)). 	Treg recently generated from spleen		RNA-Seq	TRANSCRIPTOMIC	PolyA	paired		0.0E0		Illumina HiSeq 2000	age;;8 weeks|BioSampleModel;;Model organism or animal|breed;;C57Bl6 Rag2GFP Foxp3 Thy1 1|sample_type;;SpleenGFPplusTreg|sex;;male|tissue;;Regulatory T cells		200	SpleenGFPplusTreg	SpleenGFPplusTreg	3008180604	15578134	2015-04-15 00:00:00	1452423014	3008180604	15578134	2	15578134	index:0,count:15226555,average:99.22,stdev:4.29|index:1,count:15163035,average:98.76,stdev:5.66	SpleenGFPplusTreg_Replicate2	INSERM			in_mesa	25939024	5.76	4.28	0.04	2237710373	2216101918	1937377436	1936918353	99.03	99.98	14602955	13969644	173.360	420.035	108	168754	82.72	96.01	19189578	12080093	19189578	12080093	91.34	91.98	19189578	13337825	19189578	11573290	161808576	7.23	0.69	0.09	13.64	16.82	0.42	0.72	0.18	0.12	0.00	0.00	0.81	0.09	14602955	759596	198	94	197.64	93.48	1.14	1.18	0.00	0.01	1.10	1.14	0.00	0.01	370.29	250.91	0.12	0.29	102374	722	14811456	766678	2020675	128943	62130	5482	27116	903	0	0	119255	697	2176	79	0	0	22531	791	4013225	135512	933	85	4038865	136467	84.95	82.26	12582280	630653	80671	3777520	46.826244871143	15578134.0	15362551.0	103096.0	2149618.0	67612.0	28019.0	0.0	119952.0	13212933.0	98.6	0.7	13.8	0.4	0.2	0.0	0.8	84.8	50	100	94.59	38	72521128	26.1	23.4	22.8	27.7	0.0	35.0	25.1	bulk
2778224	SRR1947323	SRP056191	SRS874599	SRX973882	SRA246770	INSERM	U1043 CPTP	Mouse regulatory T cells Transcriptome	Regulatory T-cells (Tregs) differentiate in the thymus. After selection, they migrate to the periphery where they exert their effector functions. In the thymus and in the spleen of Rag2-GFP transgenic mice, two populations of Treg are found: I. a GFP+ population (respectively, developing cells and recent thymic emigrants) II. a GFP- population (mature cells).		Spleen GFP+ Tregs replicate 3	RNA sequencing analysis Rag2-GFP+ and Rag2-GFP- CD4+CD8-Foxp3-Thy1.1+ Tregs from mouse thymus and spleen were sorted by FACS and total RNA was immediately extracted by using the RNeasy® Micro Kit (QIAGEN) (including a DNase I treatment step) and the quality of the RNA was assessed by using an Agilent 2100 BioAnalyzer (Agilent Technologies). Three biological replicates were performed per cell population. Libraries for RNA-sequencing (RNAseq) were prepared according to the TotalScript RNA-seq protocol (Epicentre), starting from 5 ng of high-quality total RNA (i.e. RIN>7) and using the Oligo(dT) primer synthesis strategy. The quality of each library was assessed by using an Agilent 2100 BioAnalyzer. Samples were indexed and sequenced on Illumina HiSeq 2000 (paired-end 2x100bp). Reads were trimmed by using Cutadapt (v1.3), removing low-quality bases (-q < 10) and clipping adapter sequences. High-quality RNAseq reads were aligned to the mouse reference genome mm10 by using TopHat (v2.0.5) (11). Mice Rag2-Gfp transgenic mice (Rag-GFP) (W. Yu et al., Nature 400, 682 (1999)) on a C57BL/6 (B6) genetic background were provided by Dr. Pamela Fink (T. E. Boursalian, J. Golob, D. M. Soper, C. J. Cooper, P. J. Fink, Nature Immunol 5, 418 (2004)), B6 Foxp3-Thy1.1 knock-in mice by Dr. Alexander Rudensky (A. Liston et al., Proc Natl Acad Sci U S A 105, 11903 (2008)), and B6 GK mice by Dr. Andrew Lew (Y. Zhan, A. J. Corbett, J. L. Brady, R. M. Sutherland, A. M. Lew, Xenotransplantation 7, 267 (2000)). 	Treg recently generated from spleen		RNA-Seq	TRANSCRIPTOMIC	PolyA	paired				Illumina HiSeq 2000	age;;8 weeks|BioSampleModel;;Model organism or animal|breed;;C57Bl6 Rag2GFP Foxp3 Thy1 1|sample_type;;SpleenGFPplusTreg|sex;;male|tissue;;Regulatory T cells		200	SpleenGFPplusTreg	SpleenGFPplusTreg	2791724460	14374137	2015-04-15 00:00:00	1355183900	2791724460	14374137	2	14374137	index:0,count:14105654,average:99.04,stdev:4.76|index:1,count:14057282,average:99.21,stdev:4.34	SpleenGFPplusTreg_replicate3	INSERM			in_mesa	25939024	7.28	3.77	0.04	2143216624	2120184577	1897622028	1892064201	98.93	99.71	13610701	12977185	181.035	439.196	120	130257	81.97	92.95	17078413	11156666	17078413	11156666	89.09	89.32	17078413	12125418	17078413	10720576	195096376	9.10	0.56	0.09	11.66	14.03	0.41	0.64	0.24	0.13	0.00	0.00	0.64	0.11	13610701	580188	198	95	197.87	94.38	1.15	1.19	0.00	0.01	1.10	1.13	0.00	0.01	280.45	191.57	0.12	0.28	76575	538	13788799	585338	1608311	82140	56373	3738	32807	765	0	0	88918	647	2415	64	0	0	27019	645	3925445	114018	994	87	3955873	114814	87.04	85.09	12002390	498048	98651	3696179	37.467222836058	14374137.0	14190889.0	77113.0	1690451.0	60111.0	33572.0	0.0	89565.0	12500438.0	98.7	0.5	11.8	0.4	0.2	0.0	0.6	87.0	50	100	95.54	38	55921437	26.1	23.4	23.0	27.5	0.0	35.2	25.4	bulk
2780401	SRR1916367	SRP056191	SRS874594	SRX957164	SRA246770	INSERM	U1043 CPTP	Mouse regulatory T cells Transcriptome	Regulatory T-cells (Tregs) differentiate in the thymus. After selection, they migrate to the periphery where they exert their effector functions. In the thymus and in the spleen of Rag2-GFP transgenic mice, two populations of Treg are found: I. a GFP+ population (respectively, developing cells and recent thymic emigrants) II. a GFP- population (mature cells).		Thymus GFP+ Tregs replicate 1	Totalscript RNA-seq kit (Illumina)	Treg recently generated from thymus		RNA-Seq	TRANSCRIPTOMIC	PolyA	paired		0.0E0		Illumina HiSeq 2000	age;;8 weeks|BioSampleModel;;Model organism or animal|breed;;C57Bl6 Rag2GFP Foxp3 Thy1 1|sample_type;;ThymusGFPplusTreg|sex;;male|tissue;;Regulatory T cells		200	ThymusGFPplusTreg	ThymusGFPplusTreg	2850250956	14901367	2015-04-15 00:00:00	1374247898	2850250956	14901367	2	14901367	index:0,count:14426439,average:99.19,stdev:4.41|index:1,count:14374421,average:98.74,stdev:5.72	RNA-seq regulatory T cells_2	INSERM			in_mesa	25939024	5.45	3.43	0.04	2054593078	1994519294	1796266137	1761549077	97.08	98.07	13690478	13025359	163.116	404.981	109	179474	81.93	94.13	18003055	11216237	18003055	11216237	88.67	90.42	18003055	12138739	18003055	10774019	187532857	9.13	0.75	0.09	12.77	22.10	0.40	0.51	0.17	0.07	0.00	0.00	0.93	0.07	13690478	995295	198	94	197.49	94.25	1.14	1.15	0.00	0.01	1.10	1.15	0.00	0.01	352.38	327.89	0.17	0.56	103906	868	13899493	1001874	1774657	221453	55442	5153	24044	675	0	0	129529	751	2679	62	0	0	30159	848	4317671	137338	1441	176	4351950	138424	85.73	77.24	11915821	773842	100803	3835180	38.046288304912	14901367.0	14685773.0	104774.0	1996110.0	60595.0	24719.0	0.0	130280.0	12689663.0	98.6	0.7	13.4	0.4	0.2	0.0	0.9	85.2	50	100	94.95	38	95127415	25.0	24.0	23.8	27.2	0.0	35.1	25.4	bulk
2780434	SRR1916368	SRP056191	SRS874599	SRX957169	SRA246770	INSERM	U1043 CPTP	Mouse regulatory T cells Transcriptome	Regulatory T-cells (Tregs) differentiate in the thymus. After selection, they migrate to the periphery where they exert their effector functions. In the thymus and in the spleen of Rag2-GFP transgenic mice, two populations of Treg are found: I. a GFP+ population (respectively, developing cells and recent thymic emigrants) II. a GFP- population (mature cells).		Spleen GFP+ Tregs replicate 1	RNA sequencing analysis Rag2-GFP+ and Rag2-GFP- CD4+CD8-Foxp3-Thy1.1+ Tregs from mouse thymus and spleen were sorted by FACS and total RNA was immediately extracted by using the RNeasy® Micro Kit (QIAGEN) (including a DNase I treatment step) and the quality of the RNA was assessed by using an Agilent 2100 BioAnalyzer (Agilent Technologies). Three biological replicates were performed per cell population. Libraries for RNA-sequencing (RNAseq) were prepared according to the TotalScript RNA-seq protocol (Epicentre), starting from 5 ng of high-quality total RNA (i.e. RIN>7) and using the Oligo(dT) primer synthesis strategy. The quality of each library was assessed by using an Agilent 2100 BioAnalyzer. Samples were indexed and sequenced on Illumina HiSeq 2000 (paired-end 2x100bp). Reads were trimmed by using Cutadapt (v1.3), removing low-quality bases (-q < 10) and clipping adapter sequences. High-quality RNAseq reads were aligned to the mouse reference genome mm10 by using TopHat (v2.0.5) (11). Mice Rag2-Gfp transgenic mice (Rag-GFP) (W. Yu et al., Nature 400, 682 (1999)) on a C57BL/6 (B6) genetic background were provided by Dr. Pamela Fink (T. E. Boursalian, J. Golob, D. M. Soper, C. J. Cooper, P. J. Fink, Nature Immunol 5, 418 (2004)), B6 Foxp3-Thy1.1 knock-in mice by Dr. Alexander Rudensky (A. Liston et al., Proc Natl Acad Sci U S A 105, 11903 (2008)), and B6 GK mice by Dr. Andrew Lew (Y. Zhan, A. J. Corbett, J. L. Brady, R. M. Sutherland, A. M. Lew, Xenotransplantation 7, 267 (2000)). 	Treg recently generated from spleen		RNA-Seq	TRANSCRIPTOMIC	PolyA	paired		0.0E0		Illumina HiSeq 2000	age;;8 weeks|BioSampleModel;;Model organism or animal|breed;;C57Bl6 Rag2GFP Foxp3 Thy1 1|sample_type;;SpleenGFPplusTreg|sex;;male|tissue;;Regulatory T cells		200	SpleenGFPplusTreg	SpleenGFPplusTreg	2987887645	15598599	2015-04-15 00:00:00	1437655460	2987887645	15598599	2	15598599	index:0,count:15120640,average:99.19,stdev:4.37|index:1,count:15060546,average:98.80,stdev:5.54	RNA-seq regulatory T cells_3	INSERM			in_mesa	25939024	5.29	3.74	0.04	2169257850	2096842039	1899657253	1853614181	96.66	97.58	14363461	13650108	165.394	433.144	109	176136	81.12	92.89	18751160	11651339	18751160	11651339	87.93	89.28	18751160	12629785	18751160	11198074	210166315	9.69	0.70	0.09	12.49	21.77	0.40	0.47	0.22	0.08	0.00	0.00	0.89	0.09	14363461	1009423	198	95	197.51	94.34	1.15	1.16	0.00	0.01	1.11	1.15	0.00	0.01	372.32	365.76	0.16	0.55	102185	879	14582587	1016012	1820843	221193	57691	4824	31665	837	0	0	129770	928	2929	106	0	0	33061	810	4596635	145915	1879	191	4634504	147022	86.01	77.58	12542618	788230	108370	4095531	37.792110362646	15598599.0	15372884.0	103064.0	2042036.0	62515.0	32502.0	0.0	130698.0	13330848.0	98.6	0.7	13.1	0.4	0.2	0.0	0.8	85.5	50	100	95.28	38	96804425	25.0	24.0	23.8	27.1	0.0	35.1	25.6	bulk
1741464	SRR2229929	SRP056666	SRS1052839	SRX1178474	SRA249145	GEO		Spatial gene expression gradients underlie prominent heterogeneity of CA1 pyramidal neurons	Tissue and organ function has been conventionally understood in terms of the interactions among discrete and homogeneous cell types.  This approach has proven difficult in neuroscience due to the marked diversity across different neuron classes, but may also be further hampered by prominent within-class variability.  Here, we considered a well-defined, canonical neuronal population – hippocampal CA1 pyramidal cells – and systematically examined the extent and spatial rules of transcriptional heterogeneity.  Using next-generation RNA sequencing, we identified striking variability in CA1 PCs, such that the differences along the dorsal-ventral axis rivaled differences across distinct pyramidal neuron classes. This variability emerged from a spectrum of continuous expression gradients, producing a profile consistent with a multifarious continuum of cells.  This work reveals an unexpected amount of variability within a canonical and narrowly defined neuronal population and suggests that continuous, within-class heterogeneity may be an important feature of neural circuits. Overall design: Hippocampal RNA profiles were generated by deep sequencing on Illumina HiSeq 2500, with three biological replicates per population		GSM1867257: deep_0; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Manual sorting to purify for fluorescent neurons from microdissected slices was performed according to previous methods (Hempel et al., 2007). Total RNA was isolated from each sample using PicoPure RNA Isolation kit (Life Technologies, Frederick, MD) including the on-column RNAseq-free DNaseI treatment (Qiagen, Hilden, Germany) following the manufacturers’ recommendations.  Eluted RNA (11 ul) was dried in a speed vac to approximately 2-4 ul.  ERCC control RNAs (Life Technologies) were added using 1 ul of 1:100,000 dilution for every 50 cells.  cDNA was amplified from this input material using Ovation RNA-seq v2 kit (NuGEN, San Carlos, CA).  Approximately half of the resulting cDNA was used to make the sequencing libraries using the Ovation Rapid DR Multiplexing kit (NuGEN).	Illumina HiSeq 2500	cell population;;Deep CA1 pyramidal cells|location;;CA1|source_name;;Deep CA1 pyramidal cells	GEO Accession;;GSM1867257		GSM1867257	deep_0	3292421000	32924210	2016-01-06 15:50:16	1551694082	3292421000	32924210	1	32924210	index:0,count:32924210,average:100,stdev:0	GSM1867257_r1				in_mesa	26777276	5.13	2.96	0.06	2985565661	2960316422	2811797715	2812938216	99.15	100.04	0	0	0	0	0	0	68.29	72.56	33816927	20910515	33816927	20910515	64.61	66.17	33816927	19782420	33816927	19068656	699730890	23.44	3.16	0	5.48	0	0.28	0	0.35	0	0.00	0	6.36	0	30620195	0	100	0	97.57	0	2.60	0	0.01	0	2.35	0	0.02	0	464.81	0	0.32	0	1039332	0	32924210	0	1803049	0	93658	0	114895	0	0	0	2095462	0	4345	0	0	0	30048	0	3333032	0	23475	0	3390900	0	87.53	0	28817146	0	110583	3509682	31.737988660101	32924210.0	30620195.0	1039332.0	1803049.0	93658.0	114895.0	0.0	2095462.0	28817146.0	93.0	3.2	5.5	0.3	0.3	0.0	6.4	87.5	100	100	100.00	8	3292421000	27.0	23.1	23.3	26.5	0.0	35.6	20.0	bulk
1741672	SRR2229936	SRP056666	SRS1052832	SRX1178481	SRA249145	GEO		Spatial gene expression gradients underlie prominent heterogeneity of CA1 pyramidal neurons	Tissue and organ function has been conventionally understood in terms of the interactions among discrete and homogeneous cell types.  This approach has proven difficult in neuroscience due to the marked diversity across different neuron classes, but may also be further hampered by prominent within-class variability.  Here, we considered a well-defined, canonical neuronal population – hippocampal CA1 pyramidal cells – and systematically examined the extent and spatial rules of transcriptional heterogeneity.  Using next-generation RNA sequencing, we identified striking variability in CA1 PCs, such that the differences along the dorsal-ventral axis rivaled differences across distinct pyramidal neuron classes. This variability emerged from a spectrum of continuous expression gradients, producing a profile consistent with a multifarious continuum of cells.  This work reveals an unexpected amount of variability within a canonical and narrowly defined neuronal population and suggests that continuous, within-class heterogeneity may be an important feature of neural circuits. Overall design: Hippocampal RNA profiles were generated by deep sequencing on Illumina HiSeq 2500, with three biological replicates per population		GSM1867264: ca3v_1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Manual sorting to purify for fluorescent neurons from microdissected slices was performed according to previous methods (Hempel et al., 2007). Total RNA was isolated from each sample using PicoPure RNA Isolation kit (Life Technologies, Frederick, MD) including the on-column RNAseq-free DNaseI treatment (Qiagen, Hilden, Germany) following the manufacturers’ recommendations.  Eluted RNA (11 ul) was dried in a speed vac to approximately 2-4 ul.  ERCC control RNAs (Life Technologies) were added using 1 ul of 1:100,000 dilution for every 50 cells.  cDNA was amplified from this input material using Ovation RNA-seq v2 kit (NuGEN, San Carlos, CA).  Approximately half of the resulting cDNA was used to make the sequencing libraries using the Ovation Rapid DR Multiplexing kit (NuGEN).	Illumina HiSeq 2500	cell population;;Ventral CA3 pyramidal cells|location;;CA3|source_name;;Ventral CA3 pyramidal cells	GEO Accession;;GSM1867264		GSM1867264	ca3v_1	4371547305	47005885	2016-01-06 15:50:16	2234710388	4371547305	47005885	1	47005885	index:0,count:47005885,average:93,stdev:0	GSM1867264_r1				in_mesa	26777276	9.32	3.12	0.06	3989176293	3979265414	3690790824	3725259250	99.75	100.93	0	0	0	0	0	0	77.42	83.74	49805029	34106653	49805029	34106653	73.83	76.62	49805029	32525473	49805029	31204143	514725363	12.90	3.34	0	7.08	0	0.31	0	0.26	0	0.00	0	5.71	0	44055016	0	93	0	90.62	0	2.77	0	0.01	0	1.31	0	0.01	0	441.83	0	0.44	0	1570128	0	47005885	0	3328166	0	147080	0	122066	0	0	0	2681723	0	6205	0	0	0	44145	0	4748351	0	29873	0	4828574	0	86.64	0	40726850	0	137726	4906629	35.626018326242	47005885.0	44055016.0	1570128.0	3328166.0	147080.0	122066.0	0.0	2681723.0	40726850.0	93.7	3.3	7.1	0.3	0.3	0.0	5.7	86.6	93	93	93.00	8	4371547305	27.2	23.1	23.3	26.4	0.0	34.0	17.7	bulk
1741688	SRR2229937	SRP056666	SRS1052831	SRX1178482	SRA249145	GEO		Spatial gene expression gradients underlie prominent heterogeneity of CA1 pyramidal neurons	Tissue and organ function has been conventionally understood in terms of the interactions among discrete and homogeneous cell types.  This approach has proven difficult in neuroscience due to the marked diversity across different neuron classes, but may also be further hampered by prominent within-class variability.  Here, we considered a well-defined, canonical neuronal population – hippocampal CA1 pyramidal cells – and systematically examined the extent and spatial rules of transcriptional heterogeneity.  Using next-generation RNA sequencing, we identified striking variability in CA1 PCs, such that the differences along the dorsal-ventral axis rivaled differences across distinct pyramidal neuron classes. This variability emerged from a spectrum of continuous expression gradients, producing a profile consistent with a multifarious continuum of cells.  This work reveals an unexpected amount of variability within a canonical and narrowly defined neuronal population and suggests that continuous, within-class heterogeneity may be an important feature of neural circuits. Overall design: Hippocampal RNA profiles were generated by deep sequencing on Illumina HiSeq 2500, with three biological replicates per population		GSM1867265: ca3v_2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Manual sorting to purify for fluorescent neurons from microdissected slices was performed according to previous methods (Hempel et al., 2007). Total RNA was isolated from each sample using PicoPure RNA Isolation kit (Life Technologies, Frederick, MD) including the on-column RNAseq-free DNaseI treatment (Qiagen, Hilden, Germany) following the manufacturers’ recommendations.  Eluted RNA (11 ul) was dried in a speed vac to approximately 2-4 ul.  ERCC control RNAs (Life Technologies) were added using 1 ul of 1:100,000 dilution for every 50 cells.  cDNA was amplified from this input material using Ovation RNA-seq v2 kit (NuGEN, San Carlos, CA).  Approximately half of the resulting cDNA was used to make the sequencing libraries using the Ovation Rapid DR Multiplexing kit (NuGEN).	Illumina HiSeq 2500	cell population;;Ventral CA3 pyramidal cells|location;;CA3|source_name;;Ventral CA3 pyramidal cells	GEO Accession;;GSM1867265		GSM1867265	ca3v_2	5067517455	54489435	2016-01-06 15:50:16	2592842981	5067517455	54489435	1	54489435	index:0,count:54489435,average:93,stdev:0	GSM1867265_r1				in_mesa	26777276	11.69	3.05	0.06	4645513348	4617303168	4327737118	4345174537	99.39	100.4	0	0	0	0	0	0	78.26	84.07	57146269	40035729	57146269	40035729	75.47	77.81	57146269	38604532	57146269	37054082	579455360	12.47	3.18	0	6.49	0	0.29	0	0.24	0	0.00	0	5.58	0	51155319	0	93	0	90.88	0	2.45	0	0.01	0	1.31	0	0.01	0	514.86	0	0.43	0	1731922	0	54489435	0	3533736	0	160375	0	132498	0	0	0	3041243	0	7469	0	0	0	47778	0	5399334	0	32047	0	5486628	0	87.40	0	47621583	0	142269	5587257	39.272483815870	54489435.0	51155319.0	1731922.0	3533736.0	160375.0	132498.0	0.0	3041243.0	47621583.0	93.9	3.2	6.5	0.3	0.2	0.0	5.6	87.4	93	93	93.00	8	5067517455	27.6	22.7	22.8	26.9	0.0	33.9	17.5	bulk
1741720	SRR2229939	SRP056666	SRS1052829	SRX1178484	SRA249145	GEO		Spatial gene expression gradients underlie prominent heterogeneity of CA1 pyramidal neurons	Tissue and organ function has been conventionally understood in terms of the interactions among discrete and homogeneous cell types.  This approach has proven difficult in neuroscience due to the marked diversity across different neuron classes, but may also be further hampered by prominent within-class variability.  Here, we considered a well-defined, canonical neuronal population – hippocampal CA1 pyramidal cells – and systematically examined the extent and spatial rules of transcriptional heterogeneity.  Using next-generation RNA sequencing, we identified striking variability in CA1 PCs, such that the differences along the dorsal-ventral axis rivaled differences across distinct pyramidal neuron classes. This variability emerged from a spectrum of continuous expression gradients, producing a profile consistent with a multifarious continuum of cells.  This work reveals an unexpected amount of variability within a canonical and narrowly defined neuronal population and suggests that continuous, within-class heterogeneity may be an important feature of neural circuits. Overall design: Hippocampal RNA profiles were generated by deep sequencing on Illumina HiSeq 2500, with three biological replicates per population		GSM1867267: sst_1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Manual sorting to purify for fluorescent neurons from microdissected slices was performed according to previous methods (Hempel et al., 2007). Total RNA was isolated from each sample using PicoPure RNA Isolation kit (Life Technologies, Frederick, MD) including the on-column RNAseq-free DNaseI treatment (Qiagen, Hilden, Germany) following the manufacturers’ recommendations.  Eluted RNA (11 ul) was dried in a speed vac to approximately 2-4 ul.  ERCC control RNAs (Life Technologies) were added using 1 ul of 1:100,000 dilution for every 50 cells.  cDNA was amplified from this input material using Ovation RNA-seq v2 kit (NuGEN, San Carlos, CA).  Approximately half of the resulting cDNA was used to make the sequencing libraries using the Ovation Rapid DR Multiplexing kit (NuGEN).	Illumina HiSeq 2500	cell population;;SST interneuron|location;;CA1|source_name;;SST interneurons	GEO Accession;;GSM1867267		GSM1867267	sst_1	3662609480	38553784	2016-01-06 15:50:16	2300346509	3662609480	38553784	1	38553784	index:0,count:38553784,average:95,stdev:0	GSM1867267_r1				in_mesa	26777276	8.4	2.79	0.06	3160910954	3200128676	2823027896	2920693198	101.24	103.46	0	0	0	0	0	0	78.79	88.31	40873800	26942575	40873800	26942575	73.17	77.36	40873800	25022832	40873800	23600795	258981361	8.19	3.59	0	9.57	0	0.33	0	0.28	0	0.00	0	10.69	0	34197247	0	95	0	92.53	0	3.67	0	0.03	0	1.26	0	0.02	0	673.76	0	0.45	0	1383562	0	38553784	0	3689435	0	126304	0	109334	0	0	0	4120899	0	4285	0	0	0	29200	0	3410513	0	25743	0	3469741	0	79.13	0	30507812	0	128795	3554510	27.598198687837	38553784.0	34197247.0	1383562.0	3689435.0	126304.0	109334.0	0.0	4120899.0	30507812.0	88.7	3.6	9.6	0.3	0.3	0.0	10.7	79.1	95	95	95.00	38	3662609480	25.8	24.2	24.2	25.8	0.0	36.3	20.1	bulk
1741848	SRR2229941	SRP056666	SRS1052827	SRX1178486	SRA249145	GEO		Spatial gene expression gradients underlie prominent heterogeneity of CA1 pyramidal neurons	Tissue and organ function has been conventionally understood in terms of the interactions among discrete and homogeneous cell types.  This approach has proven difficult in neuroscience due to the marked diversity across different neuron classes, but may also be further hampered by prominent within-class variability.  Here, we considered a well-defined, canonical neuronal population – hippocampal CA1 pyramidal cells – and systematically examined the extent and spatial rules of transcriptional heterogeneity.  Using next-generation RNA sequencing, we identified striking variability in CA1 PCs, such that the differences along the dorsal-ventral axis rivaled differences across distinct pyramidal neuron classes. This variability emerged from a spectrum of continuous expression gradients, producing a profile consistent with a multifarious continuum of cells.  This work reveals an unexpected amount of variability within a canonical and narrowly defined neuronal population and suggests that continuous, within-class heterogeneity may be an important feature of neural circuits. Overall design: Hippocampal RNA profiles were generated by deep sequencing on Illumina HiSeq 2500, with three biological replicates per population		GSM1867270: pv_0; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Manual sorting to purify for fluorescent neurons from microdissected slices was performed according to previous methods (Hempel et al., 2007). Total RNA was isolated from each sample using PicoPure RNA Isolation kit (Life Technologies, Frederick, MD) including the on-column RNAseq-free DNaseI treatment (Qiagen, Hilden, Germany) following the manufacturers’ recommendations.  Eluted RNA (11 ul) was dried in a speed vac to approximately 2-4 ul.  ERCC control RNAs (Life Technologies) were added using 1 ul of 1:100,000 dilution for every 50 cells.  cDNA was amplified from this input material using Ovation RNA-seq v2 kit (NuGEN, San Carlos, CA).  Approximately half of the resulting cDNA was used to make the sequencing libraries using the Ovation Rapid DR Multiplexing kit (NuGEN).	Illumina HiSeq 2500	cell population;;PV interneuron|location;;CA1|source_name;;PV interneurons	GEO Accession;;GSM1867270		GSM1867270	pv_0	5264918145	55420191	2016-01-06 15:50:16	2472287127	5264918145	55420191	1	55420191	index:0,count:55420191,average:95,stdev:0	GSM1867270_r1				in_mesa	26777276	13.9	2.36	0.08	4558462608	4567163642	4150894506	4236720551	100.19	102.07	0	0	0	0	0	0	73.27	80.54	56967310	36136845	56967310	36136845	68.71	71.38	56967310	33890158	56967310	32024669	698344504	15.32	3.91	0	8.04	0	0.31	0	0.41	0	0.00	0	10.28	0	49322550	0	95	0	92.52	0	3.76	0	0.04	0	1.26	0	0.02	0	475.03	0	0.39	0	2165608	0	55420191	0	4455822	0	174228	0	226133	0	0	0	5697280	0	5560	0	0	0	32499	0	3725337	0	41790	0	3805186	0	80.96	0	44866728	0	107579	3899129	36.244332072245	55420191.0	49322550.0	2165608.0	4455822.0	174228.0	226133.0	0.0	5697280.0	44866728.0	89.0	3.9	8.0	0.3	0.4	0.0	10.3	81.0	95	95	95.00	8	5264918145	27.0	23.0	23.1	26.9	0.0	35.4	19.2	bulk
1741882	SRR2229943	SRP056666	SRS1052825	SRX1178488	SRA249145	GEO		Spatial gene expression gradients underlie prominent heterogeneity of CA1 pyramidal neurons	Tissue and organ function has been conventionally understood in terms of the interactions among discrete and homogeneous cell types.  This approach has proven difficult in neuroscience due to the marked diversity across different neuron classes, but may also be further hampered by prominent within-class variability.  Here, we considered a well-defined, canonical neuronal population – hippocampal CA1 pyramidal cells – and systematically examined the extent and spatial rules of transcriptional heterogeneity.  Using next-generation RNA sequencing, we identified striking variability in CA1 PCs, such that the differences along the dorsal-ventral axis rivaled differences across distinct pyramidal neuron classes. This variability emerged from a spectrum of continuous expression gradients, producing a profile consistent with a multifarious continuum of cells.  This work reveals an unexpected amount of variability within a canonical and narrowly defined neuronal population and suggests that continuous, within-class heterogeneity may be an important feature of neural circuits. Overall design: Hippocampal RNA profiles were generated by deep sequencing on Illumina HiSeq 2500, with three biological replicates per population		GSM1867273: pv_2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Manual sorting to purify for fluorescent neurons from microdissected slices was performed according to previous methods (Hempel et al., 2007). Total RNA was isolated from each sample using PicoPure RNA Isolation kit (Life Technologies, Frederick, MD) including the on-column RNAseq-free DNaseI treatment (Qiagen, Hilden, Germany) following the manufacturers’ recommendations.  Eluted RNA (11 ul) was dried in a speed vac to approximately 2-4 ul.  ERCC control RNAs (Life Technologies) were added using 1 ul of 1:100,000 dilution for every 50 cells.  cDNA was amplified from this input material using Ovation RNA-seq v2 kit (NuGEN, San Carlos, CA).  Approximately half of the resulting cDNA was used to make the sequencing libraries using the Ovation Rapid DR Multiplexing kit (NuGEN).	Illumina HiSeq 2500	cell population;;PV interneuron|location;;CA1|source_name;;PV interneurons	GEO Accession;;GSM1867273		GSM1867273	pv_2	4841535730	50963534	2016-01-06 15:50:16	2280130312	4841535730	50963534	1	50963534	index:0,count:50963534,average:95,stdev:0	GSM1867273_r1				in_mesa	26777276	12.51	2.66	0.08	4309677143	4303183834	3957875258	4006849121	99.85	101.24	0	0	0	0	0	0	71.75	78.19	53059681	33344436	53059681	33344436	67.9	70.44	53059681	31555189	53059681	30037059	772727609	17.93	3.39	0	7.52	0	0.32	0	0.37	0	0.00	0	8.12	0	46474012	0	95	0	92.81	0	2.89	0	0.02	0	1.41	0	0.01	0	528.73	0	0.39	0	1725492	0	50963534	0	3830369	0	162683	0	187792	0	0	0	4139047	0	4864	0	0	0	34946	0	3704960	0	34580	0	3779350	0	83.67	0	42643643	0	116930	3864648	33.050953561960	50963534.0	46474012.0	1725492.0	3830369.0	162683.0	187792.0	0.0	4139047.0	42643643.0	91.2	3.4	7.5	0.3	0.4	0.0	8.1	83.7	95	95	95.00	8	4841535730	27.2	22.9	22.9	27.0	0.0	35.4	19.4	bulk
1741897	SRR2229944	SRP056666	SRS1052824	SRX1178489	SRA249145	GEO		Spatial gene expression gradients underlie prominent heterogeneity of CA1 pyramidal neurons	Tissue and organ function has been conventionally understood in terms of the interactions among discrete and homogeneous cell types.  This approach has proven difficult in neuroscience due to the marked diversity across different neuron classes, but may also be further hampered by prominent within-class variability.  Here, we considered a well-defined, canonical neuronal population – hippocampal CA1 pyramidal cells – and systematically examined the extent and spatial rules of transcriptional heterogeneity.  Using next-generation RNA sequencing, we identified striking variability in CA1 PCs, such that the differences along the dorsal-ventral axis rivaled differences across distinct pyramidal neuron classes. This variability emerged from a spectrum of continuous expression gradients, producing a profile consistent with a multifarious continuum of cells.  This work reveals an unexpected amount of variability within a canonical and narrowly defined neuronal population and suggests that continuous, within-class heterogeneity may be an important feature of neural circuits. Overall design: Hippocampal RNA profiles were generated by deep sequencing on Illumina HiSeq 2500, with three biological replicates per population		GSM1867274: amyg_0; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Manual sorting to purify for fluorescent neurons from microdissected slices was performed according to previous methods (Hempel et al., 2007). Total RNA was isolated from each sample using PicoPure RNA Isolation kit (Life Technologies, Frederick, MD) including the on-column RNAseq-free DNaseI treatment (Qiagen, Hilden, Germany) following the manufacturers’ recommendations.  Eluted RNA (11 ul) was dried in a speed vac to approximately 2-4 ul.  ERCC control RNAs (Life Technologies) were added using 1 ul of 1:100,000 dilution for every 50 cells.  cDNA was amplified from this input material using Ovation RNA-seq v2 kit (NuGEN, San Carlos, CA).  Approximately half of the resulting cDNA was used to make the sequencing libraries using the Ovation Rapid DR Multiplexing kit (NuGEN).	Illumina HiSeq 2500	cell population;;Ventral CA1 amygdala-projecting pyramidal cells|location;;CA1|source_name;;Ventral CA1 amygdala-projecting pyramidal cells	GEO Accession;;GSM1867274		GSM1867274	amyg_0	4254760020	40521524	2016-01-06 15:50:16	1949022752	4254760020	40521524	1	40521524	index:0,count:40521524,average:105,stdev:0	GSM1867274_r1				in_mesa	26777276	14.23	3.47	0.1	3689388725	3640210190	3486730624	3469739602	98.67	99.51	0	0	0	0	0	0	78.83	83.48	39621768	28679846	39621768	28679846	77.56	78.74	39621768	28219501	39621768	27053797	494689835	13.41	6.42	0	5.00	0	0.31	0	0.92	0	0.00	0	8.98	0	36382760	0	105	0	101.48	0	2.34	0	0.01	0	1.50	0	0.01	0	626.08	0	0.29	0	2599688	0	40521524	0	2025384	0	126481	0	374258	0	0	0	3638025	0	7918	0	0	0	38071	0	4074424	0	36130	0	4156543	0	84.79	0	34357376	0	103903	4331149	41.684542313504	40521524.0	36382760.0	2599688.0	2025384.0	126481.0	374258.0	0.0	3638025.0	34357376.0	89.8	6.4	5.0	0.3	0.9	0.0	9.0	84.8	105	105	105.00	7	4254760020	27.9	22.2	22.5	27.3	0.0	36.9	20.7	bulk
1741914	SRR2229945	SRP056666	SRS1052823	SRX1178490	SRA249145	GEO		Spatial gene expression gradients underlie prominent heterogeneity of CA1 pyramidal neurons	Tissue and organ function has been conventionally understood in terms of the interactions among discrete and homogeneous cell types.  This approach has proven difficult in neuroscience due to the marked diversity across different neuron classes, but may also be further hampered by prominent within-class variability.  Here, we considered a well-defined, canonical neuronal population – hippocampal CA1 pyramidal cells – and systematically examined the extent and spatial rules of transcriptional heterogeneity.  Using next-generation RNA sequencing, we identified striking variability in CA1 PCs, such that the differences along the dorsal-ventral axis rivaled differences across distinct pyramidal neuron classes. This variability emerged from a spectrum of continuous expression gradients, producing a profile consistent with a multifarious continuum of cells.  This work reveals an unexpected amount of variability within a canonical and narrowly defined neuronal population and suggests that continuous, within-class heterogeneity may be an important feature of neural circuits. Overall design: Hippocampal RNA profiles were generated by deep sequencing on Illumina HiSeq 2500, with three biological replicates per population		GSM1867276: amyg_1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Manual sorting to purify for fluorescent neurons from microdissected slices was performed according to previous methods (Hempel et al., 2007). Total RNA was isolated from each sample using PicoPure RNA Isolation kit (Life Technologies, Frederick, MD) including the on-column RNAseq-free DNaseI treatment (Qiagen, Hilden, Germany) following the manufacturers’ recommendations.  Eluted RNA (11 ul) was dried in a speed vac to approximately 2-4 ul.  ERCC control RNAs (Life Technologies) were added using 1 ul of 1:100,000 dilution for every 50 cells.  cDNA was amplified from this input material using Ovation RNA-seq v2 kit (NuGEN, San Carlos, CA).  Approximately half of the resulting cDNA was used to make the sequencing libraries using the Ovation Rapid DR Multiplexing kit (NuGEN).	Illumina HiSeq 2500	cell population;;Ventral CA1 amygdala-projecting pyramidal cells|location;;CA1|source_name;;Ventral CA1 amygdala-projecting pyramidal cells	GEO Accession;;GSM1867276		GSM1867276	amyg_1	3623131575	34506015	2016-01-06 15:50:16	1675949705	3623131575	34506015	1	34506015	index:0,count:34506015,average:105,stdev:0	GSM1867276_r1				in_mesa	26777276	9.35	2.84	0.12	3094075346	3089084572	2873881561	2897446203	99.84	100.82	0	0	0	0	0	0	69.59	75.01	34209772	21284721	34209772	21284721	65.12	66.98	34209772	19916699	34209772	19005961	636438151	20.57	6.03	0	6.41	0	0.30	0	0.86	0	0.00	0	10.20	0	30586716	0	105	0	101.28	0	3.37	0	0.03	0	2.43	0	0.03	0	528.60	0	0.37	0	2081405	0	34506015	0	2210617	0	104844	0	296274	0	0	0	3518181	0	5598	0	0	0	25355	0	3037971	0	33397	0	3102321	0	82.24	0	28376099	0	91518	3227246	35.263511003300	34506015.0	30586716.0	2081405.0	2210617.0	104844.0	296274.0	0.0	3518181.0	28376099.0	88.6	6.0	6.4	0.3	0.9	0.0	10.2	82.2	105	105	105.00	7	3623131575	26.7	23.5	23.8	26.0	0.0	36.7	20.4	bulk
1741931	SRR2229946	SRP056666	SRS1052822	SRX1178491	SRA249145	GEO		Spatial gene expression gradients underlie prominent heterogeneity of CA1 pyramidal neurons	Tissue and organ function has been conventionally understood in terms of the interactions among discrete and homogeneous cell types.  This approach has proven difficult in neuroscience due to the marked diversity across different neuron classes, but may also be further hampered by prominent within-class variability.  Here, we considered a well-defined, canonical neuronal population – hippocampal CA1 pyramidal cells – and systematically examined the extent and spatial rules of transcriptional heterogeneity.  Using next-generation RNA sequencing, we identified striking variability in CA1 PCs, such that the differences along the dorsal-ventral axis rivaled differences across distinct pyramidal neuron classes. This variability emerged from a spectrum of continuous expression gradients, producing a profile consistent with a multifarious continuum of cells.  This work reveals an unexpected amount of variability within a canonical and narrowly defined neuronal population and suggests that continuous, within-class heterogeneity may be an important feature of neural circuits. Overall design: Hippocampal RNA profiles were generated by deep sequencing on Illumina HiSeq 2500, with three biological replicates per population		GSM1867278: amyg_2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Manual sorting to purify for fluorescent neurons from microdissected slices was performed according to previous methods (Hempel et al., 2007). Total RNA was isolated from each sample using PicoPure RNA Isolation kit (Life Technologies, Frederick, MD) including the on-column RNAseq-free DNaseI treatment (Qiagen, Hilden, Germany) following the manufacturers’ recommendations.  Eluted RNA (11 ul) was dried in a speed vac to approximately 2-4 ul.  ERCC control RNAs (Life Technologies) were added using 1 ul of 1:100,000 dilution for every 50 cells.  cDNA was amplified from this input material using Ovation RNA-seq v2 kit (NuGEN, San Carlos, CA).  Approximately half of the resulting cDNA was used to make the sequencing libraries using the Ovation Rapid DR Multiplexing kit (NuGEN).	Illumina HiSeq 2500	cell population;;Ventral CA1 amygdala-projecting pyramidal cells|location;;CA1|source_name;;Ventral CA1 amygdala-projecting pyramidal cells	GEO Accession;;GSM1867278		GSM1867278	amyg_2	4980277680	47431216	2016-01-06 15:50:16	2287747916	4980277680	47431216	1	47431216	index:0,count:47431216,average:105,stdev:0	GSM1867278_r1				in_mesa	26777276	10.57	3.06	0.09	4292376709	4281651552	4028053439	4061539049	99.75	100.83	0	0	0	0	0	0	70.38	75.07	46745793	29839068	46745793	29839068	66.77	68.09	46745793	28308799	46745793	27065614	906931187	21.13	6.54	0	5.59	0	0.31	0	0.75	0	0.00	0	9.55	0	42399322	0	105	0	101.34	0	3.00	0	0.02	0	1.65	0	0.02	0	448.17	0	0.32	0	3104232	0	47431216	0	2650690	0	147049	0	357387	0	0	0	4527458	0	7126	0	0	0	37819	0	4165760	0	44300	0	4255005	0	83.80	0	39748632	0	101690	4427951	43.543622775101	47431216.0	42399322.0	3104232.0	2650690.0	147049.0	357387.0	0.0	4527458.0	39748632.0	89.4	6.5	5.6	0.3	0.8	0.0	9.5	83.8	105	105	105.00	7	4980277680	27.2	22.9	23.1	26.7	0.0	36.8	20.5	bulk
1741945	SRR2229947	SRP056666	SRS1052821	SRX1178492	SRA249145	GEO		Spatial gene expression gradients underlie prominent heterogeneity of CA1 pyramidal neurons	Tissue and organ function has been conventionally understood in terms of the interactions among discrete and homogeneous cell types.  This approach has proven difficult in neuroscience due to the marked diversity across different neuron classes, but may also be further hampered by prominent within-class variability.  Here, we considered a well-defined, canonical neuronal population – hippocampal CA1 pyramidal cells – and systematically examined the extent and spatial rules of transcriptional heterogeneity.  Using next-generation RNA sequencing, we identified striking variability in CA1 PCs, such that the differences along the dorsal-ventral axis rivaled differences across distinct pyramidal neuron classes. This variability emerged from a spectrum of continuous expression gradients, producing a profile consistent with a multifarious continuum of cells.  This work reveals an unexpected amount of variability within a canonical and narrowly defined neuronal population and suggests that continuous, within-class heterogeneity may be an important feature of neural circuits. Overall design: Hippocampal RNA profiles were generated by deep sequencing on Illumina HiSeq 2500, with three biological replicates per population		GSM1867279: nac_0; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Manual sorting to purify for fluorescent neurons from microdissected slices was performed according to previous methods (Hempel et al., 2007). Total RNA was isolated from each sample using PicoPure RNA Isolation kit (Life Technologies, Frederick, MD) including the on-column RNAseq-free DNaseI treatment (Qiagen, Hilden, Germany) following the manufacturers’ recommendations.  Eluted RNA (11 ul) was dried in a speed vac to approximately 2-4 ul.  ERCC control RNAs (Life Technologies) were added using 1 ul of 1:100,000 dilution for every 50 cells.  cDNA was amplified from this input material using Ovation RNA-seq v2 kit (NuGEN, San Carlos, CA).  Approximately half of the resulting cDNA was used to make the sequencing libraries using the Ovation Rapid DR Multiplexing kit (NuGEN).	Illumina HiSeq 2500	cell population;;Ventral CA1 nucleus accumbens-projecting pyramidal cells|location;;CA1|source_name;;Ventral CA1 nucleus accumbens-projecting pyramidal cells	GEO Accession;;GSM1867279		GSM1867279	nac_0	4249636860	40472732	2016-01-06 15:50:16	1951081264	4249636860	40472732	1	40472732	index:0,count:40472732,average:105,stdev:0	GSM1867279_r1				in_mesa	26777276	9.06	3.18	0.1	3622690484	3630964300	3381388900	3426687400	100.23	101.34	0	0	0	0	0	0	72.35	77.6	39854587	25910797	39854587	25910797	67.74	69.53	39854587	24257423	39854587	23215682	669787581	18.49	6.54	0	5.98	0	0.33	0	1.02	0	0.00	0	10.16	0	35812105	0	105	0	101.26	0	3.37	0	0.03	0	2.07	0	0.02	0	488.93	0	0.35	0	2645100	0	40472732	0	2420504	0	132835	0	414770	0	0	0	4113022	0	7892	0	0	0	33498	0	3735467	0	40019	0	3816876	0	82.50	0	33391601	0	104891	3966835	37.818640302791	40472732.0	35812105.0	2645100.0	2420504.0	132835.0	414770.0	0.0	4113022.0	33391601.0	88.5	6.5	6.0	0.3	1.0	0.0	10.2	82.5	105	105	105.00	7	4249636860	26.9	23.3	23.5	26.3	0.0	36.8	20.5	bulk
1741963	SRR2229948	SRP056666	SRS1052820	SRX1178493	SRA249145	GEO		Spatial gene expression gradients underlie prominent heterogeneity of CA1 pyramidal neurons	Tissue and organ function has been conventionally understood in terms of the interactions among discrete and homogeneous cell types.  This approach has proven difficult in neuroscience due to the marked diversity across different neuron classes, but may also be further hampered by prominent within-class variability.  Here, we considered a well-defined, canonical neuronal population – hippocampal CA1 pyramidal cells – and systematically examined the extent and spatial rules of transcriptional heterogeneity.  Using next-generation RNA sequencing, we identified striking variability in CA1 PCs, such that the differences along the dorsal-ventral axis rivaled differences across distinct pyramidal neuron classes. This variability emerged from a spectrum of continuous expression gradients, producing a profile consistent with a multifarious continuum of cells.  This work reveals an unexpected amount of variability within a canonical and narrowly defined neuronal population and suggests that continuous, within-class heterogeneity may be an important feature of neural circuits. Overall design: Hippocampal RNA profiles were generated by deep sequencing on Illumina HiSeq 2500, with three biological replicates per population		GSM1867281: nac_1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Manual sorting to purify for fluorescent neurons from microdissected slices was performed according to previous methods (Hempel et al., 2007). Total RNA was isolated from each sample using PicoPure RNA Isolation kit (Life Technologies, Frederick, MD) including the on-column RNAseq-free DNaseI treatment (Qiagen, Hilden, Germany) following the manufacturers’ recommendations.  Eluted RNA (11 ul) was dried in a speed vac to approximately 2-4 ul.  ERCC control RNAs (Life Technologies) were added using 1 ul of 1:100,000 dilution for every 50 cells.  cDNA was amplified from this input material using Ovation RNA-seq v2 kit (NuGEN, San Carlos, CA).  Approximately half of the resulting cDNA was used to make the sequencing libraries using the Ovation Rapid DR Multiplexing kit (NuGEN).	Illumina HiSeq 2500	cell population;;Ventral CA1 nucleus accumbens-projecting pyramidal cells|location;;CA1|source_name;;Ventral CA1 nucleus accumbens-projecting pyramidal cells	GEO Accession;;GSM1867281		GSM1867281	nac_1	3711764805	35350141	2016-01-06 15:50:16	1701318633	3711764805	35350141	1	35350141	index:0,count:35350141,average:105,stdev:0	GSM1867281_r1				in_mesa	26777276	8.94	3.34	0.15	3189351226	3095066657	3054937307	2986720496	97.04	97.77	0	0	0	0	0	0	62.28	65.07	33800112	19621101	33800112	19621101	61.35	61.72	33800112	19326648	33800112	18612120	981561514	30.78	6.81	0	3.82	0	0.30	0	1.50	0	0.00	0	9.08	0	31503023	0	105	0	101.31	0	1.84	0	0.01	0	1.33	0	0.01	0	400.19	0	0.30	0	2408911	0	35350141	0	1349296	0	107199	0	530091	0	0	0	3209828	0	3298	0	0	0	24563	0	2760637	0	36273	0	2824771	0	85.30	0	30153727	0	87315	2934413	33.607203802325	35350141.0	31503023.0	2408911.0	1349296.0	107199.0	530091.0	0.0	3209828.0	30153727.0	89.1	6.8	3.8	0.3	1.5	0.0	9.1	85.3	105	105	105.00	7	3711764805	28.5	21.6	22.0	27.9	0.0	36.9	20.6	bulk
1741979	SRR2229949	SRP056666	SRS1052819	SRX1178494	SRA249145	GEO		Spatial gene expression gradients underlie prominent heterogeneity of CA1 pyramidal neurons	Tissue and organ function has been conventionally understood in terms of the interactions among discrete and homogeneous cell types.  This approach has proven difficult in neuroscience due to the marked diversity across different neuron classes, but may also be further hampered by prominent within-class variability.  Here, we considered a well-defined, canonical neuronal population – hippocampal CA1 pyramidal cells – and systematically examined the extent and spatial rules of transcriptional heterogeneity.  Using next-generation RNA sequencing, we identified striking variability in CA1 PCs, such that the differences along the dorsal-ventral axis rivaled differences across distinct pyramidal neuron classes. This variability emerged from a spectrum of continuous expression gradients, producing a profile consistent with a multifarious continuum of cells.  This work reveals an unexpected amount of variability within a canonical and narrowly defined neuronal population and suggests that continuous, within-class heterogeneity may be an important feature of neural circuits. Overall design: Hippocampal RNA profiles were generated by deep sequencing on Illumina HiSeq 2500, with three biological replicates per population		GSM1867282: nac_2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Manual sorting to purify for fluorescent neurons from microdissected slices was performed according to previous methods (Hempel et al., 2007). Total RNA was isolated from each sample using PicoPure RNA Isolation kit (Life Technologies, Frederick, MD) including the on-column RNAseq-free DNaseI treatment (Qiagen, Hilden, Germany) following the manufacturers’ recommendations.  Eluted RNA (11 ul) was dried in a speed vac to approximately 2-4 ul.  ERCC control RNAs (Life Technologies) were added using 1 ul of 1:100,000 dilution for every 50 cells.  cDNA was amplified from this input material using Ovation RNA-seq v2 kit (NuGEN, San Carlos, CA).  Approximately half of the resulting cDNA was used to make the sequencing libraries using the Ovation Rapid DR Multiplexing kit (NuGEN).	Illumina HiSeq 2500	cell population;;Ventral CA1 nucleus accumbens-projecting pyramidal cells|location;;CA1|source_name;;Ventral CA1 nucleus accumbens-projecting pyramidal cells	GEO Accession;;GSM1867282		GSM1867282	nac_2	4703212920	44792504	2016-01-06 15:50:16	2159799115	4703212920	44792504	1	44792504	index:0,count:44792504,average:105,stdev:0	GSM1867282_r1				in_mesa	26777276	8.92	2.95	0.09	4035637075	3995348080	3782169022	3778847587	99.0	99.91	0	0	0	0	0	0	63.81	68.16	44110310	25437540	44110310	25437540	59.98	61.22	44110310	23910399	44110310	22849439	1088039070	26.96	6.32	0	5.68	0	0.33	0	1.01	0	0.00	0	9.66	0	39866984	0	105	0	101.34	0	2.95	0	0.02	0	2.38	0	0.02	0	411.36	0	0.35	0	2830119	0	44792504	0	2545501	0	146919	0	451788	0	0	0	4326813	0	6240	0	0	0	30496	0	3586834	0	46442	0	3670012	0	83.32	0	37321483	0	91533	3817141	41.702347787137	44792504.0	39866984.0	2830119.0	2545501.0	146919.0	451788.0	0.0	4326813.0	37321483.0	89.0	6.3	5.7	0.3	1.0	0.0	9.7	83.3	105	105	105.00	7	4703212920	27.0	23.1	23.3	26.5	0.0	36.8	20.5	bulk
1742089	SRR2229950	SRP056666	SRS1052818	SRX1178495	SRA249145	GEO		Spatial gene expression gradients underlie prominent heterogeneity of CA1 pyramidal neurons	Tissue and organ function has been conventionally understood in terms of the interactions among discrete and homogeneous cell types.  This approach has proven difficult in neuroscience due to the marked diversity across different neuron classes, but may also be further hampered by prominent within-class variability.  Here, we considered a well-defined, canonical neuronal population – hippocampal CA1 pyramidal cells – and systematically examined the extent and spatial rules of transcriptional heterogeneity.  Using next-generation RNA sequencing, we identified striking variability in CA1 PCs, such that the differences along the dorsal-ventral axis rivaled differences across distinct pyramidal neuron classes. This variability emerged from a spectrum of continuous expression gradients, producing a profile consistent with a multifarious continuum of cells.  This work reveals an unexpected amount of variability within a canonical and narrowly defined neuronal population and suggests that continuous, within-class heterogeneity may be an important feature of neural circuits. Overall design: Hippocampal RNA profiles were generated by deep sequencing on Illumina HiSeq 2500, with three biological replicates per population		GSM1867284: post_0; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Manual sorting to purify for fluorescent neurons from microdissected slices was performed according to previous methods (Hempel et al., 2007). Total RNA was isolated from each sample using PicoPure RNA Isolation kit (Life Technologies, Frederick, MD) including the on-column RNAseq-free DNaseI treatment (Qiagen, Hilden, Germany) following the manufacturers’ recommendations.  Eluted RNA (11 ul) was dried in a speed vac to approximately 2-4 ul.  ERCC control RNAs (Life Technologies) were added using 1 ul of 1:100,000 dilution for every 50 cells.  cDNA was amplified from this input material using Ovation RNA-seq v2 kit (NuGEN, San Carlos, CA).  Approximately half of the resulting cDNA was used to make the sequencing libraries using the Ovation Rapid DR Multiplexing kit (NuGEN).	Illumina HiSeq 2500	cell population;;Dorsal CA1 postsubiculum-projecting pyramidal cells|location;;CA1|source_name;;Dorsal CA1 postsubiculum-projecting pyramidal cells	GEO Accession;;GSM1867284		GSM1867284	post_0	4508965125	42942525	2016-01-06 15:50:16	2042226401	4508965125	42942525	1	42942525	index:0,count:42942525,average:105,stdev:0	GSM1867284_r1				in_mesa	26777276	7.42	3.48	0.14	3969088122	3832224894	3840671228	3729361200	96.55	97.1	0	0	0	0	0	0	58.77	60.77	41247271	22972427	41247271	22972427	58.38	58.45	41247271	22820630	41247271	22096363	1396622328	35.19	6.53	0	2.99	0	0.27	0	0.80	0	0.00	0	7.92	0	39086687	0	105	0	101.60	0	1.38	0	0.01	0	1.24	0	0.01	0	503.56	0	0.29	0	2805779	0	42942525	0	1283717	0	114004	0	342148	0	0	0	3399686	0	3299	0	0	0	29816	0	3106633	0	41519	0	3181267	0	88.03	0	37802970	0	98529	3280111	33.290817931776	42942525.0	39086687.0	2805779.0	1283717.0	114004.0	342148.0	0.0	3399686.0	37802970.0	91.0	6.5	3.0	0.3	0.8	0.0	7.9	88.0	105	105	105.00	7	4508965125	28.7	21.4	21.8	28.1	0.0	37.1	21.0	bulk
1742105	SRR2229951	SRP056666	SRS1052817	SRX1178496	SRA249145	GEO		Spatial gene expression gradients underlie prominent heterogeneity of CA1 pyramidal neurons	Tissue and organ function has been conventionally understood in terms of the interactions among discrete and homogeneous cell types.  This approach has proven difficult in neuroscience due to the marked diversity across different neuron classes, but may also be further hampered by prominent within-class variability.  Here, we considered a well-defined, canonical neuronal population – hippocampal CA1 pyramidal cells – and systematically examined the extent and spatial rules of transcriptional heterogeneity.  Using next-generation RNA sequencing, we identified striking variability in CA1 PCs, such that the differences along the dorsal-ventral axis rivaled differences across distinct pyramidal neuron classes. This variability emerged from a spectrum of continuous expression gradients, producing a profile consistent with a multifarious continuum of cells.  This work reveals an unexpected amount of variability within a canonical and narrowly defined neuronal population and suggests that continuous, within-class heterogeneity may be an important feature of neural circuits. Overall design: Hippocampal RNA profiles were generated by deep sequencing on Illumina HiSeq 2500, with three biological replicates per population		GSM1867286: post_1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Manual sorting to purify for fluorescent neurons from microdissected slices was performed according to previous methods (Hempel et al., 2007). Total RNA was isolated from each sample using PicoPure RNA Isolation kit (Life Technologies, Frederick, MD) including the on-column RNAseq-free DNaseI treatment (Qiagen, Hilden, Germany) following the manufacturers’ recommendations.  Eluted RNA (11 ul) was dried in a speed vac to approximately 2-4 ul.  ERCC control RNAs (Life Technologies) were added using 1 ul of 1:100,000 dilution for every 50 cells.  cDNA was amplified from this input material using Ovation RNA-seq v2 kit (NuGEN, San Carlos, CA).  Approximately half of the resulting cDNA was used to make the sequencing libraries using the Ovation Rapid DR Multiplexing kit (NuGEN).	Illumina HiSeq 2500	cell population;;Dorsal CA1 postsubiculum-projecting pyramidal cells|location;;CA1|source_name;;Dorsal CA1 postsubiculum-projecting pyramidal cells	GEO Accession;;GSM1867286		GSM1867286	post_1	3534090105	33658001	2016-01-06 15:50:16	1601840863	3534090105	33658001	1	33658001	index:0,count:33658001,average:105,stdev:0	GSM1867286_r1				in_mesa	26777276	7.43	3.44	0.12	3103111323	2996612623	3002148988	2915480230	96.57	97.11	0	0	0	0	0	0	59.34	61.36	32313532	18159547	32313532	18159547	58.98	59.05	32313532	18049467	32313532	17476059	1074168137	34.62	6.60	0	3.01	0	0.27	0	0.72	0	0.00	0	8.08	0	30604408	0	105	0	101.45	0	1.38	0	0.01	0	1.24	0	0.01	0	419.27	0	0.29	0	2221884	0	33658001	0	1011473	0	91334	0	242733	0	0	0	2719526	0	3007	0	0	0	23806	0	2462785	0	32137	0	2521735	0	87.92	0	29592935	0	97068	2597099	26.755460089834	33658001.0	30604408.0	2221884.0	1011473.0	91334.0	242733.0	0.0	2719526.0	29592935.0	90.9	6.6	3.0	0.3	0.7	0.0	8.1	87.9	105	105	105.00	7	3534090105	28.7	21.4	21.7	28.1	0.0	37.1	21.1	bulk
1742121	SRR2229952	SRP056666	SRS1052816	SRX1178497	SRA249145	GEO		Spatial gene expression gradients underlie prominent heterogeneity of CA1 pyramidal neurons	Tissue and organ function has been conventionally understood in terms of the interactions among discrete and homogeneous cell types.  This approach has proven difficult in neuroscience due to the marked diversity across different neuron classes, but may also be further hampered by prominent within-class variability.  Here, we considered a well-defined, canonical neuronal population – hippocampal CA1 pyramidal cells – and systematically examined the extent and spatial rules of transcriptional heterogeneity.  Using next-generation RNA sequencing, we identified striking variability in CA1 PCs, such that the differences along the dorsal-ventral axis rivaled differences across distinct pyramidal neuron classes. This variability emerged from a spectrum of continuous expression gradients, producing a profile consistent with a multifarious continuum of cells.  This work reveals an unexpected amount of variability within a canonical and narrowly defined neuronal population and suggests that continuous, within-class heterogeneity may be an important feature of neural circuits. Overall design: Hippocampal RNA profiles were generated by deep sequencing on Illumina HiSeq 2500, with three biological replicates per population		GSM1867287: post_2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Manual sorting to purify for fluorescent neurons from microdissected slices was performed according to previous methods (Hempel et al., 2007). Total RNA was isolated from each sample using PicoPure RNA Isolation kit (Life Technologies, Frederick, MD) including the on-column RNAseq-free DNaseI treatment (Qiagen, Hilden, Germany) following the manufacturers’ recommendations.  Eluted RNA (11 ul) was dried in a speed vac to approximately 2-4 ul.  ERCC control RNAs (Life Technologies) were added using 1 ul of 1:100,000 dilution for every 50 cells.  cDNA was amplified from this input material using Ovation RNA-seq v2 kit (NuGEN, San Carlos, CA).  Approximately half of the resulting cDNA was used to make the sequencing libraries using the Ovation Rapid DR Multiplexing kit (NuGEN).	Illumina HiSeq 2500	cell population;;Dorsal CA1 postsubiculum-projecting pyramidal cells|location;;CA1|source_name;;Dorsal CA1 postsubiculum-projecting pyramidal cells	GEO Accession;;GSM1867287		GSM1867287	post_2	3983612745	37939169	2016-01-06 15:50:16	1803300271	3983612745	37939169	1	37939169	index:0,count:37939169,average:105,stdev:0	GSM1867287_r1				in_mesa	26777276	6.35	3.39	0.13	3505586483	3387044415	3393708298	3297505626	96.62	97.17	0	0	0	0	0	0	59.52	61.52	36464275	20575403	36464275	20575403	59.05	59.15	36464275	20411566	36464275	19783369	1209009327	34.49	6.42	0	2.95	0	0.27	0	0.72	0	0.00	0	7.89	0	34567331	0	105	0	101.46	0	1.39	0	0.01	0	1.25	0	0.01	0	588.71	0	0.28	0	2436227	0	37939169	0	1120071	0	102648	0	273981	0	0	0	2995209	0	3401	0	0	0	26952	0	2892686	0	35942	0	2958981	0	88.16	0	33447260	0	104823	3047800	29.075679955735	37939169.0	34567331.0	2436227.0	1120071.0	102648.0	273981.0	0.0	2995209.0	33447260.0	91.1	6.4	3.0	0.3	0.7	0.0	7.9	88.2	105	105	105.00	7	3983612745	28.6	21.5	21.8	28.0	0.0	37.1	21.1	bulk
1742137	SRR2229953	SRP056666	SRS1052815	SRX1178498	SRA249145	GEO		Spatial gene expression gradients underlie prominent heterogeneity of CA1 pyramidal neurons	Tissue and organ function has been conventionally understood in terms of the interactions among discrete and homogeneous cell types.  This approach has proven difficult in neuroscience due to the marked diversity across different neuron classes, but may also be further hampered by prominent within-class variability.  Here, we considered a well-defined, canonical neuronal population – hippocampal CA1 pyramidal cells – and systematically examined the extent and spatial rules of transcriptional heterogeneity.  Using next-generation RNA sequencing, we identified striking variability in CA1 PCs, such that the differences along the dorsal-ventral axis rivaled differences across distinct pyramidal neuron classes. This variability emerged from a spectrum of continuous expression gradients, producing a profile consistent with a multifarious continuum of cells.  This work reveals an unexpected amount of variability within a canonical and narrowly defined neuronal population and suggests that continuous, within-class heterogeneity may be an important feature of neural circuits. Overall design: Hippocampal RNA profiles were generated by deep sequencing on Illumina HiSeq 2500, with three biological replicates per population		GSM1867289: dgd_0; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Manual sorting to purify for fluorescent neurons from microdissected slices was performed according to previous methods (Hempel et al., 2007). Total RNA was isolated from each sample using PicoPure RNA Isolation kit (Life Technologies, Frederick, MD) including the on-column RNAseq-free DNaseI treatment (Qiagen, Hilden, Germany) following the manufacturers’ recommendations.  Eluted RNA (11 ul) was dried in a speed vac to approximately 2-4 ul.  ERCC control RNAs (Life Technologies) were added using 1 ul of 1:100,000 dilution for every 50 cells.  cDNA was amplified from this input material using Ovation RNA-seq v2 kit (NuGEN, San Carlos, CA).  Approximately half of the resulting cDNA was used to make the sequencing libraries using the Ovation Rapid DR Multiplexing kit (NuGEN).	Illumina HiSeq 2500	cell population;;Dorsal DG granule cells|location;;DG|source_name;;Dorsal DG granule cells	GEO Accession;;GSM1867289		GSM1867289	dgd_0	3286556216	34963364	2016-01-06 15:50:16	1601660456	3286556216	34963364	1	34963364	index:0,count:34963364,average:94,stdev:0	GSM1867289_r1				in_mesa	26777276	10.67	2.93	0.09	2982697179	2937671753	2844524193	2823844873	98.49	99.27	0	0	0	0	0	0	57.17	59.98	35150360	18574229	35150360	18574229	54.77	55.32	35150360	17794683	35150360	17131685	1072796279	35.97	3.91	0	4.35	0	0.27	0	0.43	0	0.00	0	6.38	0	32488264	0	94	0	91.86	0	2.45	0	0.01	0	1.27	0	0.01	0	673.09	0	0.35	0	1365469	0	34963364	0	1522400	0	95066	0	150663	0	0	0	2229371	0	3467	0	0	0	17986	0	2032292	0	23188	0	2076933	0	88.57	0	30965864	0	111993	2107193	18.815399176734	34963364.0	32488264.0	1365469.0	1522400.0	95066.0	150663.0	0.0	2229371.0	30965864.0	92.9	3.9	4.4	0.3	0.4	0.0	6.4	88.6	94	94	94.00	8	3286556216	28.4	21.8	21.9	27.8	0.0	35.2	19.1	bulk
1742168	SRR2229955	SRP056666	SRS1052813	SRX1178500	SRA249145	GEO		Spatial gene expression gradients underlie prominent heterogeneity of CA1 pyramidal neurons	Tissue and organ function has been conventionally understood in terms of the interactions among discrete and homogeneous cell types.  This approach has proven difficult in neuroscience due to the marked diversity across different neuron classes, but may also be further hampered by prominent within-class variability.  Here, we considered a well-defined, canonical neuronal population – hippocampal CA1 pyramidal cells – and systematically examined the extent and spatial rules of transcriptional heterogeneity.  Using next-generation RNA sequencing, we identified striking variability in CA1 PCs, such that the differences along the dorsal-ventral axis rivaled differences across distinct pyramidal neuron classes. This variability emerged from a spectrum of continuous expression gradients, producing a profile consistent with a multifarious continuum of cells.  This work reveals an unexpected amount of variability within a canonical and narrowly defined neuronal population and suggests that continuous, within-class heterogeneity may be an important feature of neural circuits. Overall design: Hippocampal RNA profiles were generated by deep sequencing on Illumina HiSeq 2500, with three biological replicates per population		GSM1867293: dgd_2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Manual sorting to purify for fluorescent neurons from microdissected slices was performed according to previous methods (Hempel et al., 2007). Total RNA was isolated from each sample using PicoPure RNA Isolation kit (Life Technologies, Frederick, MD) including the on-column RNAseq-free DNaseI treatment (Qiagen, Hilden, Germany) following the manufacturers’ recommendations.  Eluted RNA (11 ul) was dried in a speed vac to approximately 2-4 ul.  ERCC control RNAs (Life Technologies) were added using 1 ul of 1:100,000 dilution for every 50 cells.  cDNA was amplified from this input material using Ovation RNA-seq v2 kit (NuGEN, San Carlos, CA).  Approximately half of the resulting cDNA was used to make the sequencing libraries using the Ovation Rapid DR Multiplexing kit (NuGEN).	Illumina HiSeq 2500	cell population;;Dorsal DG granule cells|location;;DG|source_name;;Dorsal DG granule cells	GEO Accession;;GSM1867293		GSM1867293	dgd_2	3253505534	34611761	2016-01-06 15:50:16	1589194956	3253505534	34611761	1	34611761	index:0,count:34611761,average:94,stdev:0	GSM1867293_r1				in_mesa	26777276	10.94	2.98	0.09	2951209954	2919599267	2792179211	2785188912	98.93	99.75	0	0	0	0	0	0	62.03	65.61	35081176	19926546	35081176	19926546	59.33	60.33	35081176	19058022	35081176	18323256	900259659	30.50	3.64	0	5.06	0	0.27	0	0.36	0	0.00	0	6.56	0	32121490	0	94	0	91.93	0	2.66	0	0.02	0	1.32	0	0.01	0	471.98	0	0.36	0	1258670	0	34611761	0	1749803	0	94653	0	124776	0	0	0	2270842	0	3793	0	0	0	19517	0	2281858	0	21667	0	2326835	0	87.75	0	30371687	0	116552	2369016	20.325828814606	34611761.0	32121490.0	1258670.0	1749803.0	94653.0	124776.0	0.0	2270842.0	30371687.0	92.8	3.6	5.1	0.3	0.4	0.0	6.6	87.7	94	94	94.00	8	3253505534	28.1	22.2	22.3	27.5	0.0	35.0	18.7	bulk
1742184	SRR2229956	SRP056666	SRS1052812	SRX1178501	SRA249145	GEO		Spatial gene expression gradients underlie prominent heterogeneity of CA1 pyramidal neurons	Tissue and organ function has been conventionally understood in terms of the interactions among discrete and homogeneous cell types.  This approach has proven difficult in neuroscience due to the marked diversity across different neuron classes, but may also be further hampered by prominent within-class variability.  Here, we considered a well-defined, canonical neuronal population – hippocampal CA1 pyramidal cells – and systematically examined the extent and spatial rules of transcriptional heterogeneity.  Using next-generation RNA sequencing, we identified striking variability in CA1 PCs, such that the differences along the dorsal-ventral axis rivaled differences across distinct pyramidal neuron classes. This variability emerged from a spectrum of continuous expression gradients, producing a profile consistent with a multifarious continuum of cells.  This work reveals an unexpected amount of variability within a canonical and narrowly defined neuronal population and suggests that continuous, within-class heterogeneity may be an important feature of neural circuits. Overall design: Hippocampal RNA profiles were generated by deep sequencing on Illumina HiSeq 2500, with three biological replicates per population		GSM1867296: dgv_0; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Manual sorting to purify for fluorescent neurons from microdissected slices was performed according to previous methods (Hempel et al., 2007). Total RNA was isolated from each sample using PicoPure RNA Isolation kit (Life Technologies, Frederick, MD) including the on-column RNAseq-free DNaseI treatment (Qiagen, Hilden, Germany) following the manufacturers’ recommendations.  Eluted RNA (11 ul) was dried in a speed vac to approximately 2-4 ul.  ERCC control RNAs (Life Technologies) were added using 1 ul of 1:100,000 dilution for every 50 cells.  cDNA was amplified from this input material using Ovation RNA-seq v2 kit (NuGEN, San Carlos, CA).  Approximately half of the resulting cDNA was used to make the sequencing libraries using the Ovation Rapid DR Multiplexing kit (NuGEN).	Illumina HiSeq 2500	cell population;;Ventral DG granule cells|location;;DG|source_name;;Ventral DG granule cells	GEO Accession;;GSM1867296		GSM1867296	dgv_0	2016456400	20164564	2016-01-06 15:50:16	939134131	2016456400	20164564	1	20164564	index:0,count:20164564,average:100,stdev:0	GSM1867296_r1				in_mesa	26777276	9.1	2.6	0.1	1740596681	1731463562	1636129238	1635908412	99.48	99.99	0	0	0	0	0	0	64.63	68.82	19860075	11592877	19860075	11592877	60.57	61.95	19860075	10865706	19860075	10435355	454360870	26.10	5.03	0	5.41	0	0.29	0	0.40	0	0.00	0	10.35	0	17937768	0	100	0	97.12	0	2.72	0	0.02	0	1.90	0	0.01	0	392.39	0	0.49	0	1014865	0	20164564	0	1091876	0	57753	0	81287	0	0	0	2087756	0	2518	0	0	0	13668	0	1555581	0	17695	0	1589462	0	83.54	0	16845892	0	80050	1652193	20.639512804497	20164564.0	17937768.0	1014865.0	1091876.0	57753.0	81287.0	0.0	2087756.0	16845892.0	89.0	5.0	5.4	0.3	0.4	0.0	10.4	83.5	100	100	100.00	8	2016456400	27.0	23.3	23.3	26.4	0.0	35.2	18.1	bulk
1742200	SRR2229957	SRP056666	SRS1052811	SRX1178502	SRA249145	GEO		Spatial gene expression gradients underlie prominent heterogeneity of CA1 pyramidal neurons	Tissue and organ function has been conventionally understood in terms of the interactions among discrete and homogeneous cell types.  This approach has proven difficult in neuroscience due to the marked diversity across different neuron classes, but may also be further hampered by prominent within-class variability.  Here, we considered a well-defined, canonical neuronal population – hippocampal CA1 pyramidal cells – and systematically examined the extent and spatial rules of transcriptional heterogeneity.  Using next-generation RNA sequencing, we identified striking variability in CA1 PCs, such that the differences along the dorsal-ventral axis rivaled differences across distinct pyramidal neuron classes. This variability emerged from a spectrum of continuous expression gradients, producing a profile consistent with a multifarious continuum of cells.  This work reveals an unexpected amount of variability within a canonical and narrowly defined neuronal population and suggests that continuous, within-class heterogeneity may be an important feature of neural circuits. Overall design: Hippocampal RNA profiles were generated by deep sequencing on Illumina HiSeq 2500, with three biological replicates per population		GSM1867298: dgv_1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Manual sorting to purify for fluorescent neurons from microdissected slices was performed according to previous methods (Hempel et al., 2007). Total RNA was isolated from each sample using PicoPure RNA Isolation kit (Life Technologies, Frederick, MD) including the on-column RNAseq-free DNaseI treatment (Qiagen, Hilden, Germany) following the manufacturers’ recommendations.  Eluted RNA (11 ul) was dried in a speed vac to approximately 2-4 ul.  ERCC control RNAs (Life Technologies) were added using 1 ul of 1:100,000 dilution for every 50 cells.  cDNA was amplified from this input material using Ovation RNA-seq v2 kit (NuGEN, San Carlos, CA).  Approximately half of the resulting cDNA was used to make the sequencing libraries using the Ovation Rapid DR Multiplexing kit (NuGEN).	Illumina HiSeq 2500	cell population;;Ventral DG granule cells|location;;DG|source_name;;Ventral DG granule cells	GEO Accession;;GSM1867298		GSM1867298	dgv_1	1926723700	19267237	2016-01-06 15:50:16	898284223	1926723700	19267237	1	19267237	index:0,count:19267237,average:100,stdev:0	GSM1867298_r1				in_mesa	26777276	7.55	2.7	0.07	1657186602	1645330246	1562780215	1565755189	99.28	100.19	0	0	0	0	0	0	60.99	64.72	18888924	10424575	18888924	10424575	56.76	57.8	18888924	9702638	18888924	9310438	503720726	30.40	5.55	0	5.12	0	0.28	0	0.46	0	0.00	0	10.55	0	17093505	0	100	0	97.03	0	2.95	0	0.02	0	1.55	0	0.01	0	394.10	0	0.48	0	1068673	0	19267237	0	986560	0	53127	0	87740	0	0	0	2032865	0	1890	0	0	0	11981	0	1307354	0	18037	0	1339262	0	83.60	0	16106945	0	79055	1395830	17.656441717791	19267237.0	17093505.0	1068673.0	986560.0	53127.0	87740.0	0.0	2032865.0	16106945.0	88.7	5.5	5.1	0.3	0.5	0.0	10.6	83.6	100	100	100.00	8	1926723700	27.1	23.2	23.2	26.6	0.0	35.3	18.4	bulk
1742216	SRR2229958	SRP056666	SRS1052810	SRX1178503	SRA249145	GEO		Spatial gene expression gradients underlie prominent heterogeneity of CA1 pyramidal neurons	Tissue and organ function has been conventionally understood in terms of the interactions among discrete and homogeneous cell types.  This approach has proven difficult in neuroscience due to the marked diversity across different neuron classes, but may also be further hampered by prominent within-class variability.  Here, we considered a well-defined, canonical neuronal population – hippocampal CA1 pyramidal cells – and systematically examined the extent and spatial rules of transcriptional heterogeneity.  Using next-generation RNA sequencing, we identified striking variability in CA1 PCs, such that the differences along the dorsal-ventral axis rivaled differences across distinct pyramidal neuron classes. This variability emerged from a spectrum of continuous expression gradients, producing a profile consistent with a multifarious continuum of cells.  This work reveals an unexpected amount of variability within a canonical and narrowly defined neuronal population and suggests that continuous, within-class heterogeneity may be an important feature of neural circuits. Overall design: Hippocampal RNA profiles were generated by deep sequencing on Illumina HiSeq 2500, with three biological replicates per population		GSM1867300: dgv_2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Manual sorting to purify for fluorescent neurons from microdissected slices was performed according to previous methods (Hempel et al., 2007). Total RNA was isolated from each sample using PicoPure RNA Isolation kit (Life Technologies, Frederick, MD) including the on-column RNAseq-free DNaseI treatment (Qiagen, Hilden, Germany) following the manufacturers’ recommendations.  Eluted RNA (11 ul) was dried in a speed vac to approximately 2-4 ul.  ERCC control RNAs (Life Technologies) were added using 1 ul of 1:100,000 dilution for every 50 cells.  cDNA was amplified from this input material using Ovation RNA-seq v2 kit (NuGEN, San Carlos, CA).  Approximately half of the resulting cDNA was used to make the sequencing libraries using the Ovation Rapid DR Multiplexing kit (NuGEN).	Illumina HiSeq 2500	cell population;;Ventral DG granule cells|location;;DG|source_name;;Ventral DG granule cells	GEO Accession;;GSM1867300		GSM1867300	dgv_2	1966512000	19665120	2016-01-06 15:50:16	914683542	1966512000	19665120	1	19665120	index:0,count:19665120,average:100,stdev:0	GSM1867300_r1				in_mesa	26777276	7.35	2.7	0.07	1687291635	1672291745	1590623695	1589868708	99.11	99.95	0	0	0	0	0	0	61.09	64.86	19266839	10641172	19266839	10641172	57.18	58.21	19266839	9960159	19266839	9549914	510706343	30.27	5.55	0	5.14	0	0.27	0	0.43	0	0.00	0	10.72	0	17418904	0	100	0	96.95	0	2.87	0	0.02	0	1.59	0	0.01	0	498.55	0	0.49	0	1090871	0	19665120	0	1011737	0	52649	0	84750	0	0	0	2108817	0	2338	0	0	0	12091	0	1367341	0	19328	0	1401098	0	83.43	0	16407167	0	75431	1458040	19.329453407750	19665120.0	17418904.0	1090871.0	1011737.0	52649.0	84750.0	0.0	2108817.0	16407167.0	88.6	5.5	5.1	0.3	0.4	0.0	10.7	83.4	100	100	100.00	8	1966512000	27.0	23.2	23.3	26.5	0.0	35.3	18.4	bulk
870542	SRR2229911	SRP056666	SRS1052857	SRX1178456	SRA249145	GEO		Spatial gene expression gradients underlie prominent heterogeneity of CA1 pyramidal neurons	Tissue and organ function has been conventionally understood in terms of the interactions among discrete and homogeneous cell types.  This approach has proven difficult in neuroscience due to the marked diversity across different neuron classes, but may also be further hampered by prominent within-class variability.  Here, we considered a well-defined, canonical neuronal population – hippocampal CA1 pyramidal cells – and systematically examined the extent and spatial rules of transcriptional heterogeneity.  Using next-generation RNA sequencing, we identified striking variability in CA1 PCs, such that the differences along the dorsal-ventral axis rivaled differences across distinct pyramidal neuron classes. This variability emerged from a spectrum of continuous expression gradients, producing a profile consistent with a multifarious continuum of cells.  This work reveals an unexpected amount of variability within a canonical and narrowly defined neuronal population and suggests that continuous, within-class heterogeneity may be an important feature of neural circuits. Overall design: Hippocampal RNA profiles were generated by deep sequencing on Illumina HiSeq 2500, with three biological replicates per population		GSM1867239: dorsal_0; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Manual sorting to purify for fluorescent neurons from microdissected slices was performed according to previous methods (Hempel et al., 2007). Total RNA was isolated from each sample using PicoPure RNA Isolation kit (Life Technologies, Frederick, MD) including the on-column RNAseq-free DNaseI treatment (Qiagen, Hilden, Germany) following the manufacturers’ recommendations.  Eluted RNA (11 ul) was dried in a speed vac to approximately 2-4 ul.  ERCC control RNAs (Life Technologies) were added using 1 ul of 1:100,000 dilution for every 50 cells.  cDNA was amplified from this input material using Ovation RNA-seq v2 kit (NuGEN, San Carlos, CA).  Approximately half of the resulting cDNA was used to make the sequencing libraries using the Ovation Rapid DR Multiplexing kit (NuGEN).	Illumina HiSeq 2500	cell population;;Dorsal CA1 pyramidal cells|location;;CA1|source_name;;Dorsal CA1 pyramidal cells	GEO Accession;;GSM1867239		GSM1867239	dorsal_0	4639956465	49892005	2016-01-06 15:50:16	2377398879	4639956465	49892005	1	49892005	index:0,count:49892005,average:93,stdev:0	GSM1867239_r1				in_mesa	26777276	5.86	3.03	0.07	4252979800	4238679847	3961566835	3989572957	99.66	100.71	0	0	0	0	0	0	73.29	78.74	52329117	34307446	52329117	34307446	69.37	71.75	52329117	32473275	52329117	31263087	746771291	17.56	3.28	0	6.49	0	0.29	0	0.27	0	0.00	0	5.61	0	46811554	0	93	0	90.92	0	2.72	0	0.01	0	1.28	0	0.01	0	594.74	0	0.45	0	1636490	0	49892005	0	3238603	0	144990	0	134191	0	0	0	2801270	0	5484	0	0	0	43592	0	4965554	0	32710	0	5047340	0	87.33	0	43572951	0	132872	5127972	38.593322897224	49892005.0	46811554.0	1636490.0	3238603.0	144990.0	134191.0	0.0	2801270.0	43572951.0	93.8	3.3	6.5	0.3	0.3	0.0	5.6	87.3	93	93	93.00	8	4639956465	27.2	23.1	23.2	26.5	0.0	33.8	17.4	bulk
870550	SRR2229912	SRP056666	SRS1052856	SRX1178457	SRA249145	GEO		Spatial gene expression gradients underlie prominent heterogeneity of CA1 pyramidal neurons	Tissue and organ function has been conventionally understood in terms of the interactions among discrete and homogeneous cell types.  This approach has proven difficult in neuroscience due to the marked diversity across different neuron classes, but may also be further hampered by prominent within-class variability.  Here, we considered a well-defined, canonical neuronal population – hippocampal CA1 pyramidal cells – and systematically examined the extent and spatial rules of transcriptional heterogeneity.  Using next-generation RNA sequencing, we identified striking variability in CA1 PCs, such that the differences along the dorsal-ventral axis rivaled differences across distinct pyramidal neuron classes. This variability emerged from a spectrum of continuous expression gradients, producing a profile consistent with a multifarious continuum of cells.  This work reveals an unexpected amount of variability within a canonical and narrowly defined neuronal population and suggests that continuous, within-class heterogeneity may be an important feature of neural circuits. Overall design: Hippocampal RNA profiles were generated by deep sequencing on Illumina HiSeq 2500, with three biological replicates per population		GSM1867240: dorsal_1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Manual sorting to purify for fluorescent neurons from microdissected slices was performed according to previous methods (Hempel et al., 2007). Total RNA was isolated from each sample using PicoPure RNA Isolation kit (Life Technologies, Frederick, MD) including the on-column RNAseq-free DNaseI treatment (Qiagen, Hilden, Germany) following the manufacturers’ recommendations.  Eluted RNA (11 ul) was dried in a speed vac to approximately 2-4 ul.  ERCC control RNAs (Life Technologies) were added using 1 ul of 1:100,000 dilution for every 50 cells.  cDNA was amplified from this input material using Ovation RNA-seq v2 kit (NuGEN, San Carlos, CA).  Approximately half of the resulting cDNA was used to make the sequencing libraries using the Ovation Rapid DR Multiplexing kit (NuGEN).	Illumina HiSeq 2500	cell population;;Dorsal CA1 pyramidal cells|location;;CA1|source_name;;Dorsal CA1 pyramidal cells	GEO Accession;;GSM1867240		GSM1867240	dorsal_1	5247843432	56428424	2016-01-06 15:50:16	2692916528	5247843432	56428424	1	56428424	index:0,count:56428424,average:93,stdev:0	GSM1867240_r1				in_mesa	26777276	6.14	3.08	0.07	4823397778	4798685298	4487363225	4505326195	99.49	100.4	0	0	0	0	0	0	74.46	80.1	59350713	39500474	59350713	39500474	71.0	73.45	59350713	37662784	59350713	36222432	783429658	16.24	2.98	0	6.61	0	0.29	0	0.26	0	0.00	0	5.44	0	53047694	0	93	0	90.99	0	2.63	0	0.01	0	1.28	0	0.01	0	610.04	0	0.46	0	1683398	0	56428424	0	3732563	0	164122	0	145717	0	0	0	3070891	0	5948	0	0	0	50344	0	5831808	0	34959	0	5923059	0	87.39	0	49315131	0	134126	6021509	44.894420172077	56428424.0	53047694.0	1683398.0	3732563.0	164122.0	145717.0	0.0	3070891.0	49315131.0	94.0	3.0	6.6	0.3	0.3	0.0	5.4	87.4	93	93	93.00	8	5247843432	27.1	23.2	23.3	26.4	0.0	33.7	17.2	bulk
870557	SRR2229913	SRP056666	SRS1052855	SRX1178458	SRA249145	GEO		Spatial gene expression gradients underlie prominent heterogeneity of CA1 pyramidal neurons	Tissue and organ function has been conventionally understood in terms of the interactions among discrete and homogeneous cell types.  This approach has proven difficult in neuroscience due to the marked diversity across different neuron classes, but may also be further hampered by prominent within-class variability.  Here, we considered a well-defined, canonical neuronal population – hippocampal CA1 pyramidal cells – and systematically examined the extent and spatial rules of transcriptional heterogeneity.  Using next-generation RNA sequencing, we identified striking variability in CA1 PCs, such that the differences along the dorsal-ventral axis rivaled differences across distinct pyramidal neuron classes. This variability emerged from a spectrum of continuous expression gradients, producing a profile consistent with a multifarious continuum of cells.  This work reveals an unexpected amount of variability within a canonical and narrowly defined neuronal population and suggests that continuous, within-class heterogeneity may be an important feature of neural circuits. Overall design: Hippocampal RNA profiles were generated by deep sequencing on Illumina HiSeq 2500, with three biological replicates per population		GSM1867241: dorsal_2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Manual sorting to purify for fluorescent neurons from microdissected slices was performed according to previous methods (Hempel et al., 2007). Total RNA was isolated from each sample using PicoPure RNA Isolation kit (Life Technologies, Frederick, MD) including the on-column RNAseq-free DNaseI treatment (Qiagen, Hilden, Germany) following the manufacturers’ recommendations.  Eluted RNA (11 ul) was dried in a speed vac to approximately 2-4 ul.  ERCC control RNAs (Life Technologies) were added using 1 ul of 1:100,000 dilution for every 50 cells.  cDNA was amplified from this input material using Ovation RNA-seq v2 kit (NuGEN, San Carlos, CA).  Approximately half of the resulting cDNA was used to make the sequencing libraries using the Ovation Rapid DR Multiplexing kit (NuGEN).	Illumina HiSeq 2500	cell population;;Dorsal CA1 pyramidal cells|location;;CA1|source_name;;Dorsal CA1 pyramidal cells	GEO Accession;;GSM1867241		GSM1867241	dorsal_2	4227877092	45461044	2016-01-06 15:50:16	2169524415	4227877092	45461044	1	45461044	index:0,count:45461044,average:93,stdev:0	GSM1867241_r1				in_mesa	26777276	5.55	2.98	0.08	3880168955	3855190886	3638284463	3648210280	99.36	100.27	0	0	0	0	0	0	69.58	74.26	47340118	29732151	47340118	29732151	66.14	68.0	47340118	28263070	47340118	27224284	846158281	21.81	3.23	0	5.92	0	0.29	0	0.33	0	0.00	0	5.39	0	42729323	0	93	0	90.87	0	2.47	0	0.01	0	1.26	0	0.01	0	531.36	0	0.44	0	1470193	0	45461044	0	2691605	0	132071	0	150327	0	0	0	2449323	0	4883	0	0	0	37620	0	4265253	0	29118	0	4336874	0	88.07	0	40037718	0	120873	4414350	36.520562904867	45461044.0	42729323.0	1470193.0	2691605.0	132071.0	150327.0	0.0	2449323.0	40037718.0	94.0	3.2	5.9	0.3	0.3	0.0	5.4	88.1	93	93	93.00	8	4227877092	27.5	22.9	23.0	26.7	0.0	33.9	17.5	bulk
870564	SRR2229914	SRP056666	SRS1052854	SRX1178459	SRA249145	GEO		Spatial gene expression gradients underlie prominent heterogeneity of CA1 pyramidal neurons	Tissue and organ function has been conventionally understood in terms of the interactions among discrete and homogeneous cell types.  This approach has proven difficult in neuroscience due to the marked diversity across different neuron classes, but may also be further hampered by prominent within-class variability.  Here, we considered a well-defined, canonical neuronal population – hippocampal CA1 pyramidal cells – and systematically examined the extent and spatial rules of transcriptional heterogeneity.  Using next-generation RNA sequencing, we identified striking variability in CA1 PCs, such that the differences along the dorsal-ventral axis rivaled differences across distinct pyramidal neuron classes. This variability emerged from a spectrum of continuous expression gradients, producing a profile consistent with a multifarious continuum of cells.  This work reveals an unexpected amount of variability within a canonical and narrowly defined neuronal population and suggests that continuous, within-class heterogeneity may be an important feature of neural circuits. Overall design: Hippocampal RNA profiles were generated by deep sequencing on Illumina HiSeq 2500, with three biological replicates per population		GSM1867242: intermediate_0; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Manual sorting to purify for fluorescent neurons from microdissected slices was performed according to previous methods (Hempel et al., 2007). Total RNA was isolated from each sample using PicoPure RNA Isolation kit (Life Technologies, Frederick, MD) including the on-column RNAseq-free DNaseI treatment (Qiagen, Hilden, Germany) following the manufacturers’ recommendations.  Eluted RNA (11 ul) was dried in a speed vac to approximately 2-4 ul.  ERCC control RNAs (Life Technologies) were added using 1 ul of 1:100,000 dilution for every 50 cells.  cDNA was amplified from this input material using Ovation RNA-seq v2 kit (NuGEN, San Carlos, CA).  Approximately half of the resulting cDNA was used to make the sequencing libraries using the Ovation Rapid DR Multiplexing kit (NuGEN).	Illumina HiSeq 2500	cell population;;Intermediate CA1 pyramidal cells|location;;CA1|source_name;;Intermediate CA1 pyramidal cells	GEO Accession;;GSM1867242		GSM1867242	intermediate_0	1248571400	12485714	2016-01-06 15:50:16	559220773	1248571400	12485714	1	12485714	index:0,count:12485714,average:100,stdev:0	GSM1867242_r1				in_mesa	26777276	6.36	3.18	0.04	1110705175	1109050826	1038570023	1046191998	99.85	100.73	0	0	0	0	0	0	80.48	86.16	12695087	9190104	12695087	9190104	76.91	79.37	12695087	8782382	12695087	8465787	117282120	10.56	3.52	0	6.02	0	0.24	0	0.28	0	0.00	0	8.03	0	11418427	0	100	0	97.37	0	2.54	0	0.02	0	2.56	0	0.02	0	548.15	0	0.36	0	439500	0	12485714	0	751823	0	29867	0	35079	0	0	0	1002341	0	1808	0	0	0	13706	0	1498205	0	9121	0	1522840	0	85.43	0	10666604	0	100923	1568573	15.542274803563	12485714.0	11418427.0	439500.0	751823.0	29867.0	35079.0	0.0	1002341.0	10666604.0	91.5	3.5	6.0	0.2	0.3	0.0	8.0	85.4	100	100	100.00	8	1248571400	26.9	23.4	23.4	26.3	0.0	36.1	20.6	bulk
870573	SRR2229915	SRP056666	SRS1052853	SRX1178460	SRA249145	GEO		Spatial gene expression gradients underlie prominent heterogeneity of CA1 pyramidal neurons	Tissue and organ function has been conventionally understood in terms of the interactions among discrete and homogeneous cell types.  This approach has proven difficult in neuroscience due to the marked diversity across different neuron classes, but may also be further hampered by prominent within-class variability.  Here, we considered a well-defined, canonical neuronal population – hippocampal CA1 pyramidal cells – and systematically examined the extent and spatial rules of transcriptional heterogeneity.  Using next-generation RNA sequencing, we identified striking variability in CA1 PCs, such that the differences along the dorsal-ventral axis rivaled differences across distinct pyramidal neuron classes. This variability emerged from a spectrum of continuous expression gradients, producing a profile consistent with a multifarious continuum of cells.  This work reveals an unexpected amount of variability within a canonical and narrowly defined neuronal population and suggests that continuous, within-class heterogeneity may be an important feature of neural circuits. Overall design: Hippocampal RNA profiles were generated by deep sequencing on Illumina HiSeq 2500, with three biological replicates per population		GSM1867243: intermediate_1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Manual sorting to purify for fluorescent neurons from microdissected slices was performed according to previous methods (Hempel et al., 2007). Total RNA was isolated from each sample using PicoPure RNA Isolation kit (Life Technologies, Frederick, MD) including the on-column RNAseq-free DNaseI treatment (Qiagen, Hilden, Germany) following the manufacturers’ recommendations.  Eluted RNA (11 ul) was dried in a speed vac to approximately 2-4 ul.  ERCC control RNAs (Life Technologies) were added using 1 ul of 1:100,000 dilution for every 50 cells.  cDNA was amplified from this input material using Ovation RNA-seq v2 kit (NuGEN, San Carlos, CA).  Approximately half of the resulting cDNA was used to make the sequencing libraries using the Ovation Rapid DR Multiplexing kit (NuGEN).	Illumina HiSeq 2500	cell population;;Intermediate CA1 pyramidal cells|location;;CA1|source_name;;Intermediate CA1 pyramidal cells	GEO Accession;;GSM1867243		GSM1867243	intermediate_1	1918987400	19189874	2016-01-06 15:50:16	857397334	1918987400	19189874	1	19189874	index:0,count:19189874,average:100,stdev:0	GSM1867243_r1				in_mesa	26777276	6.22	3.34	0.06	1723844906	1715148728	1619957723	1625433293	99.5	100.34	0	0	0	0	0	0	80.28	85.5	19562248	14213562	19562248	14213562	77.39	79.54	19562248	13701619	19562248	13222516	195966720	11.37	3.58	0	5.63	0	0.23	0	0.31	0	0.00	0	7.19	0	17705392	0	100	0	97.45	0	2.30	0	0.01	0	2.42	0	0.02	0	727.20	0	0.34	0	686216	0	19189874	0	1081190	0	44771	0	59982	0	0	0	1379729	0	2777	0	0	0	20427	0	2259645	0	13862	0	2296711	0	86.63	0	16624202	0	106007	2374383	22.398360485628	19189874.0	17705392.0	686216.0	1081190.0	44771.0	59982.0	0.0	1379729.0	16624202.0	92.3	3.6	5.6	0.2	0.3	0.0	7.2	86.6	100	100	100.00	8	1918987400	27.2	23.0	23.0	26.7	0.0	36.2	21.0	bulk
870581	SRR2229916	SRP056666	SRS1052852	SRX1178461	SRA249145	GEO		Spatial gene expression gradients underlie prominent heterogeneity of CA1 pyramidal neurons	Tissue and organ function has been conventionally understood in terms of the interactions among discrete and homogeneous cell types.  This approach has proven difficult in neuroscience due to the marked diversity across different neuron classes, but may also be further hampered by prominent within-class variability.  Here, we considered a well-defined, canonical neuronal population – hippocampal CA1 pyramidal cells – and systematically examined the extent and spatial rules of transcriptional heterogeneity.  Using next-generation RNA sequencing, we identified striking variability in CA1 PCs, such that the differences along the dorsal-ventral axis rivaled differences across distinct pyramidal neuron classes. This variability emerged from a spectrum of continuous expression gradients, producing a profile consistent with a multifarious continuum of cells.  This work reveals an unexpected amount of variability within a canonical and narrowly defined neuronal population and suggests that continuous, within-class heterogeneity may be an important feature of neural circuits. Overall design: Hippocampal RNA profiles were generated by deep sequencing on Illumina HiSeq 2500, with three biological replicates per population		GSM1867244: intermediate_2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Manual sorting to purify for fluorescent neurons from microdissected slices was performed according to previous methods (Hempel et al., 2007). Total RNA was isolated from each sample using PicoPure RNA Isolation kit (Life Technologies, Frederick, MD) including the on-column RNAseq-free DNaseI treatment (Qiagen, Hilden, Germany) following the manufacturers’ recommendations.  Eluted RNA (11 ul) was dried in a speed vac to approximately 2-4 ul.  ERCC control RNAs (Life Technologies) were added using 1 ul of 1:100,000 dilution for every 50 cells.  cDNA was amplified from this input material using Ovation RNA-seq v2 kit (NuGEN, San Carlos, CA).  Approximately half of the resulting cDNA was used to make the sequencing libraries using the Ovation Rapid DR Multiplexing kit (NuGEN).	Illumina HiSeq 2500	cell population;;Intermediate CA1 pyramidal cells|location;;CA1|source_name;;Intermediate CA1 pyramidal cells	GEO Accession;;GSM1867244		GSM1867244	intermediate_2	1554326600	15543266	2016-01-06 15:50:16	683740608	1554326600	15543266	1	15543266	index:0,count:15543266,average:100,stdev:0	GSM1867244_r1				in_mesa	26777276	7.25	3.36	0.07	1404477096	1393489935	1327359660	1326309368	99.22	99.92	0	0	0	0	0	0	79.3	83.98	15820050	11437926	15820050	11437926	76.76	78.57	15820050	11071815	15820050	10700778	178299046	12.70	3.69	0	5.17	0	0.27	0	0.32	0	0.00	0	6.61	0	14424046	0	100	0	97.46	0	1.92	0	0.01	0	2.46	0	0.01	0	513.36	0	0.31	0	573532	0	15543266	0	804221	0	42659	0	49701	0	0	0	1026860	0	2177	0	0	0	17634	0	1879699	0	11878	0	1911388	0	87.63	0	13619825	0	104553	1970123	18.843294788289	15543266.0	14424046.0	573532.0	804221.0	42659.0	49701.0	0.0	1026860.0	13619825.0	92.8	3.7	5.2	0.3	0.3	0.0	6.6	87.6	100	100	100.00	8	1554326600	27.4	22.7	22.9	27.0	0.0	36.5	21.7	bulk
870590	SRR2229917	SRP056666	SRS1052851	SRX1178462	SRA249145	GEO		Spatial gene expression gradients underlie prominent heterogeneity of CA1 pyramidal neurons	Tissue and organ function has been conventionally understood in terms of the interactions among discrete and homogeneous cell types.  This approach has proven difficult in neuroscience due to the marked diversity across different neuron classes, but may also be further hampered by prominent within-class variability.  Here, we considered a well-defined, canonical neuronal population – hippocampal CA1 pyramidal cells – and systematically examined the extent and spatial rules of transcriptional heterogeneity.  Using next-generation RNA sequencing, we identified striking variability in CA1 PCs, such that the differences along the dorsal-ventral axis rivaled differences across distinct pyramidal neuron classes. This variability emerged from a spectrum of continuous expression gradients, producing a profile consistent with a multifarious continuum of cells.  This work reveals an unexpected amount of variability within a canonical and narrowly defined neuronal population and suggests that continuous, within-class heterogeneity may be an important feature of neural circuits. Overall design: Hippocampal RNA profiles were generated by deep sequencing on Illumina HiSeq 2500, with three biological replicates per population		GSM1867245: ventral_0; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Manual sorting to purify for fluorescent neurons from microdissected slices was performed according to previous methods (Hempel et al., 2007). Total RNA was isolated from each sample using PicoPure RNA Isolation kit (Life Technologies, Frederick, MD) including the on-column RNAseq-free DNaseI treatment (Qiagen, Hilden, Germany) following the manufacturers’ recommendations.  Eluted RNA (11 ul) was dried in a speed vac to approximately 2-4 ul.  ERCC control RNAs (Life Technologies) were added using 1 ul of 1:100,000 dilution for every 50 cells.  cDNA was amplified from this input material using Ovation RNA-seq v2 kit (NuGEN, San Carlos, CA).  Approximately half of the resulting cDNA was used to make the sequencing libraries using the Ovation Rapid DR Multiplexing kit (NuGEN).	Illumina HiSeq 2500	cell population;;Ventral CA1 pyramidal cells|location;;CA1|source_name;;Ventral CA1 pyramidal cells	GEO Accession;;GSM1867245		GSM1867245	ventral_0	1659119600	16591196	2016-01-06 15:50:16	741854678	1659119600	16591196	1	16591196	index:0,count:16591196,average:100,stdev:0	GSM1867245_r1				in_mesa	26777276	6.44	3.0	0.06	1493442794	1484797524	1412540493	1415265503	99.42	100.19	0	0	0	0	0	0	71.26	75.4	16854872	10929357	16854872	10929357	68.13	69.69	16854872	10449221	16854872	10102225	315927078	21.15	3.77	0	5.08	0	0.27	0	0.31	0	0.00	0	6.98	0	15337597	0	100	0	97.45	0	2.17	0	0.01	0	2.43	0	0.02	0	519.38	0	0.34	0	625705	0	16591196	0	842489	0	44179	0	51183	0	0	0	1158237	0	2089	0	0	0	15157	0	1636015	0	12156	0	1665417	0	87.37	0	14495108	0	98238	1725449	17.563967100307	16591196.0	15337597.0	625705.0	842489.0	44179.0	51183.0	0.0	1158237.0	14495108.0	92.4	3.8	5.1	0.3	0.3	0.0	7.0	87.4	100	100	100.00	8	1659119600	27.3	22.9	23.0	26.8	0.0	36.2	21.1	bulk
870597	SRR2229918	SRP056666	SRS1052850	SRX1178463	SRA249145	GEO		Spatial gene expression gradients underlie prominent heterogeneity of CA1 pyramidal neurons	Tissue and organ function has been conventionally understood in terms of the interactions among discrete and homogeneous cell types.  This approach has proven difficult in neuroscience due to the marked diversity across different neuron classes, but may also be further hampered by prominent within-class variability.  Here, we considered a well-defined, canonical neuronal population – hippocampal CA1 pyramidal cells – and systematically examined the extent and spatial rules of transcriptional heterogeneity.  Using next-generation RNA sequencing, we identified striking variability in CA1 PCs, such that the differences along the dorsal-ventral axis rivaled differences across distinct pyramidal neuron classes. This variability emerged from a spectrum of continuous expression gradients, producing a profile consistent with a multifarious continuum of cells.  This work reveals an unexpected amount of variability within a canonical and narrowly defined neuronal population and suggests that continuous, within-class heterogeneity may be an important feature of neural circuits. Overall design: Hippocampal RNA profiles were generated by deep sequencing on Illumina HiSeq 2500, with three biological replicates per population		GSM1867246: ventral_1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Manual sorting to purify for fluorescent neurons from microdissected slices was performed according to previous methods (Hempel et al., 2007). Total RNA was isolated from each sample using PicoPure RNA Isolation kit (Life Technologies, Frederick, MD) including the on-column RNAseq-free DNaseI treatment (Qiagen, Hilden, Germany) following the manufacturers’ recommendations.  Eluted RNA (11 ul) was dried in a speed vac to approximately 2-4 ul.  ERCC control RNAs (Life Technologies) were added using 1 ul of 1:100,000 dilution for every 50 cells.  cDNA was amplified from this input material using Ovation RNA-seq v2 kit (NuGEN, San Carlos, CA).  Approximately half of the resulting cDNA was used to make the sequencing libraries using the Ovation Rapid DR Multiplexing kit (NuGEN).	Illumina HiSeq 2500	cell population;;Ventral CA1 pyramidal cells|location;;CA1|source_name;;Ventral CA1 pyramidal cells	GEO Accession;;GSM1867246		GSM1867246	ventral_1	1017452900	10174529	2016-01-06 15:50:16	442654960	1017452900	10174529	1	10174529	index:0,count:10174529,average:100,stdev:0	GSM1867246_r1				in_mesa	26777276	7.22	3.07	0.07	916291726	913828266	860329109	865563350	99.73	100.61	0	0	0	0	0	0	74.77	79.71	10435390	7039124	10435390	7039124	71.3	73.28	10435390	6712568	10435390	6471080	154387817	16.85	3.65	0	5.73	0	0.26	0	0.33	0	0.00	0	6.88	0	9414170	0	100	0	97.42	0	2.37	0	0.01	0	2.52	0	0.02	0	732.57	0	0.33	0	370869	0	10174529	0	583205	0	26581	0	33444	0	0	0	700334	0	1539	0	0	0	10381	0	1121161	0	7716	0	1140797	0	86.79	0	8830965	0	96996	1177209	12.136675739206	10174529.0	9414170.0	370869.0	583205.0	26581.0	33444.0	0.0	700334.0	8830965.0	92.5	3.6	5.7	0.3	0.3	0.0	6.9	86.8	100	100	100.00	8	1017452900	27.1	23.1	23.2	26.7	0.0	36.6	21.6	bulk
870607	SRR2229919	SRP056666	SRS1052849	SRX1178464	SRA249145	GEO		Spatial gene expression gradients underlie prominent heterogeneity of CA1 pyramidal neurons	Tissue and organ function has been conventionally understood in terms of the interactions among discrete and homogeneous cell types.  This approach has proven difficult in neuroscience due to the marked diversity across different neuron classes, but may also be further hampered by prominent within-class variability.  Here, we considered a well-defined, canonical neuronal population – hippocampal CA1 pyramidal cells – and systematically examined the extent and spatial rules of transcriptional heterogeneity.  Using next-generation RNA sequencing, we identified striking variability in CA1 PCs, such that the differences along the dorsal-ventral axis rivaled differences across distinct pyramidal neuron classes. This variability emerged from a spectrum of continuous expression gradients, producing a profile consistent with a multifarious continuum of cells.  This work reveals an unexpected amount of variability within a canonical and narrowly defined neuronal population and suggests that continuous, within-class heterogeneity may be an important feature of neural circuits. Overall design: Hippocampal RNA profiles were generated by deep sequencing on Illumina HiSeq 2500, with three biological replicates per population		GSM1867247: ventral_2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Manual sorting to purify for fluorescent neurons from microdissected slices was performed according to previous methods (Hempel et al., 2007). Total RNA was isolated from each sample using PicoPure RNA Isolation kit (Life Technologies, Frederick, MD) including the on-column RNAseq-free DNaseI treatment (Qiagen, Hilden, Germany) following the manufacturers’ recommendations.  Eluted RNA (11 ul) was dried in a speed vac to approximately 2-4 ul.  ERCC control RNAs (Life Technologies) were added using 1 ul of 1:100,000 dilution for every 50 cells.  cDNA was amplified from this input material using Ovation RNA-seq v2 kit (NuGEN, San Carlos, CA).  Approximately half of the resulting cDNA was used to make the sequencing libraries using the Ovation Rapid DR Multiplexing kit (NuGEN).	Illumina HiSeq 2500	cell population;;Ventral CA1 pyramidal cells|location;;CA1|source_name;;Ventral CA1 pyramidal cells	GEO Accession;;GSM1867247		GSM1867247	ventral_2	1542929300	15429293	2016-01-06 15:50:16	690282479	1542929300	15429293	1	15429293	index:0,count:15429293,average:100,stdev:0	GSM1867247_r1				in_mesa	26777276	8.61	3.16	0.06	1384125946	1383328762	1289432293	1301299306	99.94	100.92	0	0	0	0	0	0	79.68	85.61	15889628	11329324	15889628	11329324	76.2	78.72	15889628	10834769	15889628	10417054	156511920	11.31	3.52	0	6.39	0	0.27	0	0.30	0	0.00	0	7.28	0	14218627	0	100	0	97.44	0	2.54	0	0.01	0	2.54	0	0.02	0	375.31	0	0.36	0	542981	0	15429293	0	985227	0	41952	0	45949	0	0	0	1122765	0	2393	0	0	0	16012	0	1772340	0	10349	0	1801094	0	85.77	0	13233400	0	110012	1861475	16.920654110461	15429293.0	14218627.0	542981.0	985227.0	41952.0	45949.0	0.0	1122765.0	13233400.0	92.2	3.5	6.4	0.3	0.3	0.0	7.3	85.8	100	100	100.00	8	1542929300	27.0	23.3	23.3	26.4	0.0	36.1	20.7	bulk
870662	SRR2229920	SRP056666	SRS1052848	SRX1178465	SRA249145	GEO		Spatial gene expression gradients underlie prominent heterogeneity of CA1 pyramidal neurons	Tissue and organ function has been conventionally understood in terms of the interactions among discrete and homogeneous cell types.  This approach has proven difficult in neuroscience due to the marked diversity across different neuron classes, but may also be further hampered by prominent within-class variability.  Here, we considered a well-defined, canonical neuronal population – hippocampal CA1 pyramidal cells – and systematically examined the extent and spatial rules of transcriptional heterogeneity.  Using next-generation RNA sequencing, we identified striking variability in CA1 PCs, such that the differences along the dorsal-ventral axis rivaled differences across distinct pyramidal neuron classes. This variability emerged from a spectrum of continuous expression gradients, producing a profile consistent with a multifarious continuum of cells.  This work reveals an unexpected amount of variability within a canonical and narrowly defined neuronal population and suggests that continuous, within-class heterogeneity may be an important feature of neural circuits. Overall design: Hippocampal RNA profiles were generated by deep sequencing on Illumina HiSeq 2500, with three biological replicates per population		GSM1867248: proximal_0; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Manual sorting to purify for fluorescent neurons from microdissected slices was performed according to previous methods (Hempel et al., 2007). Total RNA was isolated from each sample using PicoPure RNA Isolation kit (Life Technologies, Frederick, MD) including the on-column RNAseq-free DNaseI treatment (Qiagen, Hilden, Germany) following the manufacturers’ recommendations.  Eluted RNA (11 ul) was dried in a speed vac to approximately 2-4 ul.  ERCC control RNAs (Life Technologies) were added using 1 ul of 1:100,000 dilution for every 50 cells.  cDNA was amplified from this input material using Ovation RNA-seq v2 kit (NuGEN, San Carlos, CA).  Approximately half of the resulting cDNA was used to make the sequencing libraries using the Ovation Rapid DR Multiplexing kit (NuGEN).	Illumina HiSeq 2500	cell population;;Proximal CA1 pyramidal cells|location;;CA1|source_name;;Proximal CA1 pyramidal cells	GEO Accession;;GSM1867248		GSM1867248	proximal_0	4295715415	45218057	2016-01-06 15:50:16	2025395057	4295715415	45218057	1	45218057	index:0,count:45218057,average:95,stdev:0	GSM1867248_r1				in_mesa	26777276	4.99	2.83	0.08	3803901981	3827250912	3524087954	3593476664	100.61	101.97	0	0	0	0	0	0	71.7	77.46	46563897	29518441	46563897	29518441	66.82	69.15	46563897	27507866	46563897	26352322	715654094	18.81	4.55	0	6.77	0	0.33	0	0.34	0	0.00	0	8.28	0	41168982	0	95	0	92.48	0	3.28	0	0.03	0	1.28	0	0.01	0	410.04	0	0.41	0	2056187	0	45218057	0	3062248	0	151344	0	153435	0	0	0	3744296	0	5069	0	0	0	30066	0	3675879	0	35359	0	3746373	0	84.27	0	38106734	0	109859	3824672	34.814371148472	45218057.0	41168982.0	2056187.0	3062248.0	151344.0	153435.0	0.0	3744296.0	38106734.0	91.0	4.5	6.8	0.3	0.3	0.0	8.3	84.3	95	95	95.00	8	4295715415	26.4	23.6	23.7	26.2	0.0	35.4	19.2	bulk
870671	SRR2229921	SRP056666	SRS1052847	SRX1178466	SRA249145	GEO		Spatial gene expression gradients underlie prominent heterogeneity of CA1 pyramidal neurons	Tissue and organ function has been conventionally understood in terms of the interactions among discrete and homogeneous cell types.  This approach has proven difficult in neuroscience due to the marked diversity across different neuron classes, but may also be further hampered by prominent within-class variability.  Here, we considered a well-defined, canonical neuronal population – hippocampal CA1 pyramidal cells – and systematically examined the extent and spatial rules of transcriptional heterogeneity.  Using next-generation RNA sequencing, we identified striking variability in CA1 PCs, such that the differences along the dorsal-ventral axis rivaled differences across distinct pyramidal neuron classes. This variability emerged from a spectrum of continuous expression gradients, producing a profile consistent with a multifarious continuum of cells.  This work reveals an unexpected amount of variability within a canonical and narrowly defined neuronal population and suggests that continuous, within-class heterogeneity may be an important feature of neural circuits. Overall design: Hippocampal RNA profiles were generated by deep sequencing on Illumina HiSeq 2500, with three biological replicates per population		GSM1867249: proximal_1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Manual sorting to purify for fluorescent neurons from microdissected slices was performed according to previous methods (Hempel et al., 2007). Total RNA was isolated from each sample using PicoPure RNA Isolation kit (Life Technologies, Frederick, MD) including the on-column RNAseq-free DNaseI treatment (Qiagen, Hilden, Germany) following the manufacturers’ recommendations.  Eluted RNA (11 ul) was dried in a speed vac to approximately 2-4 ul.  ERCC control RNAs (Life Technologies) were added using 1 ul of 1:100,000 dilution for every 50 cells.  cDNA was amplified from this input material using Ovation RNA-seq v2 kit (NuGEN, San Carlos, CA).  Approximately half of the resulting cDNA was used to make the sequencing libraries using the Ovation Rapid DR Multiplexing kit (NuGEN).	Illumina HiSeq 2500	cell population;;Proximal CA1 pyramidal cells|location;;CA1|source_name;;Proximal CA1 pyramidal cells	GEO Accession;;GSM1867249		GSM1867249	proximal_1	3783038795	39821461	2016-01-06 15:50:16	1788858079	3783038795	39821461	1	39821461	index:0,count:39821461,average:95,stdev:0	GSM1867249_r1				in_mesa	26777276	5.1	2.94	0.06	3367570527	3378992792	3105752308	3158592767	100.34	101.7	0	0	0	0	0	0	73.84	80.13	41384530	26879175	41384530	26879175	69.33	72.0	41384530	25237142	41384530	24151304	546218017	16.22	4.16	0	7.18	0	0.31	0	0.29	0	0.00	0	8.00	0	36400854	0	95	0	92.59	0	3.38	0	0.03	0	1.26	0	0.01	0	459.48	0	0.40	0	1658108	0	39821461	0	2857366	0	121494	0	114521	0	0	0	3184592	0	4794	0	0	0	26895	0	3392123	0	29583	0	3453395	0	84.23	0	33543488	0	110477	3520378	31.865257021824	39821461.0	36400854.0	1658108.0	2857366.0	121494.0	114521.0	0.0	3184592.0	33543488.0	91.4	4.2	7.2	0.3	0.3	0.0	8.0	84.2	95	95	95.00	8	3783038795	26.4	23.6	23.7	26.2	0.0	35.3	19.1	bulk
870677	SRR2229922	SRP056666	SRS1052846	SRX1178467	SRA249145	GEO		Spatial gene expression gradients underlie prominent heterogeneity of CA1 pyramidal neurons	Tissue and organ function has been conventionally understood in terms of the interactions among discrete and homogeneous cell types.  This approach has proven difficult in neuroscience due to the marked diversity across different neuron classes, but may also be further hampered by prominent within-class variability.  Here, we considered a well-defined, canonical neuronal population – hippocampal CA1 pyramidal cells – and systematically examined the extent and spatial rules of transcriptional heterogeneity.  Using next-generation RNA sequencing, we identified striking variability in CA1 PCs, such that the differences along the dorsal-ventral axis rivaled differences across distinct pyramidal neuron classes. This variability emerged from a spectrum of continuous expression gradients, producing a profile consistent with a multifarious continuum of cells.  This work reveals an unexpected amount of variability within a canonical and narrowly defined neuronal population and suggests that continuous, within-class heterogeneity may be an important feature of neural circuits. Overall design: Hippocampal RNA profiles were generated by deep sequencing on Illumina HiSeq 2500, with three biological replicates per population		GSM1867250: proximal_2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Manual sorting to purify for fluorescent neurons from microdissected slices was performed according to previous methods (Hempel et al., 2007). Total RNA was isolated from each sample using PicoPure RNA Isolation kit (Life Technologies, Frederick, MD) including the on-column RNAseq-free DNaseI treatment (Qiagen, Hilden, Germany) following the manufacturers’ recommendations.  Eluted RNA (11 ul) was dried in a speed vac to approximately 2-4 ul.  ERCC control RNAs (Life Technologies) were added using 1 ul of 1:100,000 dilution for every 50 cells.  cDNA was amplified from this input material using Ovation RNA-seq v2 kit (NuGEN, San Carlos, CA).  Approximately half of the resulting cDNA was used to make the sequencing libraries using the Ovation Rapid DR Multiplexing kit (NuGEN).	Illumina HiSeq 2500	cell population;;Proximal CA1 pyramidal cells|location;;CA1|source_name;;Proximal CA1 pyramidal cells	GEO Accession;;GSM1867250		GSM1867250	proximal_2	5646596225	59437855	2016-01-06 15:50:16	2652995071	5646596225	59437855	1	59437855	index:0,count:59437855,average:95,stdev:0	GSM1867250_r1				in_mesa	26777276	5.24	3.13	0.06	5080146275	5099854794	4693997174	4768297592	100.39	101.58	0	0	0	0	0	0	78.1	84.6	62180099	42848564	62180099	42848564	74.04	76.79	62180099	40616485	62180099	38889091	607925538	11.97	3.77	0	7.09	0	0.32	0	0.25	0	0.00	0	7.13	0	54860522	0	95	0	92.68	0	3.12	0	0.02	0	1.27	0	0.01	0	606.17	0	0.37	0	2243552	0	59437855	0	4213873	0	188140	0	151459	0	0	0	4237734	0	7454	0	0	0	47232	0	5756850	0	40559	0	5852095	0	85.21	0	50646649	0	133098	5966654	44.829028234834	59437855.0	54860522.0	2243552.0	4213873.0	188140.0	151459.0	0.0	4237734.0	50646649.0	92.3	3.8	7.1	0.3	0.3	0.0	7.1	85.2	95	95	95.00	8	5646596225	26.5	23.6	23.7	26.2	0.0	35.5	19.5	bulk
870686	SRR2229923	SRP056666	SRS1052845	SRX1178468	SRA249145	GEO		Spatial gene expression gradients underlie prominent heterogeneity of CA1 pyramidal neurons	Tissue and organ function has been conventionally understood in terms of the interactions among discrete and homogeneous cell types.  This approach has proven difficult in neuroscience due to the marked diversity across different neuron classes, but may also be further hampered by prominent within-class variability.  Here, we considered a well-defined, canonical neuronal population – hippocampal CA1 pyramidal cells – and systematically examined the extent and spatial rules of transcriptional heterogeneity.  Using next-generation RNA sequencing, we identified striking variability in CA1 PCs, such that the differences along the dorsal-ventral axis rivaled differences across distinct pyramidal neuron classes. This variability emerged from a spectrum of continuous expression gradients, producing a profile consistent with a multifarious continuum of cells.  This work reveals an unexpected amount of variability within a canonical and narrowly defined neuronal population and suggests that continuous, within-class heterogeneity may be an important feature of neural circuits. Overall design: Hippocampal RNA profiles were generated by deep sequencing on Illumina HiSeq 2500, with three biological replicates per population		GSM1867251: distal_0; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Manual sorting to purify for fluorescent neurons from microdissected slices was performed according to previous methods (Hempel et al., 2007). Total RNA was isolated from each sample using PicoPure RNA Isolation kit (Life Technologies, Frederick, MD) including the on-column RNAseq-free DNaseI treatment (Qiagen, Hilden, Germany) following the manufacturers’ recommendations.  Eluted RNA (11 ul) was dried in a speed vac to approximately 2-4 ul.  ERCC control RNAs (Life Technologies) were added using 1 ul of 1:100,000 dilution for every 50 cells.  cDNA was amplified from this input material using Ovation RNA-seq v2 kit (NuGEN, San Carlos, CA).  Approximately half of the resulting cDNA was used to make the sequencing libraries using the Ovation Rapid DR Multiplexing kit (NuGEN).	Illumina HiSeq 2500	cell population;;Distal CA1 pyramidal cells|location;;CA1|source_name;;Distal CA1 pyramidal cells	GEO Accession;;GSM1867251		GSM1867251	distal_0	4755264995	50055421	2016-01-06 15:50:16	2218445454	4755264995	50055421	1	50055421	index:0,count:50055421,average:95,stdev:0	GSM1867251_r1				in_mesa	26777276	4.89	3.08	0.08	4225348025	4257255030	3903595491	3990563225	100.76	102.23	0	0	0	0	0	0	73.67	79.81	51673318	33546041	51673318	33546041	69.17	71.56	51673318	31498590	51673318	30078183	707159766	16.74	3.61	0	7.00	0	0.32	0	0.35	0	0.00	0	8.35	0	45538279	0	95	0	92.87	0	3.19	0	0.02	0	1.22	0	0.01	0	563.12	0	0.41	0	1807964	0	50055421	0	3503837	0	162248	0	175417	0	0	0	4179477	0	4842	0	0	0	35440	0	4305769	0	35617	0	4381668	0	83.98	0	42034442	0	119697	4478971	37.419241919179	50055421.0	45538279.0	1807964.0	3503837.0	162248.0	175417.0	0.0	4179477.0	42034442.0	91.0	3.6	7.0	0.3	0.4	0.0	8.3	84.0	95	95	95.00	8	4755264995	26.9	23.1	23.2	26.9	0.0	35.5	19.4	bulk
870693	SRR2229924	SRP056666	SRS1052844	SRX1178469	SRA249145	GEO		Spatial gene expression gradients underlie prominent heterogeneity of CA1 pyramidal neurons	Tissue and organ function has been conventionally understood in terms of the interactions among discrete and homogeneous cell types.  This approach has proven difficult in neuroscience due to the marked diversity across different neuron classes, but may also be further hampered by prominent within-class variability.  Here, we considered a well-defined, canonical neuronal population – hippocampal CA1 pyramidal cells – and systematically examined the extent and spatial rules of transcriptional heterogeneity.  Using next-generation RNA sequencing, we identified striking variability in CA1 PCs, such that the differences along the dorsal-ventral axis rivaled differences across distinct pyramidal neuron classes. This variability emerged from a spectrum of continuous expression gradients, producing a profile consistent with a multifarious continuum of cells.  This work reveals an unexpected amount of variability within a canonical and narrowly defined neuronal population and suggests that continuous, within-class heterogeneity may be an important feature of neural circuits. Overall design: Hippocampal RNA profiles were generated by deep sequencing on Illumina HiSeq 2500, with three biological replicates per population		GSM1867252: distal_1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Manual sorting to purify for fluorescent neurons from microdissected slices was performed according to previous methods (Hempel et al., 2007). Total RNA was isolated from each sample using PicoPure RNA Isolation kit (Life Technologies, Frederick, MD) including the on-column RNAseq-free DNaseI treatment (Qiagen, Hilden, Germany) following the manufacturers’ recommendations.  Eluted RNA (11 ul) was dried in a speed vac to approximately 2-4 ul.  ERCC control RNAs (Life Technologies) were added using 1 ul of 1:100,000 dilution for every 50 cells.  cDNA was amplified from this input material using Ovation RNA-seq v2 kit (NuGEN, San Carlos, CA).  Approximately half of the resulting cDNA was used to make the sequencing libraries using the Ovation Rapid DR Multiplexing kit (NuGEN).	Illumina HiSeq 2500	cell population;;Distal CA1 pyramidal cells|location;;CA1|source_name;;Distal CA1 pyramidal cells	GEO Accession;;GSM1867252		GSM1867252	distal_1	4538355675	47772165	2016-01-06 15:50:16	2117953389	4538355675	47772165	1	47772165	index:0,count:47772165,average:95,stdev:0	GSM1867252_r1				in_mesa	26777276	4.59	3.01	0.09	4114993216	4108102635	3836035501	3878533285	99.83	101.11	0	0	0	0	0	0	68.12	73.13	49703931	30180769	49703931	30180769	64.51	66.27	49703931	28583174	49703931	27350881	952998395	23.16	3.64	0	6.35	0	0.32	0	0.44	0	0.00	0	6.49	0	44307300	0	95	0	92.95	0	2.96	0	0.02	0	1.24	0	0.01	0	534.10	0	0.39	0	1739413	0	47772165	0	3035733	0	155241	0	210670	0	0	0	3098954	0	4350	0	0	0	30433	0	3831906	0	34430	0	3901119	0	86.39	0	41271567	0	122810	3985801	32.455019949516	47772165.0	44307300.0	1739413.0	3035733.0	155241.0	210670.0	0.0	3098954.0	41271567.0	92.7	3.6	6.4	0.3	0.4	0.0	6.5	86.4	95	95	95.00	8	4538355675	27.2	22.7	22.8	27.2	0.0	35.6	19.6	bulk
870703	SRR2229925	SRP056666	SRS1052843	SRX1178470	SRA249145	GEO		Spatial gene expression gradients underlie prominent heterogeneity of CA1 pyramidal neurons	Tissue and organ function has been conventionally understood in terms of the interactions among discrete and homogeneous cell types.  This approach has proven difficult in neuroscience due to the marked diversity across different neuron classes, but may also be further hampered by prominent within-class variability.  Here, we considered a well-defined, canonical neuronal population – hippocampal CA1 pyramidal cells – and systematically examined the extent and spatial rules of transcriptional heterogeneity.  Using next-generation RNA sequencing, we identified striking variability in CA1 PCs, such that the differences along the dorsal-ventral axis rivaled differences across distinct pyramidal neuron classes. This variability emerged from a spectrum of continuous expression gradients, producing a profile consistent with a multifarious continuum of cells.  This work reveals an unexpected amount of variability within a canonical and narrowly defined neuronal population and suggests that continuous, within-class heterogeneity may be an important feature of neural circuits. Overall design: Hippocampal RNA profiles were generated by deep sequencing on Illumina HiSeq 2500, with three biological replicates per population		GSM1867253: distal_2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Manual sorting to purify for fluorescent neurons from microdissected slices was performed according to previous methods (Hempel et al., 2007). Total RNA was isolated from each sample using PicoPure RNA Isolation kit (Life Technologies, Frederick, MD) including the on-column RNAseq-free DNaseI treatment (Qiagen, Hilden, Germany) following the manufacturers’ recommendations.  Eluted RNA (11 ul) was dried in a speed vac to approximately 2-4 ul.  ERCC control RNAs (Life Technologies) were added using 1 ul of 1:100,000 dilution for every 50 cells.  cDNA was amplified from this input material using Ovation RNA-seq v2 kit (NuGEN, San Carlos, CA).  Approximately half of the resulting cDNA was used to make the sequencing libraries using the Ovation Rapid DR Multiplexing kit (NuGEN).	Illumina HiSeq 2500	cell population;;Distal CA1 pyramidal cells|location;;CA1|source_name;;Distal CA1 pyramidal cells	GEO Accession;;GSM1867253		GSM1867253	distal_2	3935061405	41421699	2016-01-06 15:50:16	1849867503	3935061405	41421699	1	41421699	index:0,count:41421699,average:95,stdev:0	GSM1867253_r1				in_mesa	26777276	5.22	3.06	0.07	3521431593	3561018130	3228771830	3318008564	101.12	102.76	0	0	0	0	0	0	76.56	83.57	43700397	29132157	43700397	29132157	71.54	74.44	43700397	27220903	43700397	25949160	459766161	13.06	3.94	0	7.71	0	0.33	0	0.37	0	0.00	0	7.43	0	38050891	0	95	0	92.63	0	3.30	0	0.02	0	1.26	0	0.01	0	540.28	0	0.43	0	1631021	0	41421699	0	3192861	0	137360	0	154215	0	0	0	3079233	0	5798	0	0	0	30015	0	3642416	0	29207	0	3707436	0	84.15	0	34858030	0	104401	3788750	36.290361203437	41421699.0	38050891.0	1631021.0	3192861.0	137360.0	154215.0	0.0	3079233.0	34858030.0	91.9	3.9	7.7	0.3	0.4	0.0	7.4	84.2	95	95	95.00	8	3935061405	26.7	23.3	23.4	26.6	0.0	35.4	19.2	bulk
870711	SRR2229926	SRP056666	SRS1052842	SRX1178471	SRA249145	GEO		Spatial gene expression gradients underlie prominent heterogeneity of CA1 pyramidal neurons	Tissue and organ function has been conventionally understood in terms of the interactions among discrete and homogeneous cell types.  This approach has proven difficult in neuroscience due to the marked diversity across different neuron classes, but may also be further hampered by prominent within-class variability.  Here, we considered a well-defined, canonical neuronal population – hippocampal CA1 pyramidal cells – and systematically examined the extent and spatial rules of transcriptional heterogeneity.  Using next-generation RNA sequencing, we identified striking variability in CA1 PCs, such that the differences along the dorsal-ventral axis rivaled differences across distinct pyramidal neuron classes. This variability emerged from a spectrum of continuous expression gradients, producing a profile consistent with a multifarious continuum of cells.  This work reveals an unexpected amount of variability within a canonical and narrowly defined neuronal population and suggests that continuous, within-class heterogeneity may be an important feature of neural circuits. Overall design: Hippocampal RNA profiles were generated by deep sequencing on Illumina HiSeq 2500, with three biological replicates per population		GSM1867254: superficial_0; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Manual sorting to purify for fluorescent neurons from microdissected slices was performed according to previous methods (Hempel et al., 2007). Total RNA was isolated from each sample using PicoPure RNA Isolation kit (Life Technologies, Frederick, MD) including the on-column RNAseq-free DNaseI treatment (Qiagen, Hilden, Germany) following the manufacturers’ recommendations.  Eluted RNA (11 ul) was dried in a speed vac to approximately 2-4 ul.  ERCC control RNAs (Life Technologies) were added using 1 ul of 1:100,000 dilution for every 50 cells.  cDNA was amplified from this input material using Ovation RNA-seq v2 kit (NuGEN, San Carlos, CA).  Approximately half of the resulting cDNA was used to make the sequencing libraries using the Ovation Rapid DR Multiplexing kit (NuGEN).	Illumina HiSeq 2500	cell population;;Superficial CA1 pyramidal cells|location;;CA1|source_name;;Superficial CA1 pyramidal cells	GEO Accession;;GSM1867254		GSM1867254	superficial_0	4858651400	48586514	2016-01-06 15:50:16	2275661278	4858651400	48586514	1	48586514	index:0,count:48586514,average:100,stdev:0	GSM1867254_r1				in_mesa	26777276	5.43	3.0	0.05	4382550826	4407622727	4082238661	4152712327	100.57	101.73	0	0	0	0	0	0	75.54	81.16	50375744	34027800	50375744	34027800	70.6	72.96	50375744	31799739	50375744	30587149	669159224	15.27	3.69	0	6.42	0	0.27	0	0.24	0	0.00	0	6.78	0	45045135	0	100	0	97.37	0	3.14	0	0.02	0	2.16	0	0.02	0	450.80	0	0.34	0	1792776	0	48586514	0	3119966	0	130107	0	116247	0	0	0	3295025	0	6887	0	0	0	46782	0	5420397	0	36667	0	5510733	0	86.29	0	41925169	0	128825	5687943	44.152478168057	48586514.0	45045135.0	1792776.0	3119966.0	130107.0	116247.0	0.0	3295025.0	41925169.0	92.7	3.7	6.4	0.3	0.2	0.0	6.8	86.3	100	100	100.00	8	4858651400	26.6	23.4	23.6	26.4	0.0	35.4	19.5	bulk
870719	SRR2229927	SRP056666	SRS1052841	SRX1178472	SRA249145	GEO		Spatial gene expression gradients underlie prominent heterogeneity of CA1 pyramidal neurons	Tissue and organ function has been conventionally understood in terms of the interactions among discrete and homogeneous cell types.  This approach has proven difficult in neuroscience due to the marked diversity across different neuron classes, but may also be further hampered by prominent within-class variability.  Here, we considered a well-defined, canonical neuronal population – hippocampal CA1 pyramidal cells – and systematically examined the extent and spatial rules of transcriptional heterogeneity.  Using next-generation RNA sequencing, we identified striking variability in CA1 PCs, such that the differences along the dorsal-ventral axis rivaled differences across distinct pyramidal neuron classes. This variability emerged from a spectrum of continuous expression gradients, producing a profile consistent with a multifarious continuum of cells.  This work reveals an unexpected amount of variability within a canonical and narrowly defined neuronal population and suggests that continuous, within-class heterogeneity may be an important feature of neural circuits. Overall design: Hippocampal RNA profiles were generated by deep sequencing on Illumina HiSeq 2500, with three biological replicates per population		GSM1867255: superficial_1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Manual sorting to purify for fluorescent neurons from microdissected slices was performed according to previous methods (Hempel et al., 2007). Total RNA was isolated from each sample using PicoPure RNA Isolation kit (Life Technologies, Frederick, MD) including the on-column RNAseq-free DNaseI treatment (Qiagen, Hilden, Germany) following the manufacturers’ recommendations.  Eluted RNA (11 ul) was dried in a speed vac to approximately 2-4 ul.  ERCC control RNAs (Life Technologies) were added using 1 ul of 1:100,000 dilution for every 50 cells.  cDNA was amplified from this input material using Ovation RNA-seq v2 kit (NuGEN, San Carlos, CA).  Approximately half of the resulting cDNA was used to make the sequencing libraries using the Ovation Rapid DR Multiplexing kit (NuGEN).	Illumina HiSeq 2500	cell population;;Superficial CA1 pyramidal cells|location;;CA1|source_name;;Superficial CA1 pyramidal cells	GEO Accession;;GSM1867255		GSM1867255	superficial_1	4976518800	49765188	2016-01-06 15:50:16	2333113735	4976518800	49765188	1	49765188	index:0,count:49765188,average:100,stdev:0	GSM1867255_r1				in_mesa	26777276	5.35	2.89	0.06	4501941130	4500877235	4213899753	4257727205	99.98	101.04	0	0	0	0	0	0	71.65	76.62	51314867	33124998	51314867	33124998	67.14	69.11	51314867	31040929	51314867	29881594	872949900	19.39	3.66	0	6.02	0	0.25	0	0.26	0	0.00	0	6.59	0	46230456	0	100	0	97.46	0	2.98	0	0.02	0	2.17	0	0.02	0	464.13	0	0.33	0	1820656	0	49765188	0	2995020	0	126535	0	130868	0	0	0	3277329	0	6899	0	0	0	45022	0	5231787	0	37153	0	5320861	0	86.88	0	43235436	0	128521	5479065	42.631671088771	49765188.0	46230456.0	1820656.0	2995020.0	126535.0	130868.0	0.0	3277329.0	43235436.0	92.9	3.7	6.0	0.3	0.3	0.0	6.6	86.9	100	100	100.00	8	4976518800	26.8	23.2	23.4	26.6	0.0	35.4	19.5	bulk
870727	SRR2229928	SRP056666	SRS1052840	SRX1178473	SRA249145	GEO		Spatial gene expression gradients underlie prominent heterogeneity of CA1 pyramidal neurons	Tissue and organ function has been conventionally understood in terms of the interactions among discrete and homogeneous cell types.  This approach has proven difficult in neuroscience due to the marked diversity across different neuron classes, but may also be further hampered by prominent within-class variability.  Here, we considered a well-defined, canonical neuronal population – hippocampal CA1 pyramidal cells – and systematically examined the extent and spatial rules of transcriptional heterogeneity.  Using next-generation RNA sequencing, we identified striking variability in CA1 PCs, such that the differences along the dorsal-ventral axis rivaled differences across distinct pyramidal neuron classes. This variability emerged from a spectrum of continuous expression gradients, producing a profile consistent with a multifarious continuum of cells.  This work reveals an unexpected amount of variability within a canonical and narrowly defined neuronal population and suggests that continuous, within-class heterogeneity may be an important feature of neural circuits. Overall design: Hippocampal RNA profiles were generated by deep sequencing on Illumina HiSeq 2500, with three biological replicates per population		GSM1867256: superficial_2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Manual sorting to purify for fluorescent neurons from microdissected slices was performed according to previous methods (Hempel et al., 2007). Total RNA was isolated from each sample using PicoPure RNA Isolation kit (Life Technologies, Frederick, MD) including the on-column RNAseq-free DNaseI treatment (Qiagen, Hilden, Germany) following the manufacturers’ recommendations.  Eluted RNA (11 ul) was dried in a speed vac to approximately 2-4 ul.  ERCC control RNAs (Life Technologies) were added using 1 ul of 1:100,000 dilution for every 50 cells.  cDNA was amplified from this input material using Ovation RNA-seq v2 kit (NuGEN, San Carlos, CA).  Approximately half of the resulting cDNA was used to make the sequencing libraries using the Ovation Rapid DR Multiplexing kit (NuGEN).	Illumina HiSeq 2500	cell population;;Superficial CA1 pyramidal cells|location;;CA1|source_name;;Superficial CA1 pyramidal cells	GEO Accession;;GSM1867256		GSM1867256	superficial_2	3891628300	38916283	2016-01-06 15:50:16	1824933093	3891628300	38916283	1	38916283	index:0,count:38916283,average:100,stdev:0	GSM1867256_r1				in_mesa	26777276	6.01	3.06	0.04	3512554575	3539753900	3258495853	3322216657	100.77	101.96	0	0	0	0	0	0	77.89	84.04	40559283	28117023	40559283	28117023	72.77	75.46	40559283	26268444	40559283	25245958	440307932	12.54	3.58	0	6.78	0	0.27	0	0.23	0	0.00	0	6.74	0	36096325	0	100	0	97.39	0	3.24	0	0.02	0	2.28	0	0.02	0	418.20	0	0.34	0	1391391	0	38916283	0	2639637	0	105344	0	91022	0	0	0	2623592	0	5977	0	0	0	39405	0	4491249	0	28860	0	4565491	0	85.97	0	33456688	0	126685	4705925	37.146662982989	38916283.0	36096325.0	1391391.0	2639637.0	105344.0	91022.0	0.0	2623592.0	33456688.0	92.8	3.6	6.8	0.3	0.2	0.0	6.7	86.0	100	100	100.00	8	3891628300	26.4	23.6	23.7	26.2	0.0	35.4	19.2	bulk
870790	SRR2229930	SRP056666	SRS1052838	SRX1178475	SRA249145	GEO		Spatial gene expression gradients underlie prominent heterogeneity of CA1 pyramidal neurons	Tissue and organ function has been conventionally understood in terms of the interactions among discrete and homogeneous cell types.  This approach has proven difficult in neuroscience due to the marked diversity across different neuron classes, but may also be further hampered by prominent within-class variability.  Here, we considered a well-defined, canonical neuronal population – hippocampal CA1 pyramidal cells – and systematically examined the extent and spatial rules of transcriptional heterogeneity.  Using next-generation RNA sequencing, we identified striking variability in CA1 PCs, such that the differences along the dorsal-ventral axis rivaled differences across distinct pyramidal neuron classes. This variability emerged from a spectrum of continuous expression gradients, producing a profile consistent with a multifarious continuum of cells.  This work reveals an unexpected amount of variability within a canonical and narrowly defined neuronal population and suggests that continuous, within-class heterogeneity may be an important feature of neural circuits. Overall design: Hippocampal RNA profiles were generated by deep sequencing on Illumina HiSeq 2500, with three biological replicates per population		GSM1867258: deep_1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Manual sorting to purify for fluorescent neurons from microdissected slices was performed according to previous methods (Hempel et al., 2007). Total RNA was isolated from each sample using PicoPure RNA Isolation kit (Life Technologies, Frederick, MD) including the on-column RNAseq-free DNaseI treatment (Qiagen, Hilden, Germany) following the manufacturers’ recommendations.  Eluted RNA (11 ul) was dried in a speed vac to approximately 2-4 ul.  ERCC control RNAs (Life Technologies) were added using 1 ul of 1:100,000 dilution for every 50 cells.  cDNA was amplified from this input material using Ovation RNA-seq v2 kit (NuGEN, San Carlos, CA).  Approximately half of the resulting cDNA was used to make the sequencing libraries using the Ovation Rapid DR Multiplexing kit (NuGEN).	Illumina HiSeq 2500	cell population;;Deep CA1 pyramidal cells|location;;CA1|source_name;;Deep CA1 pyramidal cells	GEO Accession;;GSM1867258		GSM1867258	deep_1	2770112200	27701122	2016-01-06 15:50:16	1304420328	2770112200	27701122	1	27701122	index:0,count:27701122,average:100,stdev:0	GSM1867258_r1				in_mesa	26777276	5.75	2.91	0.06	2461610928	2429478138	2325097956	2313797885	98.69	99.51	0	0	0	0	0	0	66.19	70.13	27784041	16732962	27784041	16732962	62.75	64.14	27784041	15864149	27784041	15304108	628445027	25.53	3.19	0	5.12	0	0.28	0	0.31	0	0.00	0	8.14	0	25280377	0	100	0	97.44	0	2.60	0	0.01	0	2.38	0	0.02	0	407.04	0	0.33	0	882654	0	27701122	0	1419234	0	77385	0	87106	0	0	0	2256254	0	3401	0	0	0	25667	0	2667645	0	19903	0	2716616	0	86.14	0	23861143	0	104685	2798223	26.729932655108	27701122.0	25280377.0	882654.0	1419234.0	77385.0	87106.0	0.0	2256254.0	23861143.0	91.3	3.2	5.1	0.3	0.3	0.0	8.1	86.1	100	100	100.00	8	2770112200	27.1	23.1	23.3	26.5	0.0	35.6	20.0	bulk
870798	SRR2229931	SRP056666	SRS1052837	SRX1178476	SRA249145	GEO		Spatial gene expression gradients underlie prominent heterogeneity of CA1 pyramidal neurons	Tissue and organ function has been conventionally understood in terms of the interactions among discrete and homogeneous cell types.  This approach has proven difficult in neuroscience due to the marked diversity across different neuron classes, but may also be further hampered by prominent within-class variability.  Here, we considered a well-defined, canonical neuronal population – hippocampal CA1 pyramidal cells – and systematically examined the extent and spatial rules of transcriptional heterogeneity.  Using next-generation RNA sequencing, we identified striking variability in CA1 PCs, such that the differences along the dorsal-ventral axis rivaled differences across distinct pyramidal neuron classes. This variability emerged from a spectrum of continuous expression gradients, producing a profile consistent with a multifarious continuum of cells.  This work reveals an unexpected amount of variability within a canonical and narrowly defined neuronal population and suggests that continuous, within-class heterogeneity may be an important feature of neural circuits. Overall design: Hippocampal RNA profiles were generated by deep sequencing on Illumina HiSeq 2500, with three biological replicates per population		GSM1867259: deep_2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Manual sorting to purify for fluorescent neurons from microdissected slices was performed according to previous methods (Hempel et al., 2007). Total RNA was isolated from each sample using PicoPure RNA Isolation kit (Life Technologies, Frederick, MD) including the on-column RNAseq-free DNaseI treatment (Qiagen, Hilden, Germany) following the manufacturers’ recommendations.  Eluted RNA (11 ul) was dried in a speed vac to approximately 2-4 ul.  ERCC control RNAs (Life Technologies) were added using 1 ul of 1:100,000 dilution for every 50 cells.  cDNA was amplified from this input material using Ovation RNA-seq v2 kit (NuGEN, San Carlos, CA).  Approximately half of the resulting cDNA was used to make the sequencing libraries using the Ovation Rapid DR Multiplexing kit (NuGEN).	Illumina HiSeq 2500	cell population;;Deep CA1 pyramidal cells|location;;CA1|source_name;;Deep CA1 pyramidal cells	GEO Accession;;GSM1867259		GSM1867259	deep_2	2298235200	22982352	2016-01-06 15:50:16	1085905508	2298235200	22982352	1	22982352	index:0,count:22982352,average:100,stdev:0	GSM1867259_r1				in_mesa	26777276	6.51	3.17	0.06	2073354667	2057135816	1946229940	1947786162	99.22	100.08	0	0	0	0	0	0	77.81	82.95	23548097	16543432	23548097	16543432	74.33	76.41	23548097	15805422	23548097	15239591	275001035	13.26	3.13	0	5.74	0	0.29	0	0.27	0	0.00	0	6.93	0	21262442	0	100	0	97.58	0	2.67	0	0.01	0	2.52	0	0.02	0	422.12	0	0.33	0	719746	0	22982352	0	1318384	0	65936	0	62241	0	0	0	1591733	0	3635	0	0	0	26733	0	2763028	0	16040	0	2809436	0	86.78	0	19944058	0	106001	2897449	27.334166658805	22982352.0	21262442.0	719746.0	1318384.0	65936.0	62241.0	0.0	1591733.0	19944058.0	92.5	3.1	5.7	0.3	0.3	0.0	6.9	86.8	100	100	100.00	8	2298235200	26.8	23.4	23.5	26.3	0.0	35.5	19.6	bulk
870806	SRR2229932	SRP056666	SRS1052836	SRX1178477	SRA249145	GEO		Spatial gene expression gradients underlie prominent heterogeneity of CA1 pyramidal neurons	Tissue and organ function has been conventionally understood in terms of the interactions among discrete and homogeneous cell types.  This approach has proven difficult in neuroscience due to the marked diversity across different neuron classes, but may also be further hampered by prominent within-class variability.  Here, we considered a well-defined, canonical neuronal population – hippocampal CA1 pyramidal cells – and systematically examined the extent and spatial rules of transcriptional heterogeneity.  Using next-generation RNA sequencing, we identified striking variability in CA1 PCs, such that the differences along the dorsal-ventral axis rivaled differences across distinct pyramidal neuron classes. This variability emerged from a spectrum of continuous expression gradients, producing a profile consistent with a multifarious continuum of cells.  This work reveals an unexpected amount of variability within a canonical and narrowly defined neuronal population and suggests that continuous, within-class heterogeneity may be an important feature of neural circuits. Overall design: Hippocampal RNA profiles were generated by deep sequencing on Illumina HiSeq 2500, with three biological replicates per population		GSM1867260: ca3d_0; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Manual sorting to purify for fluorescent neurons from microdissected slices was performed according to previous methods (Hempel et al., 2007). Total RNA was isolated from each sample using PicoPure RNA Isolation kit (Life Technologies, Frederick, MD) including the on-column RNAseq-free DNaseI treatment (Qiagen, Hilden, Germany) following the manufacturers’ recommendations.  Eluted RNA (11 ul) was dried in a speed vac to approximately 2-4 ul.  ERCC control RNAs (Life Technologies) were added using 1 ul of 1:100,000 dilution for every 50 cells.  cDNA was amplified from this input material using Ovation RNA-seq v2 kit (NuGEN, San Carlos, CA).  Approximately half of the resulting cDNA was used to make the sequencing libraries using the Ovation Rapid DR Multiplexing kit (NuGEN).	Illumina HiSeq 2500	cell population;;Dorsal CA3 pyramidal cells|location;;CA3|source_name;;Dorsal CA3 pyramidal cells	GEO Accession;;GSM1867260		GSM1867260	ca3d_0	3713427700	39504550	2016-01-06 15:50:16	1816207301	3713427700	39504550	1	39504550	index:0,count:39504550,average:94,stdev:0	GSM1867260_r1				in_mesa	26777276	10.52	2.91	0.04	3360267452	3390198204	3119467627	3183990465	100.89	102.07	0	0	0	0	0	0	77.95	84.03	41068436	28549038	41068436	28549038	73.56	76.13	41068436	26942934	41068436	25866212	435128432	12.95	3.25	0	6.71	0	0.32	0	0.22	0	0.00	0	6.74	0	36626473	0	94	0	91.82	0	3.02	0	0.02	0	1.34	0	0.01	0	643.51	0	0.38	0	1284650	0	39504550	0	2651754	0	127563	0	87777	0	0	0	2662737	0	5113	0	0	0	35317	0	3911076	0	25082	0	3976588	0	86.00	0	33974719	0	131523	4039076	30.710035507098	39504550.0	36626473.0	1284650.0	2651754.0	127563.0	87777.0	0.0	2662737.0	33974719.0	92.7	3.3	6.7	0.3	0.2	0.0	6.7	86.0	94	94	94.00	8	3713427700	27.1	23.2	23.3	26.4	0.0	34.8	18.4	bulk
870814	SRR2229933	SRP056666	SRS1052835	SRX1178478	SRA249145	GEO		Spatial gene expression gradients underlie prominent heterogeneity of CA1 pyramidal neurons	Tissue and organ function has been conventionally understood in terms of the interactions among discrete and homogeneous cell types.  This approach has proven difficult in neuroscience due to the marked diversity across different neuron classes, but may also be further hampered by prominent within-class variability.  Here, we considered a well-defined, canonical neuronal population – hippocampal CA1 pyramidal cells – and systematically examined the extent and spatial rules of transcriptional heterogeneity.  Using next-generation RNA sequencing, we identified striking variability in CA1 PCs, such that the differences along the dorsal-ventral axis rivaled differences across distinct pyramidal neuron classes. This variability emerged from a spectrum of continuous expression gradients, producing a profile consistent with a multifarious continuum of cells.  This work reveals an unexpected amount of variability within a canonical and narrowly defined neuronal population and suggests that continuous, within-class heterogeneity may be an important feature of neural circuits. Overall design: Hippocampal RNA profiles were generated by deep sequencing on Illumina HiSeq 2500, with three biological replicates per population		GSM1867261: ca3d_1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Manual sorting to purify for fluorescent neurons from microdissected slices was performed according to previous methods (Hempel et al., 2007). Total RNA was isolated from each sample using PicoPure RNA Isolation kit (Life Technologies, Frederick, MD) including the on-column RNAseq-free DNaseI treatment (Qiagen, Hilden, Germany) following the manufacturers’ recommendations.  Eluted RNA (11 ul) was dried in a speed vac to approximately 2-4 ul.  ERCC control RNAs (Life Technologies) were added using 1 ul of 1:100,000 dilution for every 50 cells.  cDNA was amplified from this input material using Ovation RNA-seq v2 kit (NuGEN, San Carlos, CA).  Approximately half of the resulting cDNA was used to make the sequencing libraries using the Ovation Rapid DR Multiplexing kit (NuGEN).	Illumina HiSeq 2500	cell population;;Dorsal CA3 pyramidal cells|location;;CA3|source_name;;Dorsal CA3 pyramidal cells	GEO Accession;;GSM1867261		GSM1867261	ca3d_1	4349032200	43490322	2016-01-06 15:50:16	2188193970	4349032200	43490322	1	43490322	index:0,count:43490322,average:100,stdev:0	GSM1867261_r1				in_mesa	26777276	11.71	3.34	0.04	3991161697	3940110395	3767958727	3753497396	98.72	99.62	0	0	0	0	0	0	79.04	83.77	44647371	32323603	44647371	32323603	77.41	79.02	44647371	31658633	44647371	30489575	529668430	13.27	2.87	0	5.31	0	0.27	0	0.28	0	0.00	0	5.42	0	40894993	0	100	0	97.65	0	1.92	0	0.01	0	2.07	0	0.01	0	599.87	0	0.39	0	1246145	0	43490322	0	2309353	0	116333	0	121204	0	0	0	2357792	0	6622	0	0	0	42981	0	4656207	0	25951	0	4731761	0	88.72	0	38585640	0	126880	4893151	38.565187578815	43490322.0	40894993.0	1246145.0	2309353.0	116333.0	121204.0	0.0	2357792.0	38585640.0	94.0	2.9	5.3	0.3	0.3	0.0	5.4	88.7	100	100	100.00	8	4349032200	28.3	22.3	22.3	27.1	0.0	34.1	17.8	bulk
870822	SRR2229934	SRP056666	SRS1052834	SRX1178479	SRA249145	GEO		Spatial gene expression gradients underlie prominent heterogeneity of CA1 pyramidal neurons	Tissue and organ function has been conventionally understood in terms of the interactions among discrete and homogeneous cell types.  This approach has proven difficult in neuroscience due to the marked diversity across different neuron classes, but may also be further hampered by prominent within-class variability.  Here, we considered a well-defined, canonical neuronal population – hippocampal CA1 pyramidal cells – and systematically examined the extent and spatial rules of transcriptional heterogeneity.  Using next-generation RNA sequencing, we identified striking variability in CA1 PCs, such that the differences along the dorsal-ventral axis rivaled differences across distinct pyramidal neuron classes. This variability emerged from a spectrum of continuous expression gradients, producing a profile consistent with a multifarious continuum of cells.  This work reveals an unexpected amount of variability within a canonical and narrowly defined neuronal population and suggests that continuous, within-class heterogeneity may be an important feature of neural circuits. Overall design: Hippocampal RNA profiles were generated by deep sequencing on Illumina HiSeq 2500, with three biological replicates per population		GSM1867262: ca3d_2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Manual sorting to purify for fluorescent neurons from microdissected slices was performed according to previous methods (Hempel et al., 2007). Total RNA was isolated from each sample using PicoPure RNA Isolation kit (Life Technologies, Frederick, MD) including the on-column RNAseq-free DNaseI treatment (Qiagen, Hilden, Germany) following the manufacturers’ recommendations.  Eluted RNA (11 ul) was dried in a speed vac to approximately 2-4 ul.  ERCC control RNAs (Life Technologies) were added using 1 ul of 1:100,000 dilution for every 50 cells.  cDNA was amplified from this input material using Ovation RNA-seq v2 kit (NuGEN, San Carlos, CA).  Approximately half of the resulting cDNA was used to make the sequencing libraries using the Ovation Rapid DR Multiplexing kit (NuGEN).	Illumina HiSeq 2500	cell population;;Dorsal CA3 pyramidal cells|location;;CA3|source_name;;Dorsal CA3 pyramidal cells	GEO Accession;;GSM1867262		GSM1867262	ca3d_2	4291527600	42915276	2016-01-06 15:50:16	2160326100	4291527600	42915276	1	42915276	index:0,count:42915276,average:100,stdev:0	GSM1867262_r1				in_mesa	26777276	12.12	3.25	0.06	3904032461	3857895212	3671342267	3663112385	98.82	99.78	0	0	0	0	0	0	77.36	82.32	44076650	31052136	44076650	31052136	75.57	77.24	44076650	30335176	44076650	29137979	572292809	14.66	3.04	0	5.63	0	0.27	0	0.27	0	0.00	0	5.92	0	40140343	0	100	0	97.32	0	2.15	0	0.01	0	2.08	0	0.01	0	415.31	0	0.41	0	1306566	0	42915276	0	2417131	0	117721	0	116394	0	0	0	2540818	0	6116	0	0	0	39990	0	4372065	0	27075	0	4445246	0	87.90	0	37723212	0	119922	4594695	38.314029118927	42915276.0	40140343.0	1306566.0	2417131.0	117721.0	116394.0	0.0	2540818.0	37723212.0	93.5	3.0	5.6	0.3	0.3	0.0	5.9	87.9	100	100	100.00	8	4291527600	28.2	22.4	22.4	27.0	0.0	34.1	17.7	bulk
870831	SRR2229935	SRP056666	SRS1052833	SRX1178480	SRA249145	GEO		Spatial gene expression gradients underlie prominent heterogeneity of CA1 pyramidal neurons	Tissue and organ function has been conventionally understood in terms of the interactions among discrete and homogeneous cell types.  This approach has proven difficult in neuroscience due to the marked diversity across different neuron classes, but may also be further hampered by prominent within-class variability.  Here, we considered a well-defined, canonical neuronal population – hippocampal CA1 pyramidal cells – and systematically examined the extent and spatial rules of transcriptional heterogeneity.  Using next-generation RNA sequencing, we identified striking variability in CA1 PCs, such that the differences along the dorsal-ventral axis rivaled differences across distinct pyramidal neuron classes. This variability emerged from a spectrum of continuous expression gradients, producing a profile consistent with a multifarious continuum of cells.  This work reveals an unexpected amount of variability within a canonical and narrowly defined neuronal population and suggests that continuous, within-class heterogeneity may be an important feature of neural circuits. Overall design: Hippocampal RNA profiles were generated by deep sequencing on Illumina HiSeq 2500, with three biological replicates per population		GSM1867263: ca3v_0; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Manual sorting to purify for fluorescent neurons from microdissected slices was performed according to previous methods (Hempel et al., 2007). Total RNA was isolated from each sample using PicoPure RNA Isolation kit (Life Technologies, Frederick, MD) including the on-column RNAseq-free DNaseI treatment (Qiagen, Hilden, Germany) following the manufacturers’ recommendations.  Eluted RNA (11 ul) was dried in a speed vac to approximately 2-4 ul.  ERCC control RNAs (Life Technologies) were added using 1 ul of 1:100,000 dilution for every 50 cells.  cDNA was amplified from this input material using Ovation RNA-seq v2 kit (NuGEN, San Carlos, CA).  Approximately half of the resulting cDNA was used to make the sequencing libraries using the Ovation Rapid DR Multiplexing kit (NuGEN).	Illumina HiSeq 2500	cell population;;Ventral CA3 pyramidal cells|location;;CA3|source_name;;Ventral CA3 pyramidal cells	GEO Accession;;GSM1867263		GSM1867263	ca3v_0	4303703433	46276381	2016-01-06 15:50:16	2209890151	4303703433	46276381	1	46276381	index:0,count:46276381,average:93,stdev:0	GSM1867263_r1				in_mesa	26777276	9.97	3.1	0.05	3938882777	3940354027	3649220390	3691740743	100.04	101.17	0	0	0	0	0	0	76.79	82.94	48831754	33305267	48831754	33305267	73.07	75.72	48831754	31694508	48831754	30404240	538879870	13.68	3.33	0	6.96	0	0.29	0	0.24	0	0.00	0	5.73	0	43374544	0	93	0	90.88	0	2.70	0	0.01	0	1.28	0	0.01	0	658.48	0	0.46	0	1539525	0	46276381	0	3220425	0	135753	0	113065	0	0	0	2653019	0	5922	0	0	0	41853	0	4533334	0	27771	0	4608880	0	86.77	0	40154119	0	135797	4685673	34.504981700627	46276381.0	43374544.0	1539525.0	3220425.0	135753.0	113065.0	0.0	2653019.0	40154119.0	93.7	3.3	7.0	0.3	0.2	0.0	5.7	86.8	93	93	93.00	8	4303703433	27.2	23.1	23.2	26.5	0.0	33.7	17.2	bulk
870855	SRR2229938	SRP056666	SRS1052830	SRX1178483	SRA249145	GEO		Spatial gene expression gradients underlie prominent heterogeneity of CA1 pyramidal neurons	Tissue and organ function has been conventionally understood in terms of the interactions among discrete and homogeneous cell types.  This approach has proven difficult in neuroscience due to the marked diversity across different neuron classes, but may also be further hampered by prominent within-class variability.  Here, we considered a well-defined, canonical neuronal population – hippocampal CA1 pyramidal cells – and systematically examined the extent and spatial rules of transcriptional heterogeneity.  Using next-generation RNA sequencing, we identified striking variability in CA1 PCs, such that the differences along the dorsal-ventral axis rivaled differences across distinct pyramidal neuron classes. This variability emerged from a spectrum of continuous expression gradients, producing a profile consistent with a multifarious continuum of cells.  This work reveals an unexpected amount of variability within a canonical and narrowly defined neuronal population and suggests that continuous, within-class heterogeneity may be an important feature of neural circuits. Overall design: Hippocampal RNA profiles were generated by deep sequencing on Illumina HiSeq 2500, with three biological replicates per population		GSM1867266: sst_0; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Manual sorting to purify for fluorescent neurons from microdissected slices was performed according to previous methods (Hempel et al., 2007). Total RNA was isolated from each sample using PicoPure RNA Isolation kit (Life Technologies, Frederick, MD) including the on-column RNAseq-free DNaseI treatment (Qiagen, Hilden, Germany) following the manufacturers’ recommendations.  Eluted RNA (11 ul) was dried in a speed vac to approximately 2-4 ul.  ERCC control RNAs (Life Technologies) were added using 1 ul of 1:100,000 dilution for every 50 cells.  cDNA was amplified from this input material using Ovation RNA-seq v2 kit (NuGEN, San Carlos, CA).  Approximately half of the resulting cDNA was used to make the sequencing libraries using the Ovation Rapid DR Multiplexing kit (NuGEN).	Illumina HiSeq 2500	cell population;;SST interneuron|location;;CA1|source_name;;SST interneurons	GEO Accession;;GSM1867266		GSM1867266	sst_0	3170909050	33377990	2016-01-06 15:50:16	1999306914	3170909050	33377990	1	33377990	index:0,count:33377990,average:95,stdev:0	GSM1867266_r1				in_mesa	26777276	9.51	2.69	0.06	2722717924	2764031277	2441525683	2533105379	101.52	103.75	0	0	0	0	0	0	76.41	85.32	34785509	22521777	34785509	22521777	70.33	74.04	34785509	20729705	34785509	19545205	293637871	10.78	3.58	0	9.22	0	0.31	0	0.28	0	0.00	0	11.10	0	29476440	0	95	0	92.49	0	3.91	0	0.04	0	1.21	0	0.02	0	432.23	0	0.44	0	1193472	0	33377990	0	3079064	0	102147	0	94790	0	0	0	3704613	0	3476	0	0	0	24616	0	2675001	0	21657	0	2724750	0	79.09	0	26397376	0	130538	2797433	21.430028037813	33377990.0	29476440.0	1193472.0	3079064.0	102147.0	94790.0	0.0	3704613.0	26397376.0	88.3	3.6	9.2	0.3	0.3	0.0	11.1	79.1	95	95	95.00	38	3170909050	26.0	24.1	24.1	25.9	0.0	36.3	20.1	bulk
870918	SRR2229940	SRP056666	SRS1052828	SRX1178485	SRA249145	GEO		Spatial gene expression gradients underlie prominent heterogeneity of CA1 pyramidal neurons	Tissue and organ function has been conventionally understood in terms of the interactions among discrete and homogeneous cell types.  This approach has proven difficult in neuroscience due to the marked diversity across different neuron classes, but may also be further hampered by prominent within-class variability.  Here, we considered a well-defined, canonical neuronal population – hippocampal CA1 pyramidal cells – and systematically examined the extent and spatial rules of transcriptional heterogeneity.  Using next-generation RNA sequencing, we identified striking variability in CA1 PCs, such that the differences along the dorsal-ventral axis rivaled differences across distinct pyramidal neuron classes. This variability emerged from a spectrum of continuous expression gradients, producing a profile consistent with a multifarious continuum of cells.  This work reveals an unexpected amount of variability within a canonical and narrowly defined neuronal population and suggests that continuous, within-class heterogeneity may be an important feature of neural circuits. Overall design: Hippocampal RNA profiles were generated by deep sequencing on Illumina HiSeq 2500, with three biological replicates per population		GSM1867268: sst_2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Manual sorting to purify for fluorescent neurons from microdissected slices was performed according to previous methods (Hempel et al., 2007). Total RNA was isolated from each sample using PicoPure RNA Isolation kit (Life Technologies, Frederick, MD) including the on-column RNAseq-free DNaseI treatment (Qiagen, Hilden, Germany) following the manufacturers’ recommendations.  Eluted RNA (11 ul) was dried in a speed vac to approximately 2-4 ul.  ERCC control RNAs (Life Technologies) were added using 1 ul of 1:100,000 dilution for every 50 cells.  cDNA was amplified from this input material using Ovation RNA-seq v2 kit (NuGEN, San Carlos, CA).  Approximately half of the resulting cDNA was used to make the sequencing libraries using the Ovation Rapid DR Multiplexing kit (NuGEN).	Illumina HiSeq 2500	cell population;;SST interneuron|location;;CA1|source_name;;SST interneurons	GEO Accession;;GSM1867268		GSM1867268	sst_2	4428916625	46620175	2016-01-06 15:50:16	2083435659	4428916625	46620175	1	46620175	index:0,count:46620175,average:95,stdev:0	GSM1867268_r1				in_mesa	26777276	11.91	2.75	0.06	3818576548	3857261913	3479719259	3578858362	101.01	102.85	0	0	0	0	0	0	75.21	82.65	49134328	31338642	49134328	31338642	70.01	73.26	49134328	29174847	49134328	27779289	545274186	14.28	5.21	0	8.05	0	0.30	0	0.24	0	0.00	0	10.08	0	41670207	0	95	0	91.77	0	2.17	0	0.01	0	1.44	0	0.01	0	498.02	0	0.42	0	2427255	0	46620175	0	3750977	0	139037	0	113073	0	0	0	4697858	0	5799	0	0	0	36130	0	3487819	0	37394	0	3567142	0	81.34	0	37919230	0	85744	3628634	42.319392610562	46620175.0	41670207.0	2427255.0	3750977.0	139037.0	113073.0	0.0	4697858.0	37919230.0	89.4	5.2	8.0	0.3	0.2	0.0	10.1	81.3	95	95	95.00	8	4428916625	27.1	23.1	23.2	26.7	0.0	35.3	19.0	bulk
870935	SRR2229942	SRP056666	SRS1052826	SRX1178487	SRA249145	GEO		Spatial gene expression gradients underlie prominent heterogeneity of CA1 pyramidal neurons	Tissue and organ function has been conventionally understood in terms of the interactions among discrete and homogeneous cell types.  This approach has proven difficult in neuroscience due to the marked diversity across different neuron classes, but may also be further hampered by prominent within-class variability.  Here, we considered a well-defined, canonical neuronal population – hippocampal CA1 pyramidal cells – and systematically examined the extent and spatial rules of transcriptional heterogeneity.  Using next-generation RNA sequencing, we identified striking variability in CA1 PCs, such that the differences along the dorsal-ventral axis rivaled differences across distinct pyramidal neuron classes. This variability emerged from a spectrum of continuous expression gradients, producing a profile consistent with a multifarious continuum of cells.  This work reveals an unexpected amount of variability within a canonical and narrowly defined neuronal population and suggests that continuous, within-class heterogeneity may be an important feature of neural circuits. Overall design: Hippocampal RNA profiles were generated by deep sequencing on Illumina HiSeq 2500, with three biological replicates per population		GSM1867271: pv_1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Manual sorting to purify for fluorescent neurons from microdissected slices was performed according to previous methods (Hempel et al., 2007). Total RNA was isolated from each sample using PicoPure RNA Isolation kit (Life Technologies, Frederick, MD) including the on-column RNAseq-free DNaseI treatment (Qiagen, Hilden, Germany) following the manufacturers’ recommendations.  Eluted RNA (11 ul) was dried in a speed vac to approximately 2-4 ul.  ERCC control RNAs (Life Technologies) were added using 1 ul of 1:100,000 dilution for every 50 cells.  cDNA was amplified from this input material using Ovation RNA-seq v2 kit (NuGEN, San Carlos, CA).  Approximately half of the resulting cDNA was used to make the sequencing libraries using the Ovation Rapid DR Multiplexing kit (NuGEN).	Illumina HiSeq 2500	cell population;;PV interneuron|location;;CA1|source_name;;PV interneurons	GEO Accession;;GSM1867271		GSM1867271	pv_1	4955608880	52164304	2016-01-06 15:50:16	2324403519	4955608880	52164304	1	52164304	index:0,count:52164304,average:95,stdev:0	GSM1867271_r1				in_mesa	26777276	11.06	2.78	0.08	4351030237	4309545491	4011079187	4021737166	99.05	100.27	0	0	0	0	0	0	70.52	76.57	53310052	33093139	53310052	33093139	66.93	69.03	53310052	31409353	53310052	29835531	803191782	18.46	3.24	0	7.11	0	0.33	0	0.42	0	0.00	0	9.28	0	46927363	0	95	0	92.80	0	2.91	0	0.02	0	1.35	0	0.01	0	541.19	0	0.36	0	1687722	0	52164304	0	3706349	0	174622	0	220185	0	0	0	4842134	0	5485	0	0	0	36176	0	3800410	0	41836	0	3883907	0	82.86	0	43221014	0	126750	3974123	31.354027613412	52164304.0	46927363.0	1687722.0	3706349.0	174622.0	220185.0	0.0	4842134.0	43221014.0	90.0	3.2	7.1	0.3	0.4	0.0	9.3	82.9	95	95	95.00	8	4955608880	27.3	22.8	22.8	27.2	0.0	35.5	19.6	bulk
871079	SRR2229954	SRP056666	SRS1052814	SRX1178499	SRA249145	GEO		Spatial gene expression gradients underlie prominent heterogeneity of CA1 pyramidal neurons	Tissue and organ function has been conventionally understood in terms of the interactions among discrete and homogeneous cell types.  This approach has proven difficult in neuroscience due to the marked diversity across different neuron classes, but may also be further hampered by prominent within-class variability.  Here, we considered a well-defined, canonical neuronal population – hippocampal CA1 pyramidal cells – and systematically examined the extent and spatial rules of transcriptional heterogeneity.  Using next-generation RNA sequencing, we identified striking variability in CA1 PCs, such that the differences along the dorsal-ventral axis rivaled differences across distinct pyramidal neuron classes. This variability emerged from a spectrum of continuous expression gradients, producing a profile consistent with a multifarious continuum of cells.  This work reveals an unexpected amount of variability within a canonical and narrowly defined neuronal population and suggests that continuous, within-class heterogeneity may be an important feature of neural circuits. Overall design: Hippocampal RNA profiles were generated by deep sequencing on Illumina HiSeq 2500, with three biological replicates per population		GSM1867290: dgd_1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Manual sorting to purify for fluorescent neurons from microdissected slices was performed according to previous methods (Hempel et al., 2007). Total RNA was isolated from each sample using PicoPure RNA Isolation kit (Life Technologies, Frederick, MD) including the on-column RNAseq-free DNaseI treatment (Qiagen, Hilden, Germany) following the manufacturers’ recommendations.  Eluted RNA (11 ul) was dried in a speed vac to approximately 2-4 ul.  ERCC control RNAs (Life Technologies) were added using 1 ul of 1:100,000 dilution for every 50 cells.  cDNA was amplified from this input material using Ovation RNA-seq v2 kit (NuGEN, San Carlos, CA).  Approximately half of the resulting cDNA was used to make the sequencing libraries using the Ovation Rapid DR Multiplexing kit (NuGEN).	Illumina HiSeq 2500	cell population;;Dorsal DG granule cells|location;;DG|source_name;;Dorsal DG granule cells	GEO Accession;;GSM1867290		GSM1867290	dgd_1	3757259900	39970850	2016-01-06 15:50:16	1832948568	3757259900	39970850	1	39970850	index:0,count:39970850,average:94,stdev:0	GSM1867290_r1				in_mesa	26777276	7.72	2.99	0.1	3418579996	3347870987	3256284610	3210001530	97.93	98.58	0	0	0	0	0	0	56.56	59.41	40355692	21033131	40355692	21033131	54.41	55.15	40355692	20234646	40355692	19522947	1243000505	36.36	3.25	0	4.47	0	0.28	0	0.36	0	0.00	0	6.31	0	37190433	0	94	0	91.98	0	2.42	0	0.01	0	1.31	0	0.01	0	888.24	0	0.34	0	1297223	0	39970850	0	1787550	0	111926	0	144352	0	0	0	2524139	0	3848	0	0	0	23209	0	2663863	0	24851	0	2715771	0	88.57	0	35402883	0	127524	2759821	21.641581192560	39970850.0	37190433.0	1297223.0	1787550.0	111926.0	144352.0	0.0	2524139.0	35402883.0	93.0	3.2	4.5	0.3	0.4	0.0	6.3	88.6	94	94	94.00	8	3757259900	28.0	22.3	22.4	27.4	0.0	35.1	19.1	bulk
2795632	SRR1976543	SRP057261	SRS911695	SRX997479	SRA244059	Harvard Medical School	CBDM Laboratory	ImmGen 11-cell set basic RNASeq project	Full depth directional RNA sequencing was performed on the core ImmGen populations to generate reference datasets for the tissues from 5 week-old C57BL/6J (Jackson Laboratory) males and females, double-sorted by flow cytometry, per ImmGen cell preparation SOP. RNA was prepared from 100,000 cells (final sort collected directly in Trizol). Total RNA was extracted from each sample following ImmGen RNA extraction SOP. PolyA+ RNA was isolated by bead capture (PrepX PolyA mRNA Isolation Kit, Wafergen Biosystems), following the manufacturer''s instructions. Then mRNA libraries were prepared with the PrepX RNA-Seq Library Preparation Kit (Integenex). For first strand synthesis, mRNA was fragmented and ligated to 3'' and 5'' adapters before reverse transcription. Sample libraries then underwent bead clean-up, 2nd strand synthesis and PCR amplification before final sequencing. Libraries were analyzed on an Illumina HiSeq2500 sequencer. The read depths for the 11-cell set populations range from around 8 to 25 million.		Full depth directional RNA sequencing on Spleen Dendritic Cells from Mus musculus	RNA was prepared from 100,000 cells (final sort collected directly in Trizol). Total RNA was extracted from each sample following ImmGen RNA extraction SOP. PolyA+ RNA was isolated by bead capture (PrepX PolyA mRNA Isolation Kit, Wafergen Biosystems), following the manufacturer’s instructions. Then mRNA libraries were prepared with the PrepX RNA-Seq Library Preparation Kit (Integenex). For first strand synthesis, mRNA was fragmented and ligated to 3’ and 5’ adapters before reverse transcription. Sample libraries then underwent bead clean-up, 2nd strand synthesis and PCR amplification before final sequencing. Libraries were analyzed on an Illumina HiSeq2500 sequencer.	DC (CD11c+MHCII+ FLT3+)		RNA-Seq	TRANSCRIPTOMIC	PolyA	paired				Illumina HiSeq 2500	age;;5 week-old|BioSampleModel;;Model organism or animal|cell treatment;;N/A|cell_type;;Dendritic Cell|collected_by;;Katie Rothamel|genetic variation;;N/A|organism treatment;;N/A|separation method;;FACSAria|sequencing machine;;HiSeq|sex;;male|sorting markers;;CD11c+MHCII+ FLT3+|strain;;C57BL/6J|tissue;;Spleen|treatment;;N/A		100	DC.SP#1	Spleen Dendritic Cells from Mus musculus	3118306200	31183062	2015-04-21 00:00:00	2021973378	3118306200	31183062	2	31183062	index:0,count:31183062,average:50,stdev:0|index:1,count:31183062,average:50,stdev:0	TRA00017431	Harvard Medical School			in_mesa	23631936	1.22	3.12	0.22	2752284920	2721610656	2580666588	2572639513	98.89	99.69	28303736	25062736	183.979	789.824	133	219405	77.09	82.21	31729472	21820390	31729472	21820390	78.99	79.48	31729472	22358526	31729472	21095122	465558342	16.92	4.73	0	5.65	0	0.35	0	0.23	0	0.00	0	8.65	0	28303736	0	100	0	99.03	0	1.72	0	0.01	0	1.13	0	0.00	0	492.36	0	0.29	0	1473794	0	31183062	0	1762860	0	107911	0	72858	0	0	0	2698557	0	3037	0	0	0	25977	0	4131212	0	15056	0	4175282	0	85.11	0	26540876	0	131768	4232195	32.118534090219	31183062.0	28303736.0	1473794.0	1762860.0	107911.0	72858.0	0.0	2698557.0	26540876.0	90.8	4.7	5.7	0.3	0.2	0.0	8.7	85.1	50	50	50.00	38	1559153100	26.0	23.3	24.8	25.8	0.0	37.9	30.0	bulk
2797105	SRR1976571	SRP057261	SRS911734	SRX997518	SRA244059	Harvard Medical School	CBDM Laboratory	ImmGen 11-cell set basic RNASeq project	Full depth directional RNA sequencing was performed on the core ImmGen populations to generate reference datasets for the tissues from 5 week-old C57BL/6J (Jackson Laboratory) males and females, double-sorted by flow cytometry, per ImmGen cell preparation SOP. RNA was prepared from 100,000 cells (final sort collected directly in Trizol). Total RNA was extracted from each sample following ImmGen RNA extraction SOP. PolyA+ RNA was isolated by bead capture (PrepX PolyA mRNA Isolation Kit, Wafergen Biosystems), following the manufacturer''s instructions. Then mRNA libraries were prepared with the PrepX RNA-Seq Library Preparation Kit (Integenex). For first strand synthesis, mRNA was fragmented and ligated to 3'' and 5'' adapters before reverse transcription. Sample libraries then underwent bead clean-up, 2nd strand synthesis and PCR amplification before final sequencing. Libraries were analyzed on an Illumina HiSeq2500 sequencer. The read depths for the 11-cell set populations range from around 8 to 25 million.		Full depth directional RNA sequencing on Spleen Neutrophil from Mus musculus	RNA was prepared from 100,000 cells (final sort collected directly in Trizol). Total RNA was extracted from each sample following ImmGen RNA extraction SOP. PolyA+ RNA was isolated by bead capture (PrepX PolyA mRNA Isolation Kit, Wafergen Biosystems), following the manufacturer’s instructions. Then mRNA libraries were prepared with the PrepX RNA-Seq Library Preparation Kit (Integenex). For first strand synthesis, mRNA was fragmented and ligated to 3’ and 5’ adapters before reverse transcription. Sample libraries then underwent bead clean-up, 2nd strand synthesis and PCR amplification before final sequencing. Libraries were analyzed on an Illumina HiSeq2500 sequencer.	Neutrophils (LY66+)		RNA-Seq	TRANSCRIPTOMIC	PolyA	paired				Illumina HiSeq 2500	age;;5 week-old|BioSampleModel;;Model organism or animal|cell treatment;;N/A|cell_type;;Neutrophil|collected_by;;Katie Rothamel|genetic variation;;N/A|organism treatment;;N/A|separation method;;FACSAria|sequencing machine;;HiSeq|sex;;male|sorting markers;;Ly6G+|strain;;C57BL/6J|tissue;;Spleen|treatment;;N/A		100	GN.SP#1	Spleen Neutrophil from Mus musculus	3715943800	37159438	2015-04-21 00:00:00	2415860510	3715943800	37159438	2	37159438	index:0,count:37159438,average:50,stdev:0|index:1,count:37159438,average:50,stdev:0	TRA00017430	Harvard Medical School			in_mesa	23631936	0.15	2.71	0.15	3276050043	3165589483	3124905960	3061064360	96.63	97.96	33500079	29877219	189.659	769.652	150	279255	74.54	78.14	36938664	24969906	36938664	24969906	73.6	74.86	36938664	24654575	36938664	23920437	627279250	19.15	4.35	0	4.16	0	0.62	0	0.34	0	0.00	0	8.90	0	33500079	0	100	0	99.06	0	2.00	0	0.01	0	1.13	0	0.00	0	404.15	0	0.30	0	1615744	0	37159438	0	1545956	0	228586	0	125092	0	0	0	3305681	0	2825	0	0	0	30115	0	4306874	0	20728	0	4360542	0	85.99	0	31954123	0	112289	4479488	39.892491695536	37159438.0	33500079.0	1615744.0	1545956.0	228586.0	125092.0	0.0	3305681.0	31954123.0	90.2	4.3	4.2	0.6	0.3	0.0	8.9	86.0	50	50	50.00	38	1857971900	26.0	23.4	24.4	26.2	0.0	37.9	29.7	bulk
2797841	SRR1976588	SRP057261	SRS911741	SRX997535	SRA244059	Harvard Medical School	CBDM Laboratory	ImmGen 11-cell set basic RNASeq project	Full depth directional RNA sequencing was performed on the core ImmGen populations to generate reference datasets for the tissues from 5 week-old C57BL/6J (Jackson Laboratory) males and females, double-sorted by flow cytometry, per ImmGen cell preparation SOP. RNA was prepared from 100,000 cells (final sort collected directly in Trizol). Total RNA was extracted from each sample following ImmGen RNA extraction SOP. PolyA+ RNA was isolated by bead capture (PrepX PolyA mRNA Isolation Kit, Wafergen Biosystems), following the manufacturer''s instructions. Then mRNA libraries were prepared with the PrepX RNA-Seq Library Preparation Kit (Integenex). For first strand synthesis, mRNA was fragmented and ligated to 3'' and 5'' adapters before reverse transcription. Sample libraries then underwent bead clean-up, 2nd strand synthesis and PCR amplification before final sequencing. Libraries were analyzed on an Illumina HiSeq2500 sequencer. The read depths for the 11-cell set populations range from around 8 to 25 million.		Full depth directional RNA sequencing on Peritoneal Cavity B1ab Cells from Mus musculus	RNA was prepared from 100,000 cells (final sort collected directly in Trizol). Total RNA was extracted from each sample following ImmGen RNA extraction SOP. PolyA+ RNA was isolated by bead capture (PrepX PolyA mRNA Isolation Kit, Wafergen Biosystems), following the manufacturer’s instructions. Then mRNA libraries were prepared with the PrepX RNA-Seq Library Preparation Kit (Integenex). For first strand synthesis, mRNA was fragmented and ligated to 3’ and 5’ adapters before reverse transcription. Sample libraries then underwent bead clean-up, 2nd strand synthesis and PCR amplification before final sequencing. Libraries were analyzed on an Illumina HiSeq2500 sequencer.	B1ab cells (CD19+CD43+CD5+)		RNA-Seq	TRANSCRIPTOMIC	PolyA	paired				Illumina HiSeq 2500	age;;5 week-old|BioSampleModel;;Model organism or animal|cell treatment;;N/A|cell_type;;B Cell|collected_by;;Katie Rothamel|genetic variation;;N/A|organism treatment;;N/A|separation method;;FACSAria|sequencing machine;;HiSeq|sex;;male|sorting markers;;CD19+CD43+CD5+|strain;;C57BL/6J|tissue;;Peritoneal Cavity lavage|treatment;;N/A		100	B1ab.PC#1	Peritoneal Cavity B1ab Cells from Mus musculus	4597200200	45972002	2015-04-21 00:00:00	2986998007	4597200200	45972002	2	45972002	index:0,count:45972002,average:50,stdev:0|index:1,count:45972002,average:50,stdev:0	TRA00017432	Harvard Medical School			in_mesa	23631936	2.09	3.0	0.41	4024285368	3925087226	3670710545	3631729041	97.54	98.94	41873464	37895451	172.318	770.344	114	325495	74.57	81.75	49335323	31224809	49335323	31224809	78.28	78.93	49335323	32777131	49335323	30147366	652020500	16.20	3.72	0	8.00	0	0.64	0	0.26	0	0.00	0	8.01	0	41873464	0	100	0	99.06	0	1.67	0	0.01	0	1.11	0	0.00	0	443.70	0	0.30	0	1710546	0	45972002	0	3676008	0	295020	0	119152	0	0	0	3684366	0	4860	0	0	0	41688	0	5528130	0	30464	0	5605142	0	83.09	0	38197456	0	122646	5649958	46.067201539390	45972002.0	41873464.0	1710546.0	3676008.0	295020.0	119152.0	0.0	3684366.0	38197456.0	91.1	3.7	8.0	0.6	0.3	0.0	8.0	83.1	50	50	50.00	38	2298600100	26.4	23.1	24.4	26.1	0.0	37.9	29.8	bulk
2797874	SRR1976589	SRP057261	SRS911752	SRX997537	SRA244059	Harvard Medical School	CBDM Laboratory	ImmGen 11-cell set basic RNASeq project	Full depth directional RNA sequencing was performed on the core ImmGen populations to generate reference datasets for the tissues from 5 week-old C57BL/6J (Jackson Laboratory) males and females, double-sorted by flow cytometry, per ImmGen cell preparation SOP. RNA was prepared from 100,000 cells (final sort collected directly in Trizol). Total RNA was extracted from each sample following ImmGen RNA extraction SOP. PolyA+ RNA was isolated by bead capture (PrepX PolyA mRNA Isolation Kit, Wafergen Biosystems), following the manufacturer''s instructions. Then mRNA libraries were prepared with the PrepX RNA-Seq Library Preparation Kit (Integenex). For first strand synthesis, mRNA was fragmented and ligated to 3'' and 5'' adapters before reverse transcription. Sample libraries then underwent bead clean-up, 2nd strand synthesis and PCR amplification before final sequencing. Libraries were analyzed on an Illumina HiSeq2500 sequencer. The read depths for the 11-cell set populations range from around 8 to 25 million.		Full depth directional RNA sequencing on Spleen NK Cell from Mus musculus	RNA was prepared from 100,000 cells (final sort collected directly in Trizol). Total RNA was extracted from each sample following ImmGen RNA extraction SOP. PolyA+ RNA was isolated by bead capture (PrepX PolyA mRNA Isolation Kit, Wafergen Biosystems), following the manufacturer’s instructions. Then mRNA libraries were prepared with the PrepX RNA-Seq Library Preparation Kit (Integenex). For first strand synthesis, mRNA was fragmented and ligated to 3’ and 5’ adapters before reverse transcription. Sample libraries then underwent bead clean-up, 2nd strand synthesis and PCR amplification before final sequencing. Libraries were analyzed on an Illumina HiSeq2500 sequencer.	NK (NK1.1+TCRB-)		RNA-Seq	TRANSCRIPTOMIC	PolyA	paired				Illumina HiSeq 2500	age;;5 week-old|BioSampleModel;;Model organism or animal|cell treatment;;N/A|cell_type;;NK Cell|collected_by;;Katie Rothamel|genetic variation;;N/A|organism treatment;;N/A|separation method;;FACSAria|sequencing machine;;HiSeq|sex;;male|sorting markers;;NK1.1+TCRB-|strain;;C57BL/6J|tissue;;Spleen|treatment;;N/A		100	NK.SP#1	Spleen NK Cell from Mus musculus	3568631500	35686315	2015-04-21 00:00:00	2327117199	3568631500	35686315	2	35686315	index:0,count:35686315,average:50,stdev:0|index:1,count:35686315,average:50,stdev:0	TRA00017434	Harvard Medical School			in_mesa	23631936	1.11	3.45	0.09	3123355014	3156192415	2860448068	2916613189	101.05	101.96	32485983	28556034	179.986	816.571	117	256929	85.46	93.32	37610292	27763413	37610292	27763413	87.57	88.44	37610292	28447484	37610292	26309531	191667883	6.14	3.96	0	7.67	0	0.29	0	0.15	0	0.00	0	8.52	0	32485983	0	100	0	98.89	0	2.48	0	0.01	0	1.09	0	0.00	0	511.84	0	0.32	0	1411917	0	35686315	0	2736438	0	103765	0	54963	0	0	0	3041604	0	5453	0	0	0	37984	0	5510737	0	23456	0	5577630	0	83.36	0	29749545	0	120586	5698368	47.255634982502	35686315.0	32485983.0	1411917.0	2736438.0	103765.0	54963.0	0.0	3041604.0	29749545.0	91.0	4.0	7.7	0.3	0.2	0.0	8.5	83.4	50	50	50.00	38	1784315750	26.3	23.6	25.3	24.8	0.0	37.8	29.6	bulk
2798097	SRR1976590	SRP057261	SRS911753	SRX997538	SRA244059	Harvard Medical School	CBDM Laboratory	ImmGen 11-cell set basic RNASeq project	Full depth directional RNA sequencing was performed on the core ImmGen populations to generate reference datasets for the tissues from 5 week-old C57BL/6J (Jackson Laboratory) males and females, double-sorted by flow cytometry, per ImmGen cell preparation SOP. RNA was prepared from 100,000 cells (final sort collected directly in Trizol). Total RNA was extracted from each sample following ImmGen RNA extraction SOP. PolyA+ RNA was isolated by bead capture (PrepX PolyA mRNA Isolation Kit, Wafergen Biosystems), following the manufacturer''s instructions. Then mRNA libraries were prepared with the PrepX RNA-Seq Library Preparation Kit (Integenex). For first strand synthesis, mRNA was fragmented and ligated to 3'' and 5'' adapters before reverse transcription. Sample libraries then underwent bead clean-up, 2nd strand synthesis and PCR amplification before final sequencing. Libraries were analyzed on an Illumina HiSeq2500 sequencer. The read depths for the 11-cell set populations range from around 8 to 25 million.		Full depth directional RNA sequencing on Spleen T regulatory Cells from Mus musculus	RNA was prepared from 100,000 cells (final sort collected directly in Trizol). Total RNA was extracted from each sample following ImmGen RNA extraction SOP. PolyA+ RNA was isolated by bead capture (PrepX PolyA mRNA Isolation Kit, Wafergen Biosystems), following the manufacturer’s instructions. Then mRNA libraries were prepared with the PrepX RNA-Seq Library Preparation Kit (Integenex). For first strand synthesis, mRNA was fragmented and ligated to 3’ and 5’ adapters before reverse transcription. Sample libraries then underwent bead clean-up, 2nd strand synthesis and PCR amplification before final sequencing. Libraries were analyzed on an Illumina HiSeq2500 sequencer.	Treg (TCRB+CD4+CD25+)		RNA-Seq	TRANSCRIPTOMIC	PolyA	paired				Illumina HiSeq 2500	age;;5 week-old|BioSampleModel;;Model organism or animal|cell treatment;;N/A|cell_type;;Treg|collected_by;;Katie Rothamel|genetic variation;;N/A|organism treatment;;N/A|separation method;;FACSAria|sequencing machine;;HiSeq|sex;;male|sorting markers;;CD4+CD25+CD8-CD19-|strain;;C57BL/6J|tissue;;Spleen|treatment;;N/A		100	Treg.Sp#1	Spleen T regulatory Cells from Mus musculus	3160258500	31602585	2015-04-21 00:00:00	2060143102	3160258500	31602585	2	31602585	index:0,count:31602585,average:50,stdev:0|index:1,count:31602585,average:50,stdev:0	TRA00017435	Harvard Medical School			in_mesa	23631936	1.39	2.9	0.12	2474221988	2440763475	2220210166	2231084677	98.65	100.49	25700377	23280076	178.880	819.874	117	208241	72.97	81.38	31714301	18753323	31714301	18753323	73.33	75.38	31714301	18844936	31714301	17372531	401156268	16.21	3.98	0	8.40	0	0.30	0	0.23	0	0.00	0	18.15	0	25700377	0	100	0	98.93	0	2.96	0	0.02	0	1.20	0	0.01	0	345.80	0	0.44	0	1258880	0	31602585	0	2654929	0	94818	0	72641	0	0	0	5734749	0	2424	0	0	0	21834	0	3007395	0	18185	0	3049838	0	72.92	0	23045448	0	90458	3085070	34.104999005063	31602585.0	25700377.0	1258880.0	2654929.0	94818.0	72641.0	0.0	5734749.0	23045448.0	81.3	4.0	8.4	0.3	0.2	0.0	18.1	72.9	50	50	50.00	38	1580129250	26.1	22.9	26.0	25.0	0.0	37.8	29.6	bulk
2798129	SRR1976591	SRP057261	SRS911758	SRX997539	SRA244059	Harvard Medical School	CBDM Laboratory	ImmGen 11-cell set basic RNASeq project	Full depth directional RNA sequencing was performed on the core ImmGen populations to generate reference datasets for the tissues from 5 week-old C57BL/6J (Jackson Laboratory) males and females, double-sorted by flow cytometry, per ImmGen cell preparation SOP. RNA was prepared from 100,000 cells (final sort collected directly in Trizol). Total RNA was extracted from each sample following ImmGen RNA extraction SOP. PolyA+ RNA was isolated by bead capture (PrepX PolyA mRNA Isolation Kit, Wafergen Biosystems), following the manufacturer''s instructions. Then mRNA libraries were prepared with the PrepX RNA-Seq Library Preparation Kit (Integenex). For first strand synthesis, mRNA was fragmented and ligated to 3'' and 5'' adapters before reverse transcription. Sample libraries then underwent bead clean-up, 2nd strand synthesis and PCR amplification before final sequencing. Libraries were analyzed on an Illumina HiSeq2500 sequencer. The read depths for the 11-cell set populations range from around 8 to 25 million.		Full depth directional RNA sequencing on Spleen CD4 T Cell from Mus musculus	RNA was prepared from 100,000 cells (final sort collected directly in Trizol). Total RNA was extracted from each sample following ImmGen RNA extraction SOP. PolyA+ RNA was isolated by bead capture (PrepX PolyA mRNA Isolation Kit, Wafergen Biosystems), following the manufacturer’s instructions. Then mRNA libraries were prepared with the PrepX RNA-Seq Library Preparation Kit (Integenex). For first strand synthesis, mRNA was fragmented and ligated to 3’ and 5’ adapters before reverse transcription. Sample libraries then underwent bead clean-up, 2nd strand synthesis and PCR amplification before final sequencing. Libraries were analyzed on an Illumina HiSeq2500 sequencer.	Total CD4 (TCRB+CD4+)		RNA-Seq	TRANSCRIPTOMIC	PolyA	paired				Illumina HiSeq 2500	age;;5 week-old|BioSampleModel;;Model organism or animal|cell treatment;;N/A|cell_type;;CD4 TConv Cell|collected_by;;Katie Rothamel|genetic variation;;N/A|organism treatment;;N/A|separation method;;FACSAria|sequencing machine;;HiSeq|sex;;male|sorting markers;;CD4+TCRB+|strain;;C57BL/6J|tissue;;Spleen|treatment;;N/A		100	T4.Sp#1	Spleen CD4 T Cell from Mus musculus	3227653000	32276530	2015-04-21 00:00:00	2095340910	3227653000	32276530	2	32276530	index:0,count:32276530,average:50,stdev:0|index:1,count:32276530,average:50,stdev:0	TRA00017436	Harvard Medical School			in_mesa	23631936	1.47	3.44	0.34	2836248782	2775500377	2551145824	2542417934	97.86	99.66	29233089	25849158	186.925	960.488	129	225257	79.27	88.11	35346326	23173686	35346326	23173686	83.41	84.73	35346326	24382948	35346326	22286059	288109948	10.16	4.12	0	9.08	0	0.76	0	0.29	0	0.00	0	8.38	0	29233089	0	100	0	98.97	0	1.78	0	0.01	0	1.12	0	0.00	0	478.17	0	0.30	0	1328228	0	32276530	0	2931144	0	246182	0	92459	0	0	0	2704800	0	4306	0	0	0	33446	0	4401853	0	17479	0	4457084	0	81.49	0	26301945	0	124768	4528762	36.297464093357	32276530.0	29233089.0	1328228.0	2931144.0	246182.0	92459.0	0.0	2704800.0	26301945.0	90.6	4.1	9.1	0.8	0.3	0.0	8.4	81.5	50	50	50.00	38	1613826500	26.3	23.3	25.0	25.4	0.0	37.9	29.7	bulk
2798161	SRR1976592	SRP057261	SRS911759	SRX997540	SRA244059	Harvard Medical School	CBDM Laboratory	ImmGen 11-cell set basic RNASeq project	Full depth directional RNA sequencing was performed on the core ImmGen populations to generate reference datasets for the tissues from 5 week-old C57BL/6J (Jackson Laboratory) males and females, double-sorted by flow cytometry, per ImmGen cell preparation SOP. RNA was prepared from 100,000 cells (final sort collected directly in Trizol). Total RNA was extracted from each sample following ImmGen RNA extraction SOP. PolyA+ RNA was isolated by bead capture (PrepX PolyA mRNA Isolation Kit, Wafergen Biosystems), following the manufacturer''s instructions. Then mRNA libraries were prepared with the PrepX RNA-Seq Library Preparation Kit (Integenex). For first strand synthesis, mRNA was fragmented and ligated to 3'' and 5'' adapters before reverse transcription. Sample libraries then underwent bead clean-up, 2nd strand synthesis and PCR amplification before final sequencing. Libraries were analyzed on an Illumina HiSeq2500 sequencer. The read depths for the 11-cell set populations range from around 8 to 25 million.		Full depth directional RNA sequencing on Spleen CD8 T Cell from Mus musculus	RNA was prepared from 100,000 cells (final sort collected directly in Trizol). Total RNA was extracted from each sample following ImmGen RNA extraction SOP. PolyA+ RNA was isolated by bead capture (PrepX PolyA mRNA Isolation Kit, Wafergen Biosystems), following the manufacturer’s instructions. Then mRNA libraries were prepared with the PrepX RNA-Seq Library Preparation Kit (Integenex). For first strand synthesis, mRNA was fragmented and ligated to 3’ and 5’ adapters before reverse transcription. Sample libraries then underwent bead clean-up, 2nd strand synthesis and PCR amplification before final sequencing. Libraries were analyzed on an Illumina HiSeq2500 sequencer.	Total CD8 (TCRB+CD8+)		RNA-Seq	TRANSCRIPTOMIC	PolyA	paired				Illumina HiSeq 2500	age;;5 week-old|BioSampleModel;;Model organism or animal|cell treatment;;N/A|cell_type;;CD8 T Cell|collected_by;;Katie Rothamel|genetic variation;;N/A|organism treatment;;N/A|separation method;;FACSAria|sequencing machine;;HiSeq|sex;;male|sorting markers;;TCRB+CD8+|strain;;C57BL/6J|tissue;;Spleen|treatment;;N/A		100	T8.Sp#1	Spleen CD8 T Cell from Mus musculus	5434298300	54342983	2015-04-21 00:00:00	3522187560	5434298300	54342983	2	54342983	index:0,count:54342983,average:50,stdev:0|index:1,count:54342983,average:50,stdev:0	TRA00017437	Harvard Medical School			in_mesa	23631936	1.59	3.54	0.33	4745738765	4655271272	4239814478	4229061008	98.09	99.75	49405763	44099825	175.629	886.930	117	398985	80.59	90.2	60118027	39818387	60118027	39818387	85.66	86.94	60118027	42320724	60118027	38380329	393777277	8.30	3.65	0	9.68	0	0.71	0	0.25	0	0.00	0	8.12	0	49405763	0	100	0	98.95	0	1.74	0	0.01	0	1.12	0	0.00	0	406.73	0	0.30	0	1981715	0	54342983	0	5260639	0	385042	0	138273	0	0	0	4413905	0	6926	0	0	0	58383	0	7614118	0	35761	0	7715188	0	81.23	0	44145124	0	121588	7818415	64.302521630424	54342983.0	49405763.0	1981715.0	5260639.0	385042.0	138273.0	0.0	4413905.0	44145124.0	90.9	3.6	9.7	0.7	0.3	0.0	8.1	81.2	50	50	50.00	38	2717149150	26.6	23.2	25.0	25.2	0.0	37.9	29.7	bulk
2798194	SRR1976593	SRP057261	SRS911760	SRX997541	SRA244059	Harvard Medical School	CBDM Laboratory	ImmGen 11-cell set basic RNASeq project	Full depth directional RNA sequencing was performed on the core ImmGen populations to generate reference datasets for the tissues from 5 week-old C57BL/6J (Jackson Laboratory) males and females, double-sorted by flow cytometry, per ImmGen cell preparation SOP. RNA was prepared from 100,000 cells (final sort collected directly in Trizol). Total RNA was extracted from each sample following ImmGen RNA extraction SOP. PolyA+ RNA was isolated by bead capture (PrepX PolyA mRNA Isolation Kit, Wafergen Biosystems), following the manufacturer''s instructions. Then mRNA libraries were prepared with the PrepX RNA-Seq Library Preparation Kit (Integenex). For first strand synthesis, mRNA was fragmented and ligated to 3'' and 5'' adapters before reverse transcription. Sample libraries then underwent bead clean-up, 2nd strand synthesis and PCR amplification before final sequencing. Libraries were analyzed on an Illumina HiSeq2500 sequencer. The read depths for the 11-cell set populations range from around 8 to 25 million.		Full depth directional RNA sequencing on Spleen CD19+ B Cell from Mus musculus	RNA was prepared from 100,000 cells (final sort collected directly in Trizol). Total RNA was extracted from each sample following ImmGen RNA extraction SOP. PolyA+ RNA was isolated by bead capture (PrepX PolyA mRNA Isolation Kit, Wafergen Biosystems), following the manufacturer’s instructions. Then mRNA libraries were prepared with the PrepX RNA-Seq Library Preparation Kit (Integenex). For first strand synthesis, mRNA was fragmented and ligated to 3’ and 5’ adapters before reverse transcription. Sample libraries then underwent bead clean-up, 2nd strand synthesis and PCR amplification before final sequencing. Libraries were analyzed on an Illumina HiSeq2500 sequencer.	Total CD19+ B (CD19+IgM+)		RNA-Seq	TRANSCRIPTOMIC	PolyA	paired				Illumina HiSeq 2500	age;;5 week-old|BioSampleModel;;Model organism or animal|cell treatment;;N/A|cell_type;;B Cell|collected_by;;Katie Rothamel|genetic variation;;N/A|organism treatment;;N/A|separation method;;FACSAria|sequencing machine;;HiSeq|sex;;male|sorting markers;;CD19+IgM+CD3-|strain;;C57BL/6J|tissue;;Spleen|treatment;;N/A		100	BB.SP#1	Spleen CD19+ B Cell from Mus musculus	4061577600	40615776	2015-04-21 00:00:00	2634786775	4061577600	40615776	2	40615776	index:0,count:40615776,average:50,stdev:0|index:1,count:40615776,average:50,stdev:0	TRA00017438	Harvard Medical School			in_mesa	23631936	1.99	3.18	0.19	3617312445	3635693444	3299522341	3351056320	100.51	101.56	36961220	32026926	200.048	976.408	135	266168	83.72	91.75	43284631	30943990	43284631	30943990	86.73	87.52	43284631	32057108	43284631	29517058	273745523	7.57	3.83	0	7.96	0	0.35	0	0.16	0	0.00	0	8.48	0	36961220	0	100	0	98.98	0	2.11	0	0.01	0	1.12	0	0.00	0	606.71	0	0.30	0	1554001	0	40615776	0	3233445	0	143373	0	65461	0	0	0	3445722	0	6020	0	0	0	41885	0	6101598	0	26452	0	6175955	0	83.04	0	33727775	0	116830	6244319	53.447907215612	40615776.0	36961220.0	1554001.0	3233445.0	143373.0	65461.0	0.0	3445722.0	33727775.0	91.0	3.8	8.0	0.4	0.2	0.0	8.5	83.0	50	50	50.00	38	2030788800	26.3	23.7	25.0	25.0	0.0	37.9	29.9	bulk
2798226	SRR1976594	SRP057261	SRS911761	SRX997542	SRA244059	Harvard Medical School	CBDM Laboratory	ImmGen 11-cell set basic RNASeq project	Full depth directional RNA sequencing was performed on the core ImmGen populations to generate reference datasets for the tissues from 5 week-old C57BL/6J (Jackson Laboratory) males and females, double-sorted by flow cytometry, per ImmGen cell preparation SOP. RNA was prepared from 100,000 cells (final sort collected directly in Trizol). Total RNA was extracted from each sample following ImmGen RNA extraction SOP. PolyA+ RNA was isolated by bead capture (PrepX PolyA mRNA Isolation Kit, Wafergen Biosystems), following the manufacturer''s instructions. Then mRNA libraries were prepared with the PrepX RNA-Seq Library Preparation Kit (Integenex). For first strand synthesis, mRNA was fragmented and ligated to 3'' and 5'' adapters before reverse transcription. Sample libraries then underwent bead clean-up, 2nd strand synthesis and PCR amplification before final sequencing. Libraries were analyzed on an Illumina HiSeq2500 sequencer. The read depths for the 11-cell set populations range from around 8 to 25 million.		Full depth directional RNA sequencing on Spleen TRCgd from Mus musculus	RNA was prepared from 100,000 cells (final sort collected directly in Trizol). Total RNA was extracted from each sample following ImmGen RNA extraction SOP. PolyA+ RNA was isolated by bead capture (PrepX PolyA mRNA Isolation Kit, Wafergen Biosystems), following the manufacturer’s instructions. Then mRNA libraries were prepared with the PrepX RNA-Seq Library Preparation Kit (Integenex). For first strand synthesis, mRNA was fragmented and ligated to 3’ and 5’ adapters before reverse transcription. Sample libraries then underwent bead clean-up, 2nd strand synthesis and PCR amplification before final sequencing. Libraries were analyzed on an Illumina HiSeq2500 sequencer.	TCRgd (TCRgd+TCRB-)		RNA-Seq	TRANSCRIPTOMIC	PolyA	paired				Illumina HiSeq 2500	age;;5 week-old|BioSampleModel;;Model organism or animal|cell treatment;;N/A|cell_type;;gdT Cell|collected_by;;Katie Rothamel|genetic variation;;N/A|organism treatment;;N/A|separation method;;FACSAria|sequencing machine;;HiSeq|sex;;male|sorting markers;;TCRgd+TCRB-|strain;;C57BL/6J|tissue;;Spleen|treatment;;N/A		100	Tgd.SP#1	Spleen TRCgd from Mus musculus	1595061500	15950615	2015-04-21 00:00:00	1037336639	1595061500	15950615	2	15950615	index:0,count:15950615,average:50,stdev:0|index:1,count:15950615,average:50,stdev:0	TRA00017439	Harvard Medical School			in_mesa	23631936	1.76	3.15	0.24	1291549732	1291098415	1179055678	1196302000	99.97	101.46	13310570	11807849	186.525	957.670	117	102102	77.23	84.61	15619228	10279664	15619228	10279664	77.92	79.06	15619228	10371033	15619228	9605762	177901007	13.77	4.01	0	7.28	0	0.30	0	0.24	0	0.00	0	16.01	0	13310570	0	100	0	98.90	0	2.84	0	0.02	0	1.18	0	0.01	0	455.73	0	0.44	0	639666	0	15950615	0	1160649	0	48160	0	38891	0	0	0	2552994	0	1459	0	0	0	13101	0	1709845	0	12499	0	1736904	0	76.17	0	12149921	0	68622	1756669	25.599210165836	15950615.0	13310570.0	639666.0	1160649.0	48160.0	38891.0	0.0	2552994.0	12149921.0	83.4	4.0	7.3	0.3	0.2	0.0	16.0	76.2	50	50	50.00	38	797530750	26.4	22.9	25.2	25.5	0.0	37.8	29.7	bulk
2798258	SRR1976595	SRP057261	SRS911762	SRX997543	SRA244059	Harvard Medical School	CBDM Laboratory	ImmGen 11-cell set basic RNASeq project	Full depth directional RNA sequencing was performed on the core ImmGen populations to generate reference datasets for the tissues from 5 week-old C57BL/6J (Jackson Laboratory) males and females, double-sorted by flow cytometry, per ImmGen cell preparation SOP. RNA was prepared from 100,000 cells (final sort collected directly in Trizol). Total RNA was extracted from each sample following ImmGen RNA extraction SOP. PolyA+ RNA was isolated by bead capture (PrepX PolyA mRNA Isolation Kit, Wafergen Biosystems), following the manufacturer''s instructions. Then mRNA libraries were prepared with the PrepX RNA-Seq Library Preparation Kit (Integenex). For first strand synthesis, mRNA was fragmented and ligated to 3'' and 5'' adapters before reverse transcription. Sample libraries then underwent bead clean-up, 2nd strand synthesis and PCR amplification before final sequencing. Libraries were analyzed on an Illumina HiSeq2500 sequencer. The read depths for the 11-cell set populations range from around 8 to 25 million.		Full depth directional RNA sequencing on Spleen NKT from Mus musculus	RNA was prepared from 100,000 cells (final sort collected directly in Trizol). Total RNA was extracted from each sample following ImmGen RNA extraction SOP. PolyA+ RNA was isolated by bead capture (PrepX PolyA mRNA Isolation Kit, Wafergen Biosystems), following the manufacturer’s instructions. Then mRNA libraries were prepared with the PrepX RNA-Seq Library Preparation Kit (Integenex). For first strand synthesis, mRNA was fragmented and ligated to 3’ and 5’ adapters before reverse transcription. Sample libraries then underwent bead clean-up, 2nd strand synthesis and PCR amplification before final sequencing. Libraries were analyzed on an Illumina HiSeq2500 sequencer.	NKT (CD1d Tetramer Sorted, TCRB int)		RNA-Seq	TRANSCRIPTOMIC	PolyA	paired				Illumina HiSeq 2500	age;;5 week-old|BioSampleModel;;Model organism or animal|cell treatment;;N/A|cell_type;;NKT Cell|collected_by;;Katie Rothamel|genetic variation;;N/A|organism treatment;;N/A|separation method;;FACSAria|sequencing machine;;HiSeq|sex;;male|sorting markers;;CD1dtet+|strain;;C57BL/6J|tissue;;Spleen|treatment;;N/A		100	NKT.SP.Tetramer	Spleen NKT from Mus musculus	6320546800	63205468	2015-04-21 00:00:00	4096979478	6320546800	63205468	2	63205468	index:0,count:63205468,average:50,stdev:0|index:1,count:63205468,average:50,stdev:0	TRA00025075	Harvard Medical School			in_mesa	23631936	2.32	1.38	0.07	3964955559	4369886377	3464088888	3962331364	110.21	114.38	41314077	39260442	168.824	483.799	110	572143	66.66	76.55	56463888	27537952	56463888	27537952	48.4	52.17	56463888	19994352	56463888	18767682	752235467	18.97	6.55	0	8.45	0	0.13	0	0.11	0	0.00	0	34.39	0	41314077	0	100	0	98.76	0	3.93	0	0.04	0	1.14	0	0.01	0	341.14	0	0.60	0	4139630	0	63205468	0	5340191	0	82872	0	70835	0	0	0	21737684	0	1846	0	0	0	17792	0	2467598	0	24399	0	2511635	0	56.92	0	35973886	0	69957	2518925	36.006761296225	63205468.0	41314077.0	4139630.0	5340191.0	82872.0	70835.0	0.0	21737684.0	35973886.0	65.4	6.5	8.4	0.1	0.1	0.0	34.4	56.9	50	50	50.00	38	3160273400	26.9	21.7	27.6	23.8	0.0	38.3	31.0	bulk
2798289	SRR1976596	SRP057261	SRS911764	SRX997545	SRA244059	Harvard Medical School	CBDM Laboratory	ImmGen 11-cell set basic RNASeq project	Full depth directional RNA sequencing was performed on the core ImmGen populations to generate reference datasets for the tissues from 5 week-old C57BL/6J (Jackson Laboratory) males and females, double-sorted by flow cytometry, per ImmGen cell preparation SOP. RNA was prepared from 100,000 cells (final sort collected directly in Trizol). Total RNA was extracted from each sample following ImmGen RNA extraction SOP. PolyA+ RNA was isolated by bead capture (PrepX PolyA mRNA Isolation Kit, Wafergen Biosystems), following the manufacturer''s instructions. Then mRNA libraries were prepared with the PrepX RNA-Seq Library Preparation Kit (Integenex). For first strand synthesis, mRNA was fragmented and ligated to 3'' and 5'' adapters before reverse transcription. Sample libraries then underwent bead clean-up, 2nd strand synthesis and PCR amplification before final sequencing. Libraries were analyzed on an Illumina HiSeq2500 sequencer. The read depths for the 11-cell set populations range from around 8 to 25 million.		Full depth directional RNA sequencing on Spleen NKT from Mus musculus	RNA was prepared from 100,000 cells (final sort collected directly in Trizol). Total RNA was extracted from each sample following ImmGen RNA extraction SOP. PolyA+ RNA was isolated by bead capture (PrepX PolyA mRNA Isolation Kit, Wafergen Biosystems), following the manufacturer’s instructions. Then mRNA libraries were prepared with the PrepX RNA-Seq Library Preparation Kit (Integenex). For first strand synthesis, mRNA was fragmented and ligated to 3’ and 5’ adapters before reverse transcription. Sample libraries then underwent bead clean-up, 2nd strand synthesis and PCR amplification before final sequencing. Libraries were analyzed on an Illumina HiSeq2500 sequencer.	NKT (TCRBint NK1.1int)		RNA-Seq	TRANSCRIPTOMIC	PolyA	paired				Illumina HiSeq 2500	age;;5 week-old|BioSampleModel;;Model organism or animal|cell treatment;;N/A|cell_type;;NKT Cell|collected_by;;Katie Rothamel|genetic variation;;N/A|organism treatment;;N/A|separation method;;FACSAria|sequencing machine;;HiSeq|sex;;male|sorting markers;;TCRBint NK1.1int|strain;;C57BL/6J|tissue;;Spleen|treatment;;N/A		100	NKT.SP#1	Spleen NKT from Mus musculus	2612011600	26120116	2015-04-21 00:00:00	1682061008	2612011600	26120116	2	26120116	index:0,count:26120116,average:50,stdev:0|index:1,count:26120116,average:50,stdev:0	TRA00025076	Harvard Medical School			in_mesa	23631936	1.44	2.89	0.15	2161391600	2127794369	2000666292	1992533055	98.45	99.59	22626953	20433010	172.821	781.133	117	183207	72.79	78.68	26190037	16469459	26190037	16469459	73.9	75.0	26190037	16720321	26190037	15698561	428565565	19.83	3.78	0	6.49	0	0.33	0	0.27	0	0.00	0	12.77	0	22626953	0	100	0	98.92	0	1.68	0	0.01	0	1.18	0	0.00	0	403.57	0	0.39	0	986036	0	26120116	0	1695444	0	87372	0	71184	0	0	0	3334607	0	2166	0	0	0	20297	0	2725635	0	21172	0	2769270	0	80.14	0	20931509	0	102471	2793888	27.265157947127	26120116.0	22626953.0	986036.0	1695444.0	87372.0	71184.0	0.0	3334607.0	20931509.0	86.6	3.8	6.5	0.3	0.3	0.0	12.8	80.1	50	50	50.00	38	1306005800	27.1	21.9	24.6	26.4	0.0	38.5	31.2	bulk
2798320	SRR1976597	SRP057261	SRS911767	SRX997549	SRA244059	Harvard Medical School	CBDM Laboratory	ImmGen 11-cell set basic RNASeq project	Full depth directional RNA sequencing was performed on the core ImmGen populations to generate reference datasets for the tissues from 5 week-old C57BL/6J (Jackson Laboratory) males and females, double-sorted by flow cytometry, per ImmGen cell preparation SOP. RNA was prepared from 100,000 cells (final sort collected directly in Trizol). Total RNA was extracted from each sample following ImmGen RNA extraction SOP. PolyA+ RNA was isolated by bead capture (PrepX PolyA mRNA Isolation Kit, Wafergen Biosystems), following the manufacturer''s instructions. Then mRNA libraries were prepared with the PrepX RNA-Seq Library Preparation Kit (Integenex). For first strand synthesis, mRNA was fragmented and ligated to 3'' and 5'' adapters before reverse transcription. Sample libraries then underwent bead clean-up, 2nd strand synthesis and PCR amplification before final sequencing. Libraries were analyzed on an Illumina HiSeq2500 sequencer. The read depths for the 11-cell set populations range from around 8 to 25 million.		Full depth directional RNA sequencing on Peritoneal Macrophage from Mus musculus	RNA was prepared from 100,000 cells (final sort collected directly in Trizol). Total RNA was extracted from each sample following ImmGen RNA extraction SOP. PolyA+ RNA was isolated by bead capture (PrepX PolyA mRNA Isolation Kit, Wafergen Biosystems), following the manufacturer’s instructions. Then mRNA libraries were prepared with the PrepX RNA-Seq Library Preparation Kit (Integenex). For first strand synthesis, mRNA was fragmented and ligated to 3’ and 5’ adapters before reverse transcription. Sample libraries then underwent bead clean-up, 2nd strand synthesis and PCR amplification before final sequencing. Libraries were analyzed on an Illumina HiSeq2500 sequencer.	PC Macrophages (F4/80+ICAM2+)		RNA-Seq	TRANSCRIPTOMIC	PolyA	paired				Illumina HiSeq 2500	age;;5 week-old|BioSampleModel;;Model organism or animal|cell treatment;;N/A|cell_type;;Macrophage|collected_by;;Katie Rothamel|genetic variation;;N/A|organism treatment;;N/A|separation method;;FACSAria|sequencing machine;;HiSeq|sex;;male|sorting markers;;F4/80+ICAM2+|strain;;C57BL/6J|tissue;;Peritoneal Cavity lavage|treatment;;N/A		100	MF.PC#1	Peritoneal Macrophage from Mus musculus	918492200	9184922	2015-04-21 00:00:00	591614117	918492200	9184922	2	9184922	index:0,count:9184922,average:50,stdev:0|index:1,count:9184922,average:50,stdev:0	TRA00025077	Harvard Medical School			in_mesa	23631936	1.52	2.89	0.1	776157882	770453700	721351785	721160661	99.27	99.97	8186311	7451254	161.415	642.558	145	91190	77.49	83.41	9190726	6343353	9190726	6343353	79.31	79.79	9190726	6492872	9190726	6068210	118392143	15.25	4.24	0	6.33	0	0.25	0	0.20	0	0.00	0	10.42	0	8186311	0	100	0	98.85	0	1.82	0	0.01	0	1.13	0	0.00	0	479.21	0	0.38	0	389255	0	9184922	0	580977	0	23292	0	18567	0	0	0	956752	0	917	0	0	0	5184	0	1054668	0	9017	0	1069786	0	82.80	0	7605334	0	86979	1183968	13.612113268720	9184922.0	8186311.0	389255.0	580977.0	23292.0	18567.0	0.0	956752.0	7605334.0	89.1	4.2	6.3	0.3	0.2	0.0	10.4	82.8	50	50	50.00	38	459246100	27.5	22.0	23.9	26.6	0.0	38.5	31.4	bulk
2804817	SRR3932662	SRP057261	SRS1571885	SRX1961985	SRA244059	Harvard Medical School	CBDM Laboratory	ImmGen 11-cell set basic RNASeq project	Full depth directional RNA sequencing was performed on the core ImmGen populations to generate reference datasets for the tissues from 5 week-old C57BL/6J (Jackson Laboratory) males and females, double-sorted by flow cytometry, per ImmGen cell preparation SOP. RNA was prepared from 100,000 cells (final sort collected directly in Trizol). Total RNA was extracted from each sample following ImmGen RNA extraction SOP. PolyA+ RNA was isolated by bead capture (PrepX PolyA mRNA Isolation Kit, Wafergen Biosystems), following the manufacturer''s instructions. Then mRNA libraries were prepared with the PrepX RNA-Seq Library Preparation Kit (Integenex). For first strand synthesis, mRNA was fragmented and ligated to 3'' and 5'' adapters before reverse transcription. Sample libraries then underwent bead clean-up, 2nd strand synthesis and PCR amplification before final sequencing. Libraries were analyzed on an Illumina HiSeq2500 sequencer. The read depths for the 11-cell set populations range from around 8 to 25 million.		Full depth directional RNA sequencing on Peritoneal Cavity B1ab Cells from Mus musculus (female)	RNA was prepared from 100,000 cells (final sort collected directly in Trizol). Total RNA was extracted from each sample following ImmGen RNA extraction SOP. PolyA+ RNA was isolated by bead capture (PrepX PolyA mRNA Isolation Kit, Wafergen Biosystems), following the manufacturer’s instructions. Then mRNA libraries were prepared with the PrepX RNA-Seq Library Preparation Kit (Integenex). For first strand synthesis, mRNA was fragmented and ligated to 3’ and 5’ adapters before reverse transcription. Sample libraries then underwent bead clean-up, 2nd strand synthesis and PCR amplification before final sequencing. Libraries were analyzed on an Illumina HiSeq2500 sequencer.	B1ab cells (CD19+CD43+CD5+)		RNA-Seq	TRANSCRIPTOMIC	PolyA	paired				Illumina HiSeq 2500	age;;5 week-old|BioSampleModel;;Model organism or animal|cell_type;;B Cell|separation method;;FACSAria|sequencing machine;;HiSeq|sex;;female|sorting markers;;CD19+CD43+CD5+|strain;;C57BL/6J|tissue;;Peritoneal Cavity lavage		100	B1ab.Fem.PC#1	Peritoneal Cavity B1ab Cells from Mus musculus (female)	1132008500	11320085	2016-07-20 13:08:33	549967432	1132008500	11320085	2	11320085	index:0,count:11320085,average:50,stdev:0|index:1,count:11320085,average:50,stdev:0	TRA00035661				in_mesa	23631936	1.07	3.29	0.28	830750705	819712576	738707010	738541622	98.67	99.98	9970235	9502521	113.880	520.999	75	129018	78.17	88.07	12373388	7793403	12373388	7793403	84.02	84.8	12373388	8376794	12373388	7504231	87076303	10.48	5.04	0	9.90	0	0.84	0	0.19	0	0.00	0	10.90	0	9970235	0	100	0	98.51	0	1.46	0	0.01	0	1.11	0	0.00	0	342.46	0	0.31	0	570376	0	11320085	0	1121064	0	94710	0	21132	0	0	0	1234008	0	1573	0	0	0	10486	0	1543750	0	6475	0	1562284	0	78.17	0	8849171	0	98970	1468400	14.836819238153	11320085.0	9970235.0	570376.0	1121064.0	94710.0	21132.0	0.0	1234008.0	8849171.0	88.1	5.0	9.9	0.8	0.2	0.0	10.9	78.2	50	50	50.00	17	566004250	25.7	23.9	25.9	24.5	0.0	38.4	32.9	bulk
2804851	SRR3932663	SRP057261	SRS1571886	SRX1961986	SRA244059	Harvard Medical School	CBDM Laboratory	ImmGen 11-cell set basic RNASeq project	Full depth directional RNA sequencing was performed on the core ImmGen populations to generate reference datasets for the tissues from 5 week-old C57BL/6J (Jackson Laboratory) males and females, double-sorted by flow cytometry, per ImmGen cell preparation SOP. RNA was prepared from 100,000 cells (final sort collected directly in Trizol). Total RNA was extracted from each sample following ImmGen RNA extraction SOP. PolyA+ RNA was isolated by bead capture (PrepX PolyA mRNA Isolation Kit, Wafergen Biosystems), following the manufacturer''s instructions. Then mRNA libraries were prepared with the PrepX RNA-Seq Library Preparation Kit (Integenex). For first strand synthesis, mRNA was fragmented and ligated to 3'' and 5'' adapters before reverse transcription. Sample libraries then underwent bead clean-up, 2nd strand synthesis and PCR amplification before final sequencing. Libraries were analyzed on an Illumina HiSeq2500 sequencer. The read depths for the 11-cell set populations range from around 8 to 25 million.		Full depth directional RNA sequencing on Peritoneal Macrophage from Mus musculus (female)	RNA was prepared from 100,000 cells (final sort collected directly in Trizol). Total RNA was extracted from each sample following ImmGen RNA extraction SOP. PolyA+ RNA was isolated by bead capture (PrepX PolyA mRNA Isolation Kit, Wafergen Biosystems), following the manufacturer’s instructions. Then mRNA libraries were prepared with the PrepX RNA-Seq Library Preparation Kit (Integenex). For first strand synthesis, mRNA was fragmented and ligated to 3’ and 5’ adapters before reverse transcription. Sample libraries then underwent bead clean-up, 2nd strand synthesis and PCR amplification before final sequencing. Libraries were analyzed on an Illumina HiSeq2500 sequencer.	PC Macrophages (F4/80+ICAM2+)		RNA-Seq	TRANSCRIPTOMIC	PolyA	paired				Illumina HiSeq 2500	age;;5 week-old|BioSampleModel;;Model organism or animal|cell_type;;Macrophage|separation method;;FACSAria|sequencing machine;;HiSeq|sex;;female|sorting markers;;F4/80+ICAM2+|strain;;C57BL/6J|tissue;;Peritoneal Cavity lavage		100	MF.Fem.PC#1	Peritoneal Macrophage from Mus musculus (female)	347041500	3470415	2016-07-20 12:58:18	171281266	347041500	3470415	2	3470415	index:0,count:3470415,average:50,stdev:0|index:1,count:3470415,average:50,stdev:0	TRA00035662				in_mesa	23631936	0.83	2.76	0.06	246383585	246649515	227196373	228704218	100.11	100.66	3021452	2871533	108.755	444.274	75	42096	85.75	93.11	3481898	2590825	3481898	2590825	88.46	89.27	3481898	2672760	3481898	2483877	15886402	6.45	5.52	0	6.88	0	0.35	0	0.10	0	0.00	0	12.49	0	3021452	0	100	0	98.16	0	1.46	0	0.01	0	1.11	0	0.00	0	244.97	0	0.50	0	191560	0	3470415	0	238919	0	11998	0	3466	0	0	0	433499	0	388	0	0	0	2147	0	509211	0	1771	0	513517	0	80.18	0	2782533	0	64698	496086	7.667717703793	3470415.0	3021452.0	191560.0	238919.0	11998.0	3466.0	0.0	433499.0	2782533.0	87.1	5.5	6.9	0.3	0.1	0.0	12.5	80.2	50	50	50.00	17	173520750	25.6	24.3	25.8	24.3	0.0	38.4	32.7	bulk
2804885	SRR3932664	SRP057261	SRS1571887	SRX1961987	SRA244059	Harvard Medical School	CBDM Laboratory	ImmGen 11-cell set basic RNASeq project	Full depth directional RNA sequencing was performed on the core ImmGen populations to generate reference datasets for the tissues from 5 week-old C57BL/6J (Jackson Laboratory) males and females, double-sorted by flow cytometry, per ImmGen cell preparation SOP. RNA was prepared from 100,000 cells (final sort collected directly in Trizol). Total RNA was extracted from each sample following ImmGen RNA extraction SOP. PolyA+ RNA was isolated by bead capture (PrepX PolyA mRNA Isolation Kit, Wafergen Biosystems), following the manufacturer''s instructions. Then mRNA libraries were prepared with the PrepX RNA-Seq Library Preparation Kit (Integenex). For first strand synthesis, mRNA was fragmented and ligated to 3'' and 5'' adapters before reverse transcription. Sample libraries then underwent bead clean-up, 2nd strand synthesis and PCR amplification before final sequencing. Libraries were analyzed on an Illumina HiSeq2500 sequencer. The read depths for the 11-cell set populations range from around 8 to 25 million.		Full depth directional RNA sequencing on Spleen CD19+ B Cell from Mus musculus (female)	RNA was prepared from 100,000 cells (final sort collected directly in Trizol). Total RNA was extracted from each sample following ImmGen RNA extraction SOP. PolyA+ RNA was isolated by bead capture (PrepX PolyA mRNA Isolation Kit, Wafergen Biosystems), following the manufacturer’s instructions. Then mRNA libraries were prepared with the PrepX RNA-Seq Library Preparation Kit (Integenex). For first strand synthesis, mRNA was fragmented and ligated to 3’ and 5’ adapters before reverse transcription. Sample libraries then underwent bead clean-up, 2nd strand synthesis and PCR amplification before final sequencing. Libraries were analyzed on an Illumina HiSeq2500 sequencer.	Total CD19+ B (CD19+IgM+)		RNA-Seq	TRANSCRIPTOMIC	PolyA	paired				Illumina HiSeq 2500	age;;5 week-old|BioSampleModel;;Model organism or animal|cell_type;;B Cell|separation method;;FACSAria|sequencing machine;;HiSeq|sex;;female|sorting markers;;CD19+IgM+CD3-|strain;;C57BL/6J|tissue;;Spleen		100	B.Fem.Sp#1	Spleen CD19+ B Cell from Mus musculus (female)	1013971500	10139715	2016-07-20 13:03:10	494880658	1013971500	10139715	2	10139715	index:0,count:10139715,average:50,stdev:0|index:1,count:10139715,average:50,stdev:0	TRA00035663				in_mesa	23631936	1.44	3.13	0.23	808624678	799811097	737380985	736549371	98.91	99.89	9181127	8696991	125.441	514.611	83	100949	77.31	84.87	10836520	7098163	10836520	7098163	81.03	81.59	10836520	7439419	10836520	6824073	112079355	13.86	4.75	0	8.06	0	0.47	0	0.20	0	0.00	0	8.78	0	9181127	0	100	0	98.82	0	1.60	0	0.01	0	1.14	0	0.00	0	445.16	0	0.29	0	481405	0	10139715	0	817124	0	47439	0	20407	0	0	0	890742	0	1437	0	0	0	8560	0	1322424	0	5710	0	1338131	0	82.49	0	8364003	0	98364	1290788	13.122565166118	10139715.0	9181127.0	481405.0	817124.0	47439.0	20407.0	0.0	890742.0	8364003.0	90.5	4.7	8.1	0.5	0.2	0.0	8.8	82.5	50	50	50.00	17	506985750	25.6	23.8	25.3	25.3	0.0	38.4	32.9	bulk
2804916	SRR3932665	SRP057261	SRS1571888	SRX1961988	SRA244059	Harvard Medical School	CBDM Laboratory	ImmGen 11-cell set basic RNASeq project	Full depth directional RNA sequencing was performed on the core ImmGen populations to generate reference datasets for the tissues from 5 week-old C57BL/6J (Jackson Laboratory) males and females, double-sorted by flow cytometry, per ImmGen cell preparation SOP. RNA was prepared from 100,000 cells (final sort collected directly in Trizol). Total RNA was extracted from each sample following ImmGen RNA extraction SOP. PolyA+ RNA was isolated by bead capture (PrepX PolyA mRNA Isolation Kit, Wafergen Biosystems), following the manufacturer''s instructions. Then mRNA libraries were prepared with the PrepX RNA-Seq Library Preparation Kit (Integenex). For first strand synthesis, mRNA was fragmented and ligated to 3'' and 5'' adapters before reverse transcription. Sample libraries then underwent bead clean-up, 2nd strand synthesis and PCR amplification before final sequencing. Libraries were analyzed on an Illumina HiSeq2500 sequencer. The read depths for the 11-cell set populations range from around 8 to 25 million.		Full depth directional RNA sequencing on Spleen CD4 T Cell from Mus musculus (female)	RNA was prepared from 100,000 cells (final sort collected directly in Trizol). Total RNA was extracted from each sample following ImmGen RNA extraction SOP. PolyA+ RNA was isolated by bead capture (PrepX PolyA mRNA Isolation Kit, Wafergen Biosystems), following the manufacturer’s instructions. Then mRNA libraries were prepared with the PrepX RNA-Seq Library Preparation Kit (Integenex). For first strand synthesis, mRNA was fragmented and ligated to 3’ and 5’ adapters before reverse transcription. Sample libraries then underwent bead clean-up, 2nd strand synthesis and PCR amplification before final sequencing. Libraries were analyzed on an Illumina HiSeq2500 sequencer.	Total CD4 (TCRB+CD4+)		RNA-Seq	TRANSCRIPTOMIC	PolyA	paired				Illumina HiSeq 2500	age;;5 week-old|BioSampleModel;;Model organism or animal|cell_type;;CD4 TConv Cell|separation method;;FACSAria|sequencing machine;;HiSeq|sex;;female|sorting markers;;CD4+TCRB+|strain;;C57BL/6J|tissue;;Spleen		100	T4.Fem.Sp#1	Spleen CD4 T Cell from Mus musculus (female)	1549567300	15495673	2016-07-20 13:11:08	745504851	1549567300	15495673	2	15495673	index:0,count:15495673,average:50,stdev:0|index:1,count:15495673,average:50,stdev:0	TRA00035664				in_mesa	23631936	0.45	3.33	0.31	1213984690	1194454101	1092803369	1093204262	98.39	100.04	13915895	13151459	129.395	559.730	75	147021	79.68	88.62	17011984	11088229	17011984	11088229	83.59	84.8	17011984	11631777	17011984	10610823	120369540	9.92	3.54	0	9.06	0	0.91	0	0.27	0	0.00	0	9.01	0	13915895	0	100	0	98.85	0	1.53	0	0.01	0	1.11	0	0.00	0	357.59	0	0.21	0	549126	0	15495673	0	1403794	0	141237	0	42167	0	0	0	1396374	0	2481	0	0	0	15016	0	2167565	0	7515	0	2192577	0	80.75	0	12512101	0	98929	2108652	21.314801524326	15495673.0	13915895.0	549126.0	1403794.0	141237.0	42167.0	0.0	1396374.0	12512101.0	89.8	3.5	9.1	0.9	0.3	0.0	9.0	80.7	50	50	50.00	17	774783650	24.6	23.8	27.3	24.3	0.0	38.5	33.0	bulk
2804947	SRR3932666	SRP057261	SRS1571889	SRX1961989	SRA244059	Harvard Medical School	CBDM Laboratory	ImmGen 11-cell set basic RNASeq project	Full depth directional RNA sequencing was performed on the core ImmGen populations to generate reference datasets for the tissues from 5 week-old C57BL/6J (Jackson Laboratory) males and females, double-sorted by flow cytometry, per ImmGen cell preparation SOP. RNA was prepared from 100,000 cells (final sort collected directly in Trizol). Total RNA was extracted from each sample following ImmGen RNA extraction SOP. PolyA+ RNA was isolated by bead capture (PrepX PolyA mRNA Isolation Kit, Wafergen Biosystems), following the manufacturer''s instructions. Then mRNA libraries were prepared with the PrepX RNA-Seq Library Preparation Kit (Integenex). For first strand synthesis, mRNA was fragmented and ligated to 3'' and 5'' adapters before reverse transcription. Sample libraries then underwent bead clean-up, 2nd strand synthesis and PCR amplification before final sequencing. Libraries were analyzed on an Illumina HiSeq2500 sequencer. The read depths for the 11-cell set populations range from around 8 to 25 million.		Full depth directional RNA sequencing on Spleen CD8 T Cell from Mus musculus (female)	RNA was prepared from 100,000 cells (final sort collected directly in Trizol). Total RNA was extracted from each sample following ImmGen RNA extraction SOP. PolyA+ RNA was isolated by bead capture (PrepX PolyA mRNA Isolation Kit, Wafergen Biosystems), following the manufacturer’s instructions. Then mRNA libraries were prepared with the PrepX RNA-Seq Library Preparation Kit (Integenex). For first strand synthesis, mRNA was fragmented and ligated to 3’ and 5’ adapters before reverse transcription. Sample libraries then underwent bead clean-up, 2nd strand synthesis and PCR amplification before final sequencing. Libraries were analyzed on an Illumina HiSeq2500 sequencer.	Total CD8 (TCRB+CD8+)		RNA-Seq	TRANSCRIPTOMIC	PolyA	paired				Illumina HiSeq 2500	age;;5 week-old|BioSampleModel;;Model organism or animal|cell_type;;CD8 T Cell|separation method;;FACSAria|sequencing machine;;HiSeq|sex;;female|sorting markers;;TCRB+CD8+|strain;;C57BL/6J|tissue;;Spleen		100	T8.Fem.Sp#1	Spleen CD8 T Cell from Mus musculus (female)	1260939400	12609394	2016-07-20 13:02:09	604921737	1260939400	12609394	2	12609394	index:0,count:12609394,average:50,stdev:0|index:1,count:12609394,average:50,stdev:0	TRA00035665				in_mesa	23631936	1.25	3.63	0.24	986897054	969818407	869901770	867032527	98.27	99.67	11172614	10586469	126.873	572.601	86	119714	76.04	86.36	13954025	8495668	13954025	8495668	82.25	82.87	13954025	9189732	13954025	8152267	116595931	11.81	5.38	0	10.58	0	0.78	0	0.28	0	0.00	0	10.33	0	11172614	0	100	0	98.70	0	1.54	0	0.01	0	1.12	0	0.00	0	270.20	0	0.32	0	678784	0	12609394	0	1334644	0	98748	0	35401	0	0	0	1302631	0	1579	0	0	0	11401	0	1581226	0	7663	0	1601869	0	78.02	0	9837970	0	104105	1563473	15.018231593103	12609394.0	11172614.0	678784.0	1334644.0	98748.0	35401.0	0.0	1302631.0	9837970.0	88.6	5.4	10.6	0.8	0.3	0.0	10.3	78.0	50	50	50.00	17	630469700	26.0	23.6	25.4	25.0	0.0	38.5	33.1	bulk
2804979	SRR3932667	SRP057261	SRS1571890	SRX1961990	SRA244059	Harvard Medical School	CBDM Laboratory	ImmGen 11-cell set basic RNASeq project	Full depth directional RNA sequencing was performed on the core ImmGen populations to generate reference datasets for the tissues from 5 week-old C57BL/6J (Jackson Laboratory) males and females, double-sorted by flow cytometry, per ImmGen cell preparation SOP. RNA was prepared from 100,000 cells (final sort collected directly in Trizol). Total RNA was extracted from each sample following ImmGen RNA extraction SOP. PolyA+ RNA was isolated by bead capture (PrepX PolyA mRNA Isolation Kit, Wafergen Biosystems), following the manufacturer''s instructions. Then mRNA libraries were prepared with the PrepX RNA-Seq Library Preparation Kit (Integenex). For first strand synthesis, mRNA was fragmented and ligated to 3'' and 5'' adapters before reverse transcription. Sample libraries then underwent bead clean-up, 2nd strand synthesis and PCR amplification before final sequencing. Libraries were analyzed on an Illumina HiSeq2500 sequencer. The read depths for the 11-cell set populations range from around 8 to 25 million.		Full depth directional RNA sequencing on Spleen Neutrophil from Mus musculus (female)	RNA was prepared from 100,000 cells (final sort collected directly in Trizol). Total RNA was extracted from each sample following ImmGen RNA extraction SOP. PolyA+ RNA was isolated by bead capture (PrepX PolyA mRNA Isolation Kit, Wafergen Biosystems), following the manufacturer’s instructions. Then mRNA libraries were prepared with the PrepX RNA-Seq Library Preparation Kit (Integenex). For first strand synthesis, mRNA was fragmented and ligated to 3’ and 5’ adapters before reverse transcription. Sample libraries then underwent bead clean-up, 2nd strand synthesis and PCR amplification before final sequencing. Libraries were analyzed on an Illumina HiSeq2500 sequencer.	Neutrophils (LY66+)		RNA-Seq	TRANSCRIPTOMIC	PolyA	paired				Illumina HiSeq 2500	age;;5 week-old|BioSampleModel;;Model organism or animal|cell_type;;Neutrophil|separation method;;FACSAria|sequencing machine;;HiSeq|sex;;female|sorting markers;;Ly6G+|strain;;C57BL/6J|tissue;;Spleen		100	Gn.Fem.Sp#1	Spleen Neutrophil from Mus musculus (female)	597154200	5971542	2016-07-20 12:59:10	290091218	597154200	5971542	2	5971542	index:0,count:5971542,average:50,stdev:0|index:1,count:5971542,average:50,stdev:0	TRA00035666				in_mesa	23631936	0.15	2.91	0.09	458962757	450448255	436129659	432350190	98.14	99.13	5275773	4977529	122.705	459.878	87	59113	83.34	87.79	5835870	4396656	5835870	4396656	83.57	84.73	5835870	4408707	5835870	4243725	48514576	10.57	3.46	0	4.48	0	0.65	0	0.27	0	0.00	0	10.73	0	5275773	0	100	0	98.86	0	1.38	0	0.01	0	1.10	0	0.00	0	341.23	0	0.20	0	206547	0	5971542	0	267531	0	38836	0	16214	0	0	0	640719	0	517	0	0	0	4938	0	848414	0	3416	0	857285	0	83.87	0	5008242	0	69445	829042	11.938109295126	5971542.0	5275773.0	206547.0	267531.0	38836.0	16214.0	0.0	640719.0	5008242.0	88.3	3.5	4.5	0.7	0.3	0.0	10.7	83.9	50	50	50.00	17	298577100	25.3	23.8	25.9	24.9	0.0	38.5	33.0	bulk
2805011	SRR3932668	SRP057261	SRS1571891	SRX1961991	SRA244059	Harvard Medical School	CBDM Laboratory	ImmGen 11-cell set basic RNASeq project	Full depth directional RNA sequencing was performed on the core ImmGen populations to generate reference datasets for the tissues from 5 week-old C57BL/6J (Jackson Laboratory) males and females, double-sorted by flow cytometry, per ImmGen cell preparation SOP. RNA was prepared from 100,000 cells (final sort collected directly in Trizol). Total RNA was extracted from each sample following ImmGen RNA extraction SOP. PolyA+ RNA was isolated by bead capture (PrepX PolyA mRNA Isolation Kit, Wafergen Biosystems), following the manufacturer''s instructions. Then mRNA libraries were prepared with the PrepX RNA-Seq Library Preparation Kit (Integenex). For first strand synthesis, mRNA was fragmented and ligated to 3'' and 5'' adapters before reverse transcription. Sample libraries then underwent bead clean-up, 2nd strand synthesis and PCR amplification before final sequencing. Libraries were analyzed on an Illumina HiSeq2500 sequencer. The read depths for the 11-cell set populations range from around 8 to 25 million.		Full depth directional RNA sequencing on Spleen Dendritic Cells from Mus musculus (female)	RNA was prepared from 100,000 cells (final sort collected directly in Trizol). Total RNA was extracted from each sample following ImmGen RNA extraction SOP. PolyA+ RNA was isolated by bead capture (PrepX PolyA mRNA Isolation Kit, Wafergen Biosystems), following the manufacturer’s instructions. Then mRNA libraries were prepared with the PrepX RNA-Seq Library Preparation Kit (Integenex). For first strand synthesis, mRNA was fragmented and ligated to 3’ and 5’ adapters before reverse transcription. Sample libraries then underwent bead clean-up, 2nd strand synthesis and PCR amplification before final sequencing. Libraries were analyzed on an Illumina HiSeq2500 sequencer.	DC (CD11c+MHCII+ FLT3+)		RNA-Seq	TRANSCRIPTOMIC	PolyA	paired				Illumina HiSeq 2500	age;;5 week-old|BioSampleModel;;Model organism or animal|cell_type;;Dendritic Cell|separation method;;FACSAria|sequencing machine;;HiSeq|sex;;female|sorting markers;;Cd11b+Flt3+|strain;;C57BL/6J|tissue;;Spleen		100	DC.Fem.Sp#1	Spleen Dendritic Cells from Mus musculus (female)	1559486200	15594862	2016-07-20 13:08:33	747632516	1559486200	15594862	2	15594862	index:0,count:15594862,average:50,stdev:0|index:1,count:15594862,average:50,stdev:0	TRA00035667				in_mesa	23631936	0.74	3.13	0.15	1277232826	1269208880	1189174037	1190703419	99.37	100.13	14368435	13326688	137.474	552.100	90	137409	80.39	86.39	16311275	11550083	16311275	11550083	83.18	83.71	16311275	11951871	16311275	11192325	163666030	12.81	3.58	0	6.40	0	0.40	0	0.19	0	0.00	0	7.27	0	14368435	0	100	0	98.93	0	1.39	0	0.01	0	1.10	0	0.00	0	359.88	0	0.20	0	558018	0	15594862	0	998774	0	62266	0	30362	0	0	0	1133799	0	1864	0	0	0	13845	0	2350090	0	10215	0	2376014	0	85.73	0	13369661	0	110651	2296545	20.754850837317	15594862.0	14368435.0	558018.0	998774.0	62266.0	30362.0	0.0	1133799.0	13369661.0	92.1	3.6	6.4	0.4	0.2	0.0	7.3	85.7	50	50	50.00	17	779743100	25.3	24.1	25.4	25.2	0.0	38.5	33.2	bulk
2805042	SRR3932669	SRP057261	SRS1571892	SRX1961992	SRA244059	Harvard Medical School	CBDM Laboratory	ImmGen 11-cell set basic RNASeq project	Full depth directional RNA sequencing was performed on the core ImmGen populations to generate reference datasets for the tissues from 5 week-old C57BL/6J (Jackson Laboratory) males and females, double-sorted by flow cytometry, per ImmGen cell preparation SOP. RNA was prepared from 100,000 cells (final sort collected directly in Trizol). Total RNA was extracted from each sample following ImmGen RNA extraction SOP. PolyA+ RNA was isolated by bead capture (PrepX PolyA mRNA Isolation Kit, Wafergen Biosystems), following the manufacturer''s instructions. Then mRNA libraries were prepared with the PrepX RNA-Seq Library Preparation Kit (Integenex). For first strand synthesis, mRNA was fragmented and ligated to 3'' and 5'' adapters before reverse transcription. Sample libraries then underwent bead clean-up, 2nd strand synthesis and PCR amplification before final sequencing. Libraries were analyzed on an Illumina HiSeq2500 sequencer. The read depths for the 11-cell set populations range from around 8 to 25 million.		Full depth directional RNA sequencing on Spleen NK Cell from Mus musculus (female)	RNA was prepared from 100,000 cells (final sort collected directly in Trizol). Total RNA was extracted from each sample following ImmGen RNA extraction SOP. PolyA+ RNA was isolated by bead capture (PrepX PolyA mRNA Isolation Kit, Wafergen Biosystems), following the manufacturer’s instructions. Then mRNA libraries were prepared with the PrepX RNA-Seq Library Preparation Kit (Integenex). For first strand synthesis, mRNA was fragmented and ligated to 3’ and 5’ adapters before reverse transcription. Sample libraries then underwent bead clean-up, 2nd strand synthesis and PCR amplification before final sequencing. Libraries were analyzed on an Illumina HiSeq2500 sequencer.	NK (NK1.1+TCRB-)		RNA-Seq	TRANSCRIPTOMIC	PolyA	paired				Illumina HiSeq 2500	age;;5 week-old|BioSampleModel;;Model organism or animal|cell_type;;NK Cell|separation method;;FACSAria|sequencing machine;;HiSeq|sex;;female|sorting markers;;NK1.1+TCRB-|strain;;C57BL/6J|tissue;;Spleen		100	NK.Fem.Sp#1	Spleen NK Cell from Mus musculus (female)	1341782100	13417821	2016-07-20 13:06:34	646342812	1341782100	13417821	2	13417821	index:0,count:13417821,average:50,stdev:0|index:1,count:13417821,average:50,stdev:0	TRA00035668				in_mesa	23631936	0.84	3.46	0.1	1062936352	1064376066	960922953	971735204	100.14	101.13	12154172	11469032	131.832	451.385	83	136090	83.61	92.67	14446399	10162429	14446399	10162429	87.13	88.17	14446399	10590487	14446399	9669395	71137768	6.69	2.96	0	8.85	0	0.37	0	0.13	0	0.00	0	8.92	0	12154172	0	100	0	98.97	0	1.48	0	0.01	0	1.10	0	0.00	0	303.80	0	0.22	0	397296	0	13417821	0	1187999	0	49704	0	17077	0	0	0	1196868	0	1861	0	0	0	9628	0	1731758	0	6278	0	1749525	0	81.73	0	10966173	0	75504	1706349	22.599451684679	13417821.0	12154172.0	397296.0	1187999.0	49704.0	17077.0	0.0	1196868.0	10966173.0	90.6	3.0	8.9	0.4	0.1	0.0	8.9	81.7	50	50	50.00	17	670891050	24.9	23.7	26.2	25.2	0.0	38.5	33.1	bulk
2805268	SRR3932670	SRP057261	SRS1571893	SRX1961993	SRA244059	Harvard Medical School	CBDM Laboratory	ImmGen 11-cell set basic RNASeq project	Full depth directional RNA sequencing was performed on the core ImmGen populations to generate reference datasets for the tissues from 5 week-old C57BL/6J (Jackson Laboratory) males and females, double-sorted by flow cytometry, per ImmGen cell preparation SOP. RNA was prepared from 100,000 cells (final sort collected directly in Trizol). Total RNA was extracted from each sample following ImmGen RNA extraction SOP. PolyA+ RNA was isolated by bead capture (PrepX PolyA mRNA Isolation Kit, Wafergen Biosystems), following the manufacturer''s instructions. Then mRNA libraries were prepared with the PrepX RNA-Seq Library Preparation Kit (Integenex). For first strand synthesis, mRNA was fragmented and ligated to 3'' and 5'' adapters before reverse transcription. Sample libraries then underwent bead clean-up, 2nd strand synthesis and PCR amplification before final sequencing. Libraries were analyzed on an Illumina HiSeq2500 sequencer. The read depths for the 11-cell set populations range from around 8 to 25 million.		Full depth directional RNA sequencing on Spleen NKT from Mus musculus (female)	RNA was prepared from 100,000 cells (final sort collected directly in Trizol). Total RNA was extracted from each sample following ImmGen RNA extraction SOP. PolyA+ RNA was isolated by bead capture (PrepX PolyA mRNA Isolation Kit, Wafergen Biosystems), following the manufacturer’s instructions. Then mRNA libraries were prepared with the PrepX RNA-Seq Library Preparation Kit (Integenex). For first strand synthesis, mRNA was fragmented and ligated to 3’ and 5’ adapters before reverse transcription. Sample libraries then underwent bead clean-up, 2nd strand synthesis and PCR amplification before final sequencing. Libraries were analyzed on an Illumina HiSeq2500 sequencer.	NKT (TCRBint NK1.1int)		RNA-Seq	TRANSCRIPTOMIC	PolyA	paired				Illumina HiSeq 2500	age;;5 week-old|BioSampleModel;;Model organism or animal|cell_type;;NKT Cell|separation method;;FACSAria|sequencing machine;;HiSeq|sex;;female|sorting markers;;TCRBint NK1.1int|strain;;C57BL/6J|tissue;;Spleen		100	NKT.Fem.Sp#1	Spleen NKT from Mus musculus (female)	1600282800	16002828	2016-07-20 13:11:08	768063898	1600282800	16002828	2	16002828	index:0,count:16002828,average:50,stdev:0|index:1,count:16002828,average:50,stdev:0	TRA00035669				in_mesa	23631936	1.33	3.38	0.12	1300058097	1297068614	1163797894	1173502871	99.77	100.83	14720311	13802994	135.565	572.607	83	158088	83.5	93.41	17722065	12290769	17722065	12290769	88.62	89.58	17722065	13045301	17722065	11786561	77118515	5.93	3.16	0	9.77	0	0.50	0	0.12	0	0.00	0	7.39	0	14720311	0	100	0	98.94	0	1.44	0	0.01	0	1.10	0	0.00	0	357.83	0	0.22	0	505090	0	16002828	0	1562706	0	79669	0	19900	0	0	0	1182948	0	2519	0	0	0	14536	0	2302240	0	9749	0	2329044	0	82.22	0	13157605	0	96974	2268607	23.393971580011	16002828.0	14720311.0	505090.0	1562706.0	79669.0	19900.0	0.0	1182948.0	13157605.0	92.0	3.2	9.8	0.5	0.1	0.0	7.4	82.2	50	50	50.00	17	800141400	25.4	24.1	25.8	24.7	0.0	38.5	33.1	bulk
2805299	SRR3932671	SRP057261	SRS1571896	SRX1961994	SRA244059	Harvard Medical School	CBDM Laboratory	ImmGen 11-cell set basic RNASeq project	Full depth directional RNA sequencing was performed on the core ImmGen populations to generate reference datasets for the tissues from 5 week-old C57BL/6J (Jackson Laboratory) males and females, double-sorted by flow cytometry, per ImmGen cell preparation SOP. RNA was prepared from 100,000 cells (final sort collected directly in Trizol). Total RNA was extracted from each sample following ImmGen RNA extraction SOP. PolyA+ RNA was isolated by bead capture (PrepX PolyA mRNA Isolation Kit, Wafergen Biosystems), following the manufacturer''s instructions. Then mRNA libraries were prepared with the PrepX RNA-Seq Library Preparation Kit (Integenex). For first strand synthesis, mRNA was fragmented and ligated to 3'' and 5'' adapters before reverse transcription. Sample libraries then underwent bead clean-up, 2nd strand synthesis and PCR amplification before final sequencing. Libraries were analyzed on an Illumina HiSeq2500 sequencer. The read depths for the 11-cell set populations range from around 8 to 25 million.		Full depth directional RNA sequencing on Spleen TCRgd from Mus musculus (female)	RNA was prepared from 100,000 cells (final sort collected directly in Trizol). Total RNA was extracted from each sample following ImmGen RNA extraction SOP. PolyA+ RNA was isolated by bead capture (PrepX PolyA mRNA Isolation Kit, Wafergen Biosystems), following the manufacturer’s instructions. Then mRNA libraries were prepared with the PrepX RNA-Seq Library Preparation Kit (Integenex). For first strand synthesis, mRNA was fragmented and ligated to 3’ and 5’ adapters before reverse transcription. Sample libraries then underwent bead clean-up, 2nd strand synthesis and PCR amplification before final sequencing. Libraries were analyzed on an Illumina HiSeq2500 sequencer.	TCRgd (TCRgd+TCRB-)		RNA-Seq	TRANSCRIPTOMIC	PolyA	paired				Illumina HiSeq 2500	age;;5 week-old|BioSampleModel;;Model organism or animal|cell_type;;gdT Cell|separation method;;FACSAria|sequencing machine;;HiSeq|sex;;female|sorting markers;;TCRgd+TCRB-|strain;;C57BL/6J|tissue;;Spleen		100	Tgd.Fem.Sp#1	Spleen TCRgd from Mus musculus (female)	905865500	9058655	2016-07-20 13:04:09	438582523	905865500	9058655	2	9058655	index:0,count:9058655,average:50,stdev:0|index:1,count:9058655,average:50,stdev:0	TRA00035670				in_mesa	23631936	1.08	3.43	0.13	672956525	671297901	611501200	615735809	99.75	100.69	8045028	7586590	119.902	593.897	72	98656	83.58	92.15	9520794	6724035	9520794	6724035	87.62	88.47	9520794	7049288	9520794	6455194	47556051	7.07	4.38	0	8.26	0	0.52	0	0.19	0	0.00	0	10.48	0	8045028	0	100	0	98.66	0	1.40	0	0.01	0	1.11	0	0.00	0	304.78	0	0.20	0	396891	0	9058655	0	748246	0	47301	0	17207	0	0	0	949119	0	1559	0	0	0	8991	0	1360745	0	4911	0	1376206	0	80.55	0	7296782	0	97145	1288210	13.260692778836	9058655.0	8045028.0	396891.0	748246.0	47301.0	17207.0	0.0	949119.0	7296782.0	88.8	4.4	8.3	0.5	0.2	0.0	10.5	80.6	50	50	50.00	17	452932750	25.5	24.1	26.1	24.3	0.0	38.5	33.0	bulk
2805331	SRR3932672	SRP057261	SRS1571898	SRX1961995	SRA244059	Harvard Medical School	CBDM Laboratory	ImmGen 11-cell set basic RNASeq project	Full depth directional RNA sequencing was performed on the core ImmGen populations to generate reference datasets for the tissues from 5 week-old C57BL/6J (Jackson Laboratory) males and females, double-sorted by flow cytometry, per ImmGen cell preparation SOP. RNA was prepared from 100,000 cells (final sort collected directly in Trizol). Total RNA was extracted from each sample following ImmGen RNA extraction SOP. PolyA+ RNA was isolated by bead capture (PrepX PolyA mRNA Isolation Kit, Wafergen Biosystems), following the manufacturer''s instructions. Then mRNA libraries were prepared with the PrepX RNA-Seq Library Preparation Kit (Integenex). For first strand synthesis, mRNA was fragmented and ligated to 3'' and 5'' adapters before reverse transcription. Sample libraries then underwent bead clean-up, 2nd strand synthesis and PCR amplification before final sequencing. Libraries were analyzed on an Illumina HiSeq2500 sequencer. The read depths for the 11-cell set populations range from around 8 to 25 million.		Full depth directional RNA sequencing on Spleen T regulatory Cells from Mus musculus (female)	RNA was prepared from 100,000 cells (final sort collected directly in Trizol). Total RNA was extracted from each sample following ImmGen RNA extraction SOP. PolyA+ RNA was isolated by bead capture (PrepX PolyA mRNA Isolation Kit, Wafergen Biosystems), following the manufacturer’s instructions. Then mRNA libraries were prepared with the PrepX RNA-Seq Library Preparation Kit (Integenex). For first strand synthesis, mRNA was fragmented and ligated to 3’ and 5’ adapters before reverse transcription. Sample libraries then underwent bead clean-up, 2nd strand synthesis and PCR amplification before final sequencing. Libraries were analyzed on an Illumina HiSeq2500 sequencer.	Treg (TCRB+CD4+CD25+)		RNA-Seq	TRANSCRIPTOMIC	PolyA	paired				Illumina HiSeq 2500	age;;5 week-old|BioSampleModel;;Model organism or animal|cell_type;;Treg|separation method;;FACSAria|sequencing machine;;HiSeq|sex;;female|sorting markers;;CD4+CD25+CD8-CD19-|strain;;C57BL/6J|tissue;;Spleen		100	Treg.Fem.Sp#1	Spleen T regulatory Cells from Mus musculus (female)	1849224800	18492248	2016-07-20 13:11:08	899733437	1849224800	18492248	2	18492248	index:0,count:18492248,average:50,stdev:0|index:1,count:18492248,average:50,stdev:0	TRA00035671				in_mesa	23631936	1.19	3.69	0.11	1489708380	1484696124	1312774713	1321644007	99.66	100.68	16854510	15857117	132.308	588.434	83	183579	80.54	91.51	20958839	13574150	20958839	13574150	86.76	87.67	20958839	14622218	20958839	13004743	113416358	7.61	3.75	0	10.93	0	0.49	0	0.18	0	0.00	0	8.19	0	16854510	0	100	0	98.89	0	1.78	0	0.01	0	1.15	0	0.00	0	455.97	0	0.22	0	693706	0	18492248	0	2020833	0	91454	0	32541	0	0	0	1513743	0	2758	0	0	0	18165	0	2686590	0	8625	0	2716138	0	80.22	0	14833677	0	111858	2645871	23.653837901625	18492248.0	16854510.0	693706.0	2020833.0	91454.0	32541.0	0.0	1513743.0	14833677.0	91.1	3.8	10.9	0.5	0.2	0.0	8.2	80.2	50	50	50.00	17	924612400	25.4	24.3	26.1	24.3	0.0	38.5	33.1	bulk
1675820	SRR3532922	SRP059295	SRS1440206	SRX1767514	SRA272264	GEO		RNAseq in E18.5 wild-type, Nova2-KO, and Nova1-KO mouse cortex and mid- and hind-brain	We sequenced mRNA from E18.5 mouse cortex (3 wild-type vs 3 Nova2-/- and 3 wild-type vs 3 Nova1-/-) and from E18.5 mouse mid- and hind-brain (3 wild-type vs 3 Nova1-/-) to compare gene expression level and alternative splicing events between wild-type and Nova mutant mice. Overall design: Mouse cortex or mid- and hind-brain mRNA profiles of embryonic 18.5 day wild type (WT), Nova2-/-, and Nova1-/- mice were generated by deep sequencing using Illumina Hiseq2500.		GSM2154666: RNAseq_WT1_cortex; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Trizol extraction Illumina High-throughput TruSeq RNA Sample preparation: ribozero selection	Illumina HiSeq 2500	developmental stage;;E18.5|genotype;;wild-type|source_name;;cortex|strain background;;CD1|tissue compartment;;cortex|tissue;;brain	GEO Accession;;GSM2154666		GSM2154666	RNAseq_WT1_cortex	12168924750	48675699	2016-05-26 12:42:58	7345053325	12168924750	48675699	2	48675699	index:0,count:48675699,average:125,stdev:0|index:1,count:48675699,average:125,stdev:0	GSM2154666_r1						8.25	2.83	0.09	7531694445	7307718803	6734018937	6560840664	97.03	97.43	42264497	39832250	195.200	827.056	158	389189	58.56	65.91	51578409	24748327	51578409	24748327	62.55	63.0	51578409	26435472	51578409	23654433	2211596840	29.36	1.80	0	9.69	0	0.80	0	0.76	0	0.00	0	11.61	0	42264497	0	250	0	245.45	0	2.24	0	0.02	0	1.90	0	0.02	0	133.56	0	0.66	0	875968	0	48675699	0	4715599	0	391268	0	371010	0	0	0	5648924	0	9787	0	0	0	156788	0	11130059	0	79840	0	11376474	0	77.14	0	37548898	0	252296	9324622	36.959056029426	48675699.0	42264497.0	875968.0	4715599.0	391268.0	371010.0	0.0	5648924.0	37548898.0	86.8	1.8	9.7	0.8	0.8	0.0	11.6	77.1	125	125	125.00	24	6084462375	27.6	22.4	22.2	27.8	0.0	33.5	23.9	bulk
1675835	SRR3532923	SRP059295	SRS1440208	SRX1767515	SRA272264	GEO		RNAseq in E18.5 wild-type, Nova2-KO, and Nova1-KO mouse cortex and mid- and hind-brain	We sequenced mRNA from E18.5 mouse cortex (3 wild-type vs 3 Nova2-/- and 3 wild-type vs 3 Nova1-/-) and from E18.5 mouse mid- and hind-brain (3 wild-type vs 3 Nova1-/-) to compare gene expression level and alternative splicing events between wild-type and Nova mutant mice. Overall design: Mouse cortex or mid- and hind-brain mRNA profiles of embryonic 18.5 day wild type (WT), Nova2-/-, and Nova1-/- mice were generated by deep sequencing using Illumina Hiseq2500.		GSM2154667: RNAseq_WT2_cortex; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Trizol extraction Illumina High-throughput TruSeq RNA Sample preparation: ribozero selection	Illumina HiSeq 2500	developmental stage;;E18.5|genotype;;wild-type|source_name;;cortex|strain background;;CD1|tissue compartment;;cortex|tissue;;brain	GEO Accession;;GSM2154667		GSM2154667	RNAseq_WT2_cortex	10558170750	42232683	2016-05-26 12:42:58	6358366582	10558170750	42232683	2	42232683	index:0,count:42232683,average:125,stdev:0|index:1,count:42232683,average:125,stdev:0	GSM2154667_r1						5.87	2.68	0.44	6331184048	5638708037	5567535699	4987641860	89.06	89.58	35380387	33474479	196.890	889.440	158	339440	47.65	54.37	44762403	16857508	44762403	16857508	52.9	52.04	44762403	18716460	44762403	16136474	2107090824	33.28	1.85	0	10.36	0	1.26	0	2.36	0	0.00	0	12.61	0	35380387	0	250	0	244.95	0	2.16	0	0.03	0	1.93	0	0.02	0	70.16	0	0.78	0	781001	0	42232683	0	4375325	0	531694	0	994633	0	0	0	5325969	0	7095	0	0	0	127615	0	7297788	0	137511	0	7570009	0	73.41	0	31005062	0	268156	7361131	27.450927818136	42232683.0	35380387.0	781001.0	4375325.0	531694.0	994633.0	0.0	5325969.0	31005062.0	83.8	1.8	10.4	1.3	2.4	0.0	12.6	73.4	125	125	125.00	24	5279085375	28.3	21.6	21.5	28.5	0.0	33.4	23.8	bulk
1675852	SRR3532924	SRP059295	SRS1440207	SRX1767516	SRA272264	GEO		RNAseq in E18.5 wild-type, Nova2-KO, and Nova1-KO mouse cortex and mid- and hind-brain	We sequenced mRNA from E18.5 mouse cortex (3 wild-type vs 3 Nova2-/- and 3 wild-type vs 3 Nova1-/-) and from E18.5 mouse mid- and hind-brain (3 wild-type vs 3 Nova1-/-) to compare gene expression level and alternative splicing events between wild-type and Nova mutant mice. Overall design: Mouse cortex or mid- and hind-brain mRNA profiles of embryonic 18.5 day wild type (WT), Nova2-/-, and Nova1-/- mice were generated by deep sequencing using Illumina Hiseq2500.		GSM2154668: RNAseq_WT3_cortex; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Trizol extraction Illumina High-throughput TruSeq RNA Sample preparation: ribozero selection	Illumina HiSeq 2500	developmental stage;;E18.5|genotype;;wild-type|source_name;;cortex|strain background;;CD1|tissue compartment;;cortex|tissue;;brain	GEO Accession;;GSM2154668		GSM2154668	RNAseq_WT3_cortex	14817256750	59269027	2016-05-26 12:42:58	8925238783	14817256750	59269027	2	59269027	index:0,count:59269027,average:125,stdev:0|index:1,count:59269027,average:125,stdev:0	GSM2154668_r1						8.2	2.76	0.08	9129270573	8879203225	8412808411	8198933131	97.26	97.46	51773720	49026638	192.830	801.931	144	496652	54.84	59.81	60027215	28394749	60027215	28394749	57.51	57.3	60027215	29776307	60027215	27203013	3265964284	35.77	2.04	0	7.25	0	0.50	0	0.35	0	0.00	0	11.80	0	51773720	0	250	0	245.98	0	1.47	0	0.01	0	1.17	0	0.00	0	145.64	0	0.53	0	1208313	0	59269027	0	4299874	0	296376	0	207015	0	0	0	6991916	0	10185	0	0	0	99529	0	12866833	0	47491	0	13024038	0	80.10	0	47473846	0	249392	10070899	40.381804548662	59269027.0	51773720.0	1208313.0	4299874.0	296376.0	207015.0	0.0	6991916.0	47473846.0	87.4	2.0	7.3	0.5	0.3	0.0	11.8	80.1	125	125	125.00	24	7408628375	27.8	22.3	22.1	27.8	0.0	33.5	23.9	bulk
1675869	SRR3532925	SRP059295	SRS1440211	SRX1767517	SRA272264	GEO		RNAseq in E18.5 wild-type, Nova2-KO, and Nova1-KO mouse cortex and mid- and hind-brain	We sequenced mRNA from E18.5 mouse cortex (3 wild-type vs 3 Nova2-/- and 3 wild-type vs 3 Nova1-/-) and from E18.5 mouse mid- and hind-brain (3 wild-type vs 3 Nova1-/-) to compare gene expression level and alternative splicing events between wild-type and Nova mutant mice. Overall design: Mouse cortex or mid- and hind-brain mRNA profiles of embryonic 18.5 day wild type (WT), Nova2-/-, and Nova1-/- mice were generated by deep sequencing using Illumina Hiseq2500.		GSM2154669: RNAseq_Nova2-KO1_cortex; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Trizol extraction Illumina High-throughput TruSeq RNA Sample preparation: ribozero selection	Illumina HiSeq 2500	developmental stage;;E18.5|genotype;;Nova2-ko|source_name;;cortex|strain background;;CD1|tissue compartment;;cortex|tissue;;brain	GEO Accession;;GSM2154669		GSM2154669	RNAseq_Nova2-KO1_cortex	11092251750	44369007	2016-05-26 12:42:58	6691280245	11092251750	44369007	2	44369007	index:0,count:44369007,average:125,stdev:0|index:1,count:44369007,average:125,stdev:0	GSM2154669_r1						6.63	2.91	0.14	7084952134	6894062530	6469243215	6311065995	97.31	97.55	39115034	37151168	198.958	792.984	158	360589	52.56	57.9	45735323	20559121	45735323	20559121	55.56	55.34	45735323	21730427	45735323	19650981	2657199441	37.50	1.80	0	8.13	0	0.48	0	0.33	0	0.00	0	11.03	0	39115034	0	250	0	245.86	0	2.32	0	0.02	0	1.93	0	0.02	0	156.75	0	0.65	0	800657	0	44369007	0	3607160	0	215046	0	145114	0	0	0	4893813	0	7899	0	0	0	109836	0	9377972	0	62274	0	9557981	0	80.03	0	35507874	0	222555	7617689	34.228343555526	44369007.0	39115034.0	800657.0	3607160.0	215046.0	145114.0	0.0	4893813.0	35507874.0	88.2	1.8	8.1	0.5	0.3	0.0	11.0	80.0	125	125	125.00	24	5546125875	27.6	22.4	22.2	27.8	0.0	33.5	24.0	bulk
1675885	SRR3532926	SRP059295	SRS1440210	SRX1767518	SRA272264	GEO		RNAseq in E18.5 wild-type, Nova2-KO, and Nova1-KO mouse cortex and mid- and hind-brain	We sequenced mRNA from E18.5 mouse cortex (3 wild-type vs 3 Nova2-/- and 3 wild-type vs 3 Nova1-/-) and from E18.5 mouse mid- and hind-brain (3 wild-type vs 3 Nova1-/-) to compare gene expression level and alternative splicing events between wild-type and Nova mutant mice. Overall design: Mouse cortex or mid- and hind-brain mRNA profiles of embryonic 18.5 day wild type (WT), Nova2-/-, and Nova1-/- mice were generated by deep sequencing using Illumina Hiseq2500.		GSM2154670: RNAseq_Nova2-KO2_cortex; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Trizol extraction Illumina High-throughput TruSeq RNA Sample preparation: ribozero selection	Illumina HiSeq 2500	developmental stage;;E18.5|genotype;;Nova2-ko|source_name;;cortex|strain background;;CD1|tissue compartment;;cortex|tissue;;brain	GEO Accession;;GSM2154670		GSM2154670	RNAseq_Nova2-KO2_cortex	11355152000	45420608	2016-05-26 12:42:58	6871546149	11355152000	45420608	2	45420608	index:0,count:45420608,average:125,stdev:0|index:1,count:45420608,average:125,stdev:0	GSM2154670_r1						6.66	2.86	0.14	7091928338	6898188324	6475398751	6315196025	97.27	97.53	39756607	37749651	194.991	796.514	158	377171	52.33	57.62	46667129	20804892	46667129	20804892	55.2	55.04	46667129	21945490	46667129	19875251	2674389336	37.71	1.81	0	8.03	0	0.53	0	0.33	0	0.00	0	11.61	0	39756607	0	250	0	245.80	0	2.30	0	0.02	0	1.95	0	0.02	0	172.85	0	0.65	0	821496	0	45420608	0	3648814	0	241121	0	151578	0	0	0	5271302	0	8015	0	0	0	110275	0	9460512	0	63567	0	9642369	0	79.50	0	36107793	0	221605	7603932	34.312998352925	45420608.0	39756607.0	821496.0	3648814.0	241121.0	151578.0	0.0	5271302.0	36107793.0	87.5	1.8	8.0	0.5	0.3	0.0	11.6	79.5	125	125	125.00	24	5677576000	27.6	22.4	22.1	27.8	0.0	33.4	23.8	bulk
1675901	SRR3532927	SRP059295	SRS1440209	SRX1767519	SRA272264	GEO		RNAseq in E18.5 wild-type, Nova2-KO, and Nova1-KO mouse cortex and mid- and hind-brain	We sequenced mRNA from E18.5 mouse cortex (3 wild-type vs 3 Nova2-/- and 3 wild-type vs 3 Nova1-/-) and from E18.5 mouse mid- and hind-brain (3 wild-type vs 3 Nova1-/-) to compare gene expression level and alternative splicing events between wild-type and Nova mutant mice. Overall design: Mouse cortex or mid- and hind-brain mRNA profiles of embryonic 18.5 day wild type (WT), Nova2-/-, and Nova1-/- mice were generated by deep sequencing using Illumina Hiseq2500.		GSM2154671: RNAseq_Nova2-KO3_cortex; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Trizol extraction Illumina High-throughput TruSeq RNA Sample preparation: ribozero selection	Illumina HiSeq 2500	developmental stage;;E18.5|genotype;;Nova2-ko|source_name;;cortex|strain background;;CD1|tissue compartment;;cortex|tissue;;brain	GEO Accession;;GSM2154671		GSM2154671	RNAseq_Nova2-KO3_cortex	12301019750	49204079	2016-05-26 12:42:58	7406928821	12301019750	49204079	2	49204079	index:0,count:49204079,average:125,stdev:0|index:1,count:49204079,average:125,stdev:0	GSM2154671_r1						6.05	2.85	0.13	7306348626	7093825175	6699909935	6523907344	97.09	97.37	42200479	40074470	188.963	847.526	139	425382	49.67	54.41	49570987	20960046	49570987	20960046	52.18	51.9	49570987	22021720	49570987	19994065	2985974036	40.87	2.28	0	7.47	0	0.61	0	0.35	0	0.00	0	13.28	0	42200479	0	250	0	245.07	0	2.30	0	0.02	0	1.97	0	0.02	0	120.83	0	0.65	0	1124286	0	49204079	0	3677035	0	299479	0	171390	0	0	0	6532731	0	7895	0	0	0	108869	0	9435610	0	72247	0	9624621	0	78.29	0	38523444	0	228756	7368166	32.209716903600	49204079.0	42200479.0	1124286.0	3677035.0	299479.0	171390.0	0.0	6532731.0	38523444.0	85.8	2.3	7.5	0.6	0.3	0.0	13.3	78.3	125	125	125.00	24	6150509875	27.7	22.4	22.2	27.7	0.0	33.5	23.9	bulk
1675916	SRR3532928	SRP059295	SRS1440212	SRX1767520	SRA272264	GEO		RNAseq in E18.5 wild-type, Nova2-KO, and Nova1-KO mouse cortex and mid- and hind-brain	We sequenced mRNA from E18.5 mouse cortex (3 wild-type vs 3 Nova2-/- and 3 wild-type vs 3 Nova1-/-) and from E18.5 mouse mid- and hind-brain (3 wild-type vs 3 Nova1-/-) to compare gene expression level and alternative splicing events between wild-type and Nova mutant mice. Overall design: Mouse cortex or mid- and hind-brain mRNA profiles of embryonic 18.5 day wild type (WT), Nova2-/-, and Nova1-/- mice were generated by deep sequencing using Illumina Hiseq2500.		GSM2154672: RNAseq_WT4_cortex; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Trizol extraction Illumina High-throughput TruSeq RNA Sample preparation: ribozero selection	Illumina HiSeq 2500	developmental stage;;E18.5|genotype;;wild-type|source_name;;cortex|strain background;;CD1|tissue compartment;;cortex|tissue;;brain	GEO Accession;;GSM2154672		GSM2154672	RNAseq_WT4_cortex	13678916500	54715666	2016-05-26 12:42:59	7497957475	13678916500	54715666	2	54715666	index:0,count:54715666,average:125,stdev:0|index:1,count:54715666,average:125,stdev:0	GSM2154672_r1						2.49	2.88	0.36	9200595051	8950674853	8221657729	8018443711	97.28	97.53	48516886	45516918	222.618	952.793	160	351925	48.47	54.66	58356166	23515078	58356166	23515078	52.38	51.67	58356166	25411510	58356166	22230467	3654686602	39.72	1.87	0	10.04	0	0.76	0	0.42	0	0.00	0	10.15	0	48516886	0	250	0	246.11	0	2.41	0	0.02	0	2.10	0	0.02	0	129.08	0	0.46	0	1021233	0	54715666	0	5492811	0	415453	0	228189	0	0	0	5555138	0	9909	0	0	0	162710	0	11679627	0	80157	0	11932403	0	78.63	0	43024075	0	245201	9925331	40.478346336271	54715666.0	48516886.0	1021233.0	5492811.0	415453.0	228189.0	0.0	5555138.0	43024075.0	88.7	1.9	10.0	0.8	0.4	0.0	10.2	78.6	125	125	125.00	24	6839458250	27.0	23.0	22.9	27.2	0.0	34.7	25.3	bulk
1675931	SRR3532929	SRP059295	SRS1440214	SRX1767521	SRA272264	GEO		RNAseq in E18.5 wild-type, Nova2-KO, and Nova1-KO mouse cortex and mid- and hind-brain	We sequenced mRNA from E18.5 mouse cortex (3 wild-type vs 3 Nova2-/- and 3 wild-type vs 3 Nova1-/-) and from E18.5 mouse mid- and hind-brain (3 wild-type vs 3 Nova1-/-) to compare gene expression level and alternative splicing events between wild-type and Nova mutant mice. Overall design: Mouse cortex or mid- and hind-brain mRNA profiles of embryonic 18.5 day wild type (WT), Nova2-/-, and Nova1-/- mice were generated by deep sequencing using Illumina Hiseq2500.		GSM2154673: RNAseq_WT5_cortex; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Trizol extraction Illumina High-throughput TruSeq RNA Sample preparation: ribozero selection	Illumina HiSeq 2500	developmental stage;;E18.5|genotype;;wild-type|source_name;;cortex|strain background;;CD1|tissue compartment;;cortex|tissue;;brain	GEO Accession;;GSM2154673		GSM2154673	RNAseq_WT5_cortex	11869306250	47477225	2016-05-26 12:42:59	6531803337	11869306250	47477225	2	47477225	index:0,count:47477225,average:125,stdev:0|index:1,count:47477225,average:125,stdev:0	GSM2154673_r1						1.85	2.94	0.55	7886206253	7650835559	7101970516	6910492082	97.02	97.3	41795852	39334525	219.322	951.288	139	313670	46.45	51.93	49907041	19415722	49907041	19415722	49.92	49.18	49907041	20866125	49907041	18386778	3345529869	42.42	2.01	0	9.28	0	0.66	0	0.51	0	0.00	0	10.79	0	41795852	0	250	0	246.16	0	2.43	0	0.03	0	2.06	0	0.02	0	156.81	0	0.46	0	953473	0	47477225	0	4406847	0	315168	0	241082	0	0	0	5125123	0	8480	0	0	0	154857	0	9857869	0	78781	0	10099987	0	78.75	0	37389005	0	237371	8302817	34.978228174461	47477225.0	41795852.0	953473.0	4406847.0	315168.0	241082.0	0.0	5125123.0	37389005.0	88.0	2.0	9.3	0.7	0.5	0.0	10.8	78.8	125	125	125.00	24	5934653125	27.1	22.9	22.7	27.2	0.0	34.4	24.9	bulk
1676044	SRR3532930	SRP059295	SRS1440213	SRX1767522	SRA272264	GEO		RNAseq in E18.5 wild-type, Nova2-KO, and Nova1-KO mouse cortex and mid- and hind-brain	We sequenced mRNA from E18.5 mouse cortex (3 wild-type vs 3 Nova2-/- and 3 wild-type vs 3 Nova1-/-) and from E18.5 mouse mid- and hind-brain (3 wild-type vs 3 Nova1-/-) to compare gene expression level and alternative splicing events between wild-type and Nova mutant mice. Overall design: Mouse cortex or mid- and hind-brain mRNA profiles of embryonic 18.5 day wild type (WT), Nova2-/-, and Nova1-/- mice were generated by deep sequencing using Illumina Hiseq2500.		GSM2154674: RNAseq_WT6_cortex; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Trizol extraction Illumina High-throughput TruSeq RNA Sample preparation: ribozero selection	Illumina HiSeq 2500	developmental stage;;E18.5|genotype;;wild-type|source_name;;cortex|strain background;;CD1|tissue compartment;;cortex|tissue;;brain	GEO Accession;;GSM2154674		GSM2154674	RNAseq_WT6_cortex	15580238250	62320953	2016-05-26 12:42:58	8509292653	15580238250	62320953	2	62320953	index:0,count:62320953,average:125,stdev:0|index:1,count:62320953,average:125,stdev:0	GSM2154674_r1						2.03	2.97	0.37	10547136266	10215892643	9658345320	9383588020	96.86	97.16	55702892	52748684	216.948	876.804	160	416223	45.41	49.88	64601330	25297262	64601330	25297262	48.32	47.44	64601330	26917635	64601330	24059869	4726315064	44.81	1.94	0	8.00	0	0.54	0	0.46	0	0.00	0	9.61	0	55702892	0	250	0	246.42	0	2.43	0	0.03	0	2.06	0	0.02	0	210.86	0	0.46	0	1209794	0	62320953	0	4986089	0	339311	0	289572	0	0	0	5989178	0	11141	0	0	0	192406	0	12812764	0	102062	0	13118373	0	81.38	0	50716803	0	260062	10781139	41.456033561228	62320953.0	55702892.0	1209794.0	4986089.0	339311.0	289572.0	0.0	5989178.0	50716803.0	89.4	1.9	8.0	0.5	0.5	0.0	9.6	81.4	125	125	125.00	24	7790119125	27.3	22.7	22.6	27.4	0.0	34.6	25.2	bulk
1676060	SRR3532931	SRP059295	SRS1440215	SRX1767523	SRA272264	GEO		RNAseq in E18.5 wild-type, Nova2-KO, and Nova1-KO mouse cortex and mid- and hind-brain	We sequenced mRNA from E18.5 mouse cortex (3 wild-type vs 3 Nova2-/- and 3 wild-type vs 3 Nova1-/-) and from E18.5 mouse mid- and hind-brain (3 wild-type vs 3 Nova1-/-) to compare gene expression level and alternative splicing events between wild-type and Nova mutant mice. Overall design: Mouse cortex or mid- and hind-brain mRNA profiles of embryonic 18.5 day wild type (WT), Nova2-/-, and Nova1-/- mice were generated by deep sequencing using Illumina Hiseq2500.		GSM2154675: RNAseq_Nova1-KO1_cortex; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Trizol extraction Illumina High-throughput TruSeq RNA Sample preparation: ribozero selection	Illumina HiSeq 2500	developmental stage;;E18.5|genotype;;Nova1-ko|source_name;;cortex|strain background;;CD1|tissue compartment;;cortex|tissue;;brain	GEO Accession;;GSM2154675		GSM2154675	RNAseq_Nova1-KO1_cortex	13493587250	53974349	2016-05-26 12:42:59	7414236812	13493587250	53974349	2	53974349	index:0,count:53974349,average:125,stdev:0|index:1,count:53974349,average:125,stdev:0	GSM2154675_r1						2.24	2.89	0.32	9065360959	8774147380	8246556880	8002366826	96.79	97.04	47999103	45299398	219.593	919.769	160	361326	45.54	50.38	56052682	21858075	56052682	21858075	48.86	47.84	56052682	23450297	56052682	20756637	3987737969	43.99	1.86	0	8.55	0	0.64	0	0.46	0	0.00	0	9.98	0	47999103	0	250	0	246.38	0	2.45	0	0.03	0	2.17	0	0.02	0	154.95	0	0.46	0	1004061	0	53974349	0	4612682	0	344994	0	245901	0	0	0	5384351	0	9191	0	0	0	180669	0	10972367	0	85295	0	11247522	0	80.38	0	43386421	0	249875	9192748	36.789386693347	53974349.0	47999103.0	1004061.0	4612682.0	344994.0	245901.0	0.0	5384351.0	43386421.0	88.9	1.9	8.5	0.6	0.5	0.0	10.0	80.4	125	125	125.00	24	6746793625	27.1	22.9	22.8	27.2	0.0	34.5	25.1	bulk
1676077	SRR3532932	SRP059295	SRS1440216	SRX1767524	SRA272264	GEO		RNAseq in E18.5 wild-type, Nova2-KO, and Nova1-KO mouse cortex and mid- and hind-brain	We sequenced mRNA from E18.5 mouse cortex (3 wild-type vs 3 Nova2-/- and 3 wild-type vs 3 Nova1-/-) and from E18.5 mouse mid- and hind-brain (3 wild-type vs 3 Nova1-/-) to compare gene expression level and alternative splicing events between wild-type and Nova mutant mice. Overall design: Mouse cortex or mid- and hind-brain mRNA profiles of embryonic 18.5 day wild type (WT), Nova2-/-, and Nova1-/- mice were generated by deep sequencing using Illumina Hiseq2500.		GSM2154676: RNAseq_Nova1-KO2_cortex; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Trizol extraction Illumina High-throughput TruSeq RNA Sample preparation: ribozero selection	Illumina HiSeq 2500	developmental stage;;E18.5|genotype;;Nova1-ko|source_name;;cortex|strain background;;CD1|tissue compartment;;cortex|tissue;;brain	GEO Accession;;GSM2154676		GSM2154676	RNAseq_Nova1-KO2_cortex	14287017500	57148070	2016-05-26 12:42:59	7847776409	14287017500	57148070	2	57148070	index:0,count:57148070,average:125,stdev:0|index:1,count:57148070,average:125,stdev:0	GSM2154676_r1						2.08	2.79	0.5	9607204226	9324792676	8610843463	8378189341	97.06	97.3	50626227	47637391	220.692	932.770	160	372937	47.36	53.23	60663714	23974247	60663714	23974247	51.12	50.33	60663714	25881220	60663714	22666250	3944194157	41.05	1.85	0	9.78	0	0.73	0	0.45	0	0.00	0	10.24	0	50626227	0	250	0	246.25	0	2.43	0	0.02	0	2.10	0	0.02	0	179.37	0	0.46	0	1058878	0	57148070	0	5588839	0	417192	0	255455	0	0	0	5849196	0	10523	0	0	0	211051	0	12065845	0	87364	0	12374783	0	78.81	0	45037388	0	254136	10205481	40.157557370857	57148070.0	50626227.0	1058878.0	5588839.0	417192.0	255455.0	0.0	5849196.0	45037388.0	88.6	1.9	9.8	0.7	0.4	0.0	10.2	78.8	125	125	125.00	24	7143508750	26.9	23.1	23.0	27.0	0.0	34.6	25.2	bulk
1676093	SRR3532933	SRP059295	SRS1440217	SRX1767525	SRA272264	GEO		RNAseq in E18.5 wild-type, Nova2-KO, and Nova1-KO mouse cortex and mid- and hind-brain	We sequenced mRNA from E18.5 mouse cortex (3 wild-type vs 3 Nova2-/- and 3 wild-type vs 3 Nova1-/-) and from E18.5 mouse mid- and hind-brain (3 wild-type vs 3 Nova1-/-) to compare gene expression level and alternative splicing events between wild-type and Nova mutant mice. Overall design: Mouse cortex or mid- and hind-brain mRNA profiles of embryonic 18.5 day wild type (WT), Nova2-/-, and Nova1-/- mice were generated by deep sequencing using Illumina Hiseq2500.		GSM2154677: RNAseq_Nova1-KO3_cortex; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Trizol extraction Illumina High-throughput TruSeq RNA Sample preparation: ribozero selection	Illumina HiSeq 2500	developmental stage;;E18.5|genotype;;Nova1-ko|source_name;;cortex|strain background;;CD1|tissue compartment;;cortex|tissue;;brain	GEO Accession;;GSM2154677		GSM2154677	RNAseq_Nova1-KO3_cortex	12118093250	48472373	2016-05-26 12:42:59	6837764870	12118093250	48472373	2	48472373	index:0,count:48472373,average:125,stdev:0|index:1,count:48472373,average:125,stdev:0	GSM2154677_r1						2.19	2.85	0.42	7839239842	7616634322	6998118376	6814560551	97.16	97.38	41805990	39194673	220.103	981.575	139	308845	47.69	53.83	50685382	19936859	50685382	19936859	51.55	50.75	50685382	21552326	50685382	18795807	3164892638	40.37	1.92	0	9.84	0	0.84	0	0.41	0	0.00	0	12.50	0	41805990	0	250	0	245.59	0	2.42	0	0.02	0	2.11	0	0.02	0	209.74	0	0.49	0	930743	0	48472373	0	4768739	0	406825	0	200736	0	0	0	6058822	0	8143	0	0	0	180112	0	9770791	0	70816	0	10029862	0	76.41	0	37037251	0	239109	8194207	34.269755634460	48472373.0	41805990.0	930743.0	4768739.0	406825.0	200736.0	0.0	6058822.0	37037251.0	86.2	1.9	9.8	0.8	0.4	0.0	12.5	76.4	125	125	125.00	24	6059046625	26.9	23.1	23.0	27.0	0.0	34.2	24.7	bulk
1676109	SRR3532934	SRP059295	SRS1440218	SRX1767526	SRA272264	GEO		RNAseq in E18.5 wild-type, Nova2-KO, and Nova1-KO mouse cortex and mid- and hind-brain	We sequenced mRNA from E18.5 mouse cortex (3 wild-type vs 3 Nova2-/- and 3 wild-type vs 3 Nova1-/-) and from E18.5 mouse mid- and hind-brain (3 wild-type vs 3 Nova1-/-) to compare gene expression level and alternative splicing events between wild-type and Nova mutant mice. Overall design: Mouse cortex or mid- and hind-brain mRNA profiles of embryonic 18.5 day wild type (WT), Nova2-/-, and Nova1-/- mice were generated by deep sequencing using Illumina Hiseq2500.		GSM2154678: RNAseq_WT4_midhindbrain; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Trizol extraction Illumina High-throughput TruSeq RNA Sample preparation: ribozero selection	Illumina HiSeq 2500	developmental stage;;E18.5|genotype;;wild-type|source_name;;mid- and hind-brain|strain background;;CD1|tissue compartment;;mid- and hind-brain|tissue;;brain	GEO Accession;;GSM2154678		GSM2154678	RNAseq_WT4_midhindbrain	12745142000	50980568	2016-05-26 12:42:59	7035327833	12745142000	50980568	2	50980568	index:0,count:50980568,average:125,stdev:0|index:1,count:50980568,average:125,stdev:0	GSM2154678_r1						3.3	3.05	0.22	8799153521	8572527828	7697032438	7511303927	97.42	97.59	45330388	42176391	231.842	1005.203	160	335784	53.9	62.24	55001715	24434290	55001715	24434290	59.16	59.1	55001715	26818397	55001715	23201048	2812300321	31.96	1.64	0	11.92	0	0.60	0	0.39	0	0.00	0	10.09	0	45330388	0	250	0	246.46	0	2.39	0	0.02	0	2.06	0	0.02	0	171.20	0	0.47	0	835005	0	50980568	0	6074427	0	304298	0	199907	0	0	0	5145975	0	10929	0	0	0	168629	0	12383630	0	78920	0	12642108	0	77.00	0	39255961	0	248381	10693184	43.051537758524	50980568.0	45330388.0	835005.0	6074427.0	304298.0	199907.0	0.0	5145975.0	39255961.0	88.9	1.6	11.9	0.6	0.4	0.0	10.1	77.0	125	125	125.00	24	6372571000	26.6	23.4	23.2	26.9	0.0	34.6	25.1	bulk
1676125	SRR3532935	SRP059295	SRS1440219	SRX1767527	SRA272264	GEO		RNAseq in E18.5 wild-type, Nova2-KO, and Nova1-KO mouse cortex and mid- and hind-brain	We sequenced mRNA from E18.5 mouse cortex (3 wild-type vs 3 Nova2-/- and 3 wild-type vs 3 Nova1-/-) and from E18.5 mouse mid- and hind-brain (3 wild-type vs 3 Nova1-/-) to compare gene expression level and alternative splicing events between wild-type and Nova mutant mice. Overall design: Mouse cortex or mid- and hind-brain mRNA profiles of embryonic 18.5 day wild type (WT), Nova2-/-, and Nova1-/- mice were generated by deep sequencing using Illumina Hiseq2500.		GSM2154679: RNAseq_WT5_midhindbrain; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Trizol extraction Illumina High-throughput TruSeq RNA Sample preparation: ribozero selection	Illumina HiSeq 2500	developmental stage;;E18.5|genotype;;wild-type|source_name;;mid- and hind-brain|strain background;;CD1|tissue compartment;;mid- and hind-brain|tissue;;brain	GEO Accession;;GSM2154679		GSM2154679	RNAseq_WT5_midhindbrain	12136617250	48546469	2016-05-26 12:42:59	6701350679	12136617250	48546469	2	48546469	index:0,count:48546469,average:125,stdev:0|index:1,count:48546469,average:125,stdev:0	GSM2154679_r1						2.74	3.09	0.34	8135358557	7902781906	7213884484	7021864893	97.14	97.34	42887967	40094504	221.118	979.786	160	329873	51.68	58.79	51542610	22166622	51542610	22166622	55.97	55.89	51542610	24004918	51542610	21075035	2879203542	35.39	1.74	0	10.68	0	0.60	0	0.46	0	0.00	0	10.60	0	42887967	0	250	0	246.34	0	2.38	0	0.02	0	2.08	0	0.02	0	156.32	0	0.47	0	844149	0	48546469	0	5183020	0	291104	0	222127	0	0	0	5145271	0	10224	0	0	0	171655	0	11440424	0	78349	0	11700652	0	77.67	0	37704947	0	242853	9633645	39.668626700103	48546469.0	42887967.0	844149.0	5183020.0	291104.0	222127.0	0.0	5145271.0	37704947.0	88.3	1.7	10.7	0.6	0.5	0.0	10.6	77.7	125	125	125.00	24	6068308625	26.8	23.2	23.0	27.0	0.0	34.5	25.0	bulk
1676141	SRR3532936	SRP059295	SRS1440220	SRX1767528	SRA272264	GEO		RNAseq in E18.5 wild-type, Nova2-KO, and Nova1-KO mouse cortex and mid- and hind-brain	We sequenced mRNA from E18.5 mouse cortex (3 wild-type vs 3 Nova2-/- and 3 wild-type vs 3 Nova1-/-) and from E18.5 mouse mid- and hind-brain (3 wild-type vs 3 Nova1-/-) to compare gene expression level and alternative splicing events between wild-type and Nova mutant mice. Overall design: Mouse cortex or mid- and hind-brain mRNA profiles of embryonic 18.5 day wild type (WT), Nova2-/-, and Nova1-/- mice were generated by deep sequencing using Illumina Hiseq2500.		GSM2154680: RNAseq_WT6_midhindbrain; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Trizol extraction Illumina High-throughput TruSeq RNA Sample preparation: ribozero selection	Illumina HiSeq 2500	developmental stage;;E18.5|genotype;;wild-type|source_name;;mid- and hind-brain|strain background;;CD1|tissue compartment;;mid- and hind-brain|tissue;;brain	GEO Accession;;GSM2154680		GSM2154680	RNAseq_WT6_midhindbrain	13866006750	55464027	2016-05-26 12:42:59	7550088769	13866006750	55464027	2	55464027	index:0,count:55464027,average:125,stdev:0|index:1,count:55464027,average:125,stdev:0	GSM2154680_r1						2.95	3.13	0.24	9501130011	9242094163	8506739041	8293322992	97.27	97.49	49898553	46730074	220.171	934.982	160	384284	52.92	59.53	59102098	26406949	59102098	26406949	56.74	56.68	59102098	28312330	59102098	25144785	3335663693	35.11	1.80	0	9.98	0	0.49	0	0.44	0	0.00	0	9.11	0	49898553	0	250	0	246.58	0	2.38	0	0.02	0	2.00	0	0.02	0	217.27	0	0.45	0	996785	0	55464027	0	5536434	0	269569	0	242736	0	0	0	5053169	0	12501	0	0	0	194461	0	13807647	0	96742	0	14111351	0	79.98	0	44362119	0	260553	11620985	44.601232762624	55464027.0	49898553.0	996785.0	5536434.0	269569.0	242736.0	0.0	5053169.0	44362119.0	90.0	1.8	10.0	0.5	0.4	0.0	9.1	80.0	125	125	125.00	24	6933003375	26.9	23.0	22.8	27.2	0.0	34.6	25.2	bulk
1676158	SRR3532937	SRP059295	SRS1440221	SRX1767529	SRA272264	GEO		RNAseq in E18.5 wild-type, Nova2-KO, and Nova1-KO mouse cortex and mid- and hind-brain	We sequenced mRNA from E18.5 mouse cortex (3 wild-type vs 3 Nova2-/- and 3 wild-type vs 3 Nova1-/-) and from E18.5 mouse mid- and hind-brain (3 wild-type vs 3 Nova1-/-) to compare gene expression level and alternative splicing events between wild-type and Nova mutant mice. Overall design: Mouse cortex or mid- and hind-brain mRNA profiles of embryonic 18.5 day wild type (WT), Nova2-/-, and Nova1-/- mice were generated by deep sequencing using Illumina Hiseq2500.		GSM2154681: RNAseq_Nova1-KO1_midhindbrain; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Trizol extraction Illumina High-throughput TruSeq RNA Sample preparation: ribozero selection	Illumina HiSeq 2500	developmental stage;;E18.5|genotype;;Nova1-ko|source_name;;mid- and hind-brain|strain background;;CD1|tissue compartment;;mid- and hind-brain|tissue;;brain	GEO Accession;;GSM2154681		GSM2154681	RNAseq_Nova1-KO1_midhindbrain	16099683750	64398735	2016-05-26 12:42:59	8789281420	16099683750	64398735	2	64398735	index:0,count:64398735,average:125,stdev:0|index:1,count:64398735,average:125,stdev:0	GSM2154681_r1						2.66	3.18	0.22	11012453674	10675220467	9945988252	9662287258	96.94	97.15	58161051	54687535	216.819	900.826	160	462616	51.14	56.97	68033662	29745104	68033662	29745104	54.65	54.32	68033662	31784367	68033662	28360044	4122439348	37.43	1.75	0	9.24	0	0.46	0	0.45	0	0.00	0	8.78	0	58161051	0	250	0	246.66	0	2.41	0	0.02	0	2.01	0	0.02	0	158.03	0	0.46	0	1126329	0	64398735	0	5953214	0	293840	0	291433	0	0	0	5652411	0	13958	0	0	0	220856	0	15662015	0	112184	0	16009013	0	81.07	0	52207837	0	273890	13108864	47.861783927854	64398735.0	58161051.0	1126329.0	5953214.0	293840.0	291433.0	0.0	5652411.0	52207837.0	90.3	1.7	9.2	0.5	0.5	0.0	8.8	81.1	125	125	125.00	24	8049841875	27.0	22.9	22.8	27.3	0.0	34.6	25.2	bulk
1676175	SRR3532938	SRP059295	SRS1440223	SRX1767530	SRA272264	GEO		RNAseq in E18.5 wild-type, Nova2-KO, and Nova1-KO mouse cortex and mid- and hind-brain	We sequenced mRNA from E18.5 mouse cortex (3 wild-type vs 3 Nova2-/- and 3 wild-type vs 3 Nova1-/-) and from E18.5 mouse mid- and hind-brain (3 wild-type vs 3 Nova1-/-) to compare gene expression level and alternative splicing events between wild-type and Nova mutant mice. Overall design: Mouse cortex or mid- and hind-brain mRNA profiles of embryonic 18.5 day wild type (WT), Nova2-/-, and Nova1-/- mice were generated by deep sequencing using Illumina Hiseq2500.		GSM2154682: RNAseq_Nova1-KO2_midhindbrain; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Trizol extraction Illumina High-throughput TruSeq RNA Sample preparation: ribozero selection	Illumina HiSeq 2500	developmental stage;;E18.5|genotype;;Nova1-ko|source_name;;mid- and hind-brain|strain background;;CD1|tissue compartment;;mid- and hind-brain|tissue;;brain	GEO Accession;;GSM2154682		GSM2154682	RNAseq_Nova1-KO2_midhindbrain	12687851000	50751404	2016-05-26 12:42:59	6992385785	12687851000	50751404	2	50751404	index:0,count:50751404,average:125,stdev:0|index:1,count:50751404,average:125,stdev:0	GSM2154682_r1						2.56	3.02	0.35	7732671365	7487176973	6906604333	6702320393	96.83	97.04	43512795	40758263	200.170	1003.001	139	387149	49.85	56.12	52870885	21692554	52870885	21692554	53.22	53.31	52870885	23156309	52870885	20607743	2925398141	37.83	2.63	0	9.58	0	0.63	0	0.44	0	0.00	0	13.19	0	43512795	0	250	0	244.81	0	2.36	0	0.02	0	1.94	0	0.02	0	175.00	0	0.47	0	1334569	0	50751404	0	4859652	0	319623	0	224396	0	0	0	6694590	0	10016	0	0	0	147513	0	11107018	0	86903	0	11351450	0	76.16	0	38653143	0	245366	8856677	36.095779366334	50751404.0	43512795.0	1334569.0	4859652.0	319623.0	224396.0	0.0	6694590.0	38653143.0	85.7	2.6	9.6	0.6	0.4	0.0	13.2	76.2	125	125	125.00	24	6343925500	27.4	22.7	22.5	27.3	0.0	34.5	25.0	bulk
1676190	SRR3532939	SRP059295	SRS1440222	SRX1767531	SRA272264	GEO		RNAseq in E18.5 wild-type, Nova2-KO, and Nova1-KO mouse cortex and mid- and hind-brain	We sequenced mRNA from E18.5 mouse cortex (3 wild-type vs 3 Nova2-/- and 3 wild-type vs 3 Nova1-/-) and from E18.5 mouse mid- and hind-brain (3 wild-type vs 3 Nova1-/-) to compare gene expression level and alternative splicing events between wild-type and Nova mutant mice. Overall design: Mouse cortex or mid- and hind-brain mRNA profiles of embryonic 18.5 day wild type (WT), Nova2-/-, and Nova1-/- mice were generated by deep sequencing using Illumina Hiseq2500.		GSM2154683: RNAseq_Nova1-KO3_midhindbrain; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Trizol extraction Illumina High-throughput TruSeq RNA Sample preparation: ribozero selection	Illumina HiSeq 2500	developmental stage;;E18.5|genotype;;Nova1-ko|source_name;;mid- and hind-brain|strain background;;CD1|tissue compartment;;mid- and hind-brain|tissue;;brain	GEO Accession;;GSM2154683		GSM2154683	RNAseq_Nova1-KO3_midhindbrain	12286273000	49145092	2016-05-26 12:42:59	6712804096	12286273000	49145092	2	49145092	index:0,count:49145092,average:125,stdev:0|index:1,count:49145092,average:125,stdev:0	GSM2154683_r1						2.73	3.08	0.26	7458592476	7236791326	6626213372	6442745092	97.03	97.23	41966814	39142328	201.140	1028.709	138	371079	52.17	59.08	51553506	21893658	51553506	21893658	55.78	56.1	51553506	23409873	51553506	20788547	2620292892	35.13	2.56	0	9.99	0	0.63	0	0.43	0	0.00	0	13.55	0	41966814	0	250	0	244.77	0	2.37	0	0.02	0	1.91	0	0.02	0	179.25	0	0.46	0	1257548	0	49145092	0	4909930	0	309262	0	211175	0	0	0	6657841	0	10308	0	0	0	148881	0	11338226	0	87891	0	11585306	0	75.40	0	37056884	0	246254	9017538	36.618848830882	49145092.0	41966814.0	1257548.0	4909930.0	309262.0	211175.0	0.0	6657841.0	37056884.0	85.4	2.6	10.0	0.6	0.4	0.0	13.5	75.4	125	125	125.00	24	6143136500	27.3	22.8	22.7	27.1	0.0	34.5	25.0	bulk
1910858	SRR2063284	SRP059509	SRS961430	SRX1059057	SRA272961	GEO		Genome-wide Circadian Control of Transcription at Active Enhancers Regulates Insulin Secretion and Diabetes Risk	The molecular clock is a transcriptional oscillator present in brain and peripheral cells that coordinates behavior and physiology with the solar cycle. Here we reveal that the clock gates insulin secretion through genome-wide transcriptional control of the pancreatic exocyst across species. Clock transcription factors bind to unique enhancer sites in cycling genes in beta cells that diverge from those in liver, revealing the dynamics of inter-tissue clock control of genomic and physiologic processes important in glucose homeostasis. Overall design: Transcriptome profiling in mouse and human islets at serial 4-hour time intervals by polyA RNA-Seq		GSM1711965: Mouse islet polyA RNA-Seq biological replicate 1 CT0; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Mouse islets were isolated by perfusing the pancreatic bile duct with collagenase Illumina stranded LT kit for RNA-Seq	NextSeq 500	cell type;;Pancreatic islet cells|genotype;;wild type|source_name;;C57BL/6 wild type mice|strain;;C57BL/6	GEO Accession;;GSM1711965		GSM1711965	Mouse islet polyA RNA-Seq biological replicate 1 CT0	12503799388	44829893	2015-11-10 17:09:03	6214012868	12503799388	44829893	2	44829893	index:0,count:44829893,average:138.91,stdev:17.65|index:1,count:44829893,average:140.01,stdev:17.00	GSM1711965_r1				in_mesa	26542580	5.63	3.22	0.05	6452385043	6435061406	5992496040	6003786941	99.73	100.19	39416075	34202204	198.131	1012.886	128	272891	87.35	94.26	43649891	34428954	43649891	34428954	89.98	90.33	43649891	35465005	43649891	32995528	288120226	4.47	0.28	0	6.45	0	0.22	0	0.07	0	0.00	0	11.79	0	39416449	0	278	0	272.61	0	1.95	0	0.01	0	1.24	0	0.01	0	106.53	0	0.78	0	125084	0	44829893	0	2890625	0	99311	0	29407	0	0	0	5284726	0	13329	0	0	0	136532	0	28220910	0	43211	0	28413982	0	81.48	0	36525824	0	217071	18426983	84.889197543661	44829893.0	39416449.0	125084.0	2890625.0	99311.0	29407.0	0.0	5284726.0	36525824.0	87.9	0.3	6.4	0.2	0.1	0.0	11.8	81.5	35	151	138.91	7	6227154776	25.6	24.1	25.2	25.1	0.0	32.9	20.9	bulk
1910873	SRR2063285	SRP059509	SRS961429	SRX1059058	SRA272961	GEO		Genome-wide Circadian Control of Transcription at Active Enhancers Regulates Insulin Secretion and Diabetes Risk	The molecular clock is a transcriptional oscillator present in brain and peripheral cells that coordinates behavior and physiology with the solar cycle. Here we reveal that the clock gates insulin secretion through genome-wide transcriptional control of the pancreatic exocyst across species. Clock transcription factors bind to unique enhancer sites in cycling genes in beta cells that diverge from those in liver, revealing the dynamics of inter-tissue clock control of genomic and physiologic processes important in glucose homeostasis. Overall design: Transcriptome profiling in mouse and human islets at serial 4-hour time intervals by polyA RNA-Seq		GSM1711966: Mouse islet polyA RNA-Seq biological replicate 1 CT4; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Mouse islets were isolated by perfusing the pancreatic bile duct with collagenase Illumina stranded LT kit for RNA-Seq	NextSeq 500	cell type;;Pancreatic islet cells|genotype;;wild type|source_name;;C57BL/6 wild type mice|strain;;C57BL/6	GEO Accession;;GSM1711966		GSM1711966	Mouse islet polyA RNA-Seq biological replicate 1 CT4	9550346890	34369796	2015-11-10 17:09:03	4732016493	9550346890	34369796	2	34369796	index:0,count:34369796,average:138.39,stdev:17.83|index:1,count:34369796,average:139.48,stdev:17.23	GSM1711966_r1				in_mesa	26542580	4.13	3.25	0.05	4902071457	4887447548	4611405354	4616831940	99.7	100.12	30467983	26180998	196.848	1084.549	128	214412	88.17	93.89	33332812	26863269	33332812	26863269	89.57	90.0	33332812	27291294	33332812	25750795	239726429	4.89	0.13	0	5.40	0	0.26	0	0.07	0	0.00	0	11.02	0	30468261	0	277	0	271.68	0	1.82	0	0.01	0	1.24	0	0.00	0	122.75	0	0.76	0	43828	0	34369796	0	1855717	0	89542	0	23367	0	0	0	3788626	0	10423	0	0	0	113140	0	22163833	0	32301	0	22319697	0	83.25	0	28612544	0	213752	14220480	66.527938919870	34369796.0	30468261.0	43828.0	1855717.0	89542.0	23367.0	0.0	3788626.0	28612544.0	88.6	0.1	5.4	0.3	0.1	0.0	11.0	83.2	35	151	138.39	7	4756442731	25.6	24.4	25.1	24.9	0.0	32.9	20.9	bulk
1910889	SRR2063286	SRP059509	SRS961428	SRX1059059	SRA272961	GEO		Genome-wide Circadian Control of Transcription at Active Enhancers Regulates Insulin Secretion and Diabetes Risk	The molecular clock is a transcriptional oscillator present in brain and peripheral cells that coordinates behavior and physiology with the solar cycle. Here we reveal that the clock gates insulin secretion through genome-wide transcriptional control of the pancreatic exocyst across species. Clock transcription factors bind to unique enhancer sites in cycling genes in beta cells that diverge from those in liver, revealing the dynamics of inter-tissue clock control of genomic and physiologic processes important in glucose homeostasis. Overall design: Transcriptome profiling in mouse and human islets at serial 4-hour time intervals by polyA RNA-Seq		GSM1711967: Mouse islet polyA RNA-Seq biological replicate 1 CT8; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Mouse islets were isolated by perfusing the pancreatic bile duct with collagenase Illumina stranded LT kit for RNA-Seq	NextSeq 500	cell type;;Pancreatic islet cells|genotype;;wild type|source_name;;C57BL/6 wild type mice|strain;;C57BL/6	GEO Accession;;GSM1711967		GSM1711967	Mouse islet polyA RNA-Seq biological replicate 1 CT8	9926992414	35915373	2015-11-10 17:09:03	4928604306	9926992414	35915373	2	35915373	index:0,count:35915373,average:137.60,stdev:18.19|index:1,count:35915373,average:138.80,stdev:17.60	GSM1711967_r1				in_mesa	26542580	3.71	3.16	0.05	4996567498	4982338723	4725956571	4730864085	99.72	100.1	31677006	27288635	193.453	1069.626	128	238585	87.76	92.97	34427670	27801237	34427670	27801237	88.73	89.11	34427670	28106994	34427670	26649229	290224655	5.81	0.19	0	4.94	0	0.24	0	0.07	0	0.00	0	11.49	0	31677320	0	276	0	269.99	0	1.80	0	0.01	0	1.20	0	0.01	0	119.50	0	0.76	0	67969	0	35915373	0	1772828	0	85685	0	25346	0	0	0	4127022	0	10357	0	0	0	115679	0	22573255	0	34272	0	22733563	0	83.26	0	29904492	0	216899	14284691	65.858722262436	35915373.0	31677320.0	67969.0	1772828.0	85685.0	25346.0	0.0	4127022.0	29904492.0	88.2	0.2	4.9	0.2	0.1	0.0	11.5	83.3	35	151	137.60	7	4942027474	25.7	24.4	25.2	24.7	0.0	32.9	20.8	bulk
1910907	SRR2063287	SRP059509	SRS961425	SRX1059060	SRA272961	GEO		Genome-wide Circadian Control of Transcription at Active Enhancers Regulates Insulin Secretion and Diabetes Risk	The molecular clock is a transcriptional oscillator present in brain and peripheral cells that coordinates behavior and physiology with the solar cycle. Here we reveal that the clock gates insulin secretion through genome-wide transcriptional control of the pancreatic exocyst across species. Clock transcription factors bind to unique enhancer sites in cycling genes in beta cells that diverge from those in liver, revealing the dynamics of inter-tissue clock control of genomic and physiologic processes important in glucose homeostasis. Overall design: Transcriptome profiling in mouse and human islets at serial 4-hour time intervals by polyA RNA-Seq		GSM1711968: Mouse islet polyA RNA-Seq biological replicate 1 CT12; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Mouse islets were isolated by perfusing the pancreatic bile duct with collagenase Illumina stranded LT kit for RNA-Seq	NextSeq 500	cell type;;Pancreatic islet cells|genotype;;wild type|source_name;;C57BL/6 wild type mice|strain;;C57BL/6	GEO Accession;;GSM1711968		GSM1711968	Mouse islet polyA RNA-Seq biological replicate 1 CT12	7859666572	28093413	2015-11-10 17:09:03	3909023124	7859666572	28093413	2	28093413	index:0,count:28093413,average:139.35,stdev:16.97|index:1,count:28093413,average:140.41,stdev:16.33	GSM1711968_r1				in_mesa	26542580	3.78	3.11	0.05	4027878609	4007969789	3822822715	3817266642	99.51	99.85	24720148	21438019	197.393	1053.765	128	182091	86.65	91.46	26695694	21420407	26695694	21420407	87.45	87.74	26695694	21617226	26695694	20549020	290891470	7.22	0.20	0	4.63	0	0.21	0	0.07	0	0.00	0	11.73	0	24720410	0	279	0	273.45	0	1.76	0	0.01	0	1.22	0	0.01	0	144.69	0	0.78	0	55851	0	28093413	0	1301081	0	57875	0	21037	0	0	0	3294091	0	8048	0	0	0	90507	0	17445556	0	27133	0	17571244	0	83.36	0	23419329	0	205471	11259363	54.797820617021	28093413.0	24720410.0	55851.0	1301081.0	57875.0	21037.0	0.0	3294091.0	23419329.0	88.0	0.2	4.6	0.2	0.1	0.0	11.7	83.4	35	151	139.35	7	3914933178	25.7	24.5	25.2	24.6	0.0	32.8	20.8	bulk
1910924	SRR2063288	SRP059509	SRS961427	SRX1059061	SRA272961	GEO		Genome-wide Circadian Control of Transcription at Active Enhancers Regulates Insulin Secretion and Diabetes Risk	The molecular clock is a transcriptional oscillator present in brain and peripheral cells that coordinates behavior and physiology with the solar cycle. Here we reveal that the clock gates insulin secretion through genome-wide transcriptional control of the pancreatic exocyst across species. Clock transcription factors bind to unique enhancer sites in cycling genes in beta cells that diverge from those in liver, revealing the dynamics of inter-tissue clock control of genomic and physiologic processes important in glucose homeostasis. Overall design: Transcriptome profiling in mouse and human islets at serial 4-hour time intervals by polyA RNA-Seq		GSM1711969: Mouse islet polyA RNA-Seq biological replicate 1 CT16; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Mouse islets were isolated by perfusing the pancreatic bile duct with collagenase Illumina stranded LT kit for RNA-Seq	NextSeq 500	cell type;;Pancreatic islet cells|genotype;;wild type|source_name;;C57BL/6 wild type mice|strain;;C57BL/6	GEO Accession;;GSM1711969		GSM1711969	Mouse islet polyA RNA-Seq biological replicate 1 CT16	6986279816	25294936	2015-11-10 17:09:03	3478265914	6986279816	25294936	2	25294936	index:0,count:25294936,average:137.41,stdev:18.20|index:1,count:25294936,average:138.78,stdev:17.55	GSM1711969_r1				in_mesa	26542580	4.98	3.0	0.04	3441118972	3434870566	3223118886	3231177148	99.82	100.25	21955699	19127145	191.710	991.882	127	169593	87.86	93.97	24068456	19290955	24068456	19290955	89.45	89.88	24068456	19640594	24068456	18451776	160180854	4.65	0.33	0	5.64	0	0.19	0	0.06	0	0.00	0	12.95	0	21955914	0	276	0	269.25	0	2.07	0	0.01	0	1.30	0	0.01	0	58.08	0	0.79	0	83008	0	25294936	0	1426208	0	47290	0	15481	0	0	0	3276251	0	6755	0	0	0	72740	0	15518209	0	24594	0	15622298	0	81.16	0	20529706	0	190516	9762972	51.244892817401	25294936.0	21955914.0	83008.0	1426208.0	47290.0	15481.0	0.0	3276251.0	20529706.0	86.8	0.3	5.6	0.2	0.1	0.0	13.0	81.2	35	151	137.41	7	3475822634	25.7	24.3	25.5	24.6	0.0	32.8	20.8	bulk
1910940	SRR2063289	SRP059509	SRS961426	SRX1059062	SRA272961	GEO		Genome-wide Circadian Control of Transcription at Active Enhancers Regulates Insulin Secretion and Diabetes Risk	The molecular clock is a transcriptional oscillator present in brain and peripheral cells that coordinates behavior and physiology with the solar cycle. Here we reveal that the clock gates insulin secretion through genome-wide transcriptional control of the pancreatic exocyst across species. Clock transcription factors bind to unique enhancer sites in cycling genes in beta cells that diverge from those in liver, revealing the dynamics of inter-tissue clock control of genomic and physiologic processes important in glucose homeostasis. Overall design: Transcriptome profiling in mouse and human islets at serial 4-hour time intervals by polyA RNA-Seq		GSM1711970: Mouse islet polyA RNA-Seq biological replicate 1 CT020; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Mouse islets were isolated by perfusing the pancreatic bile duct with collagenase Illumina stranded LT kit for RNA-Seq	NextSeq 500	cell type;;Pancreatic islet cells|genotype;;wild type|source_name;;C57BL/6 wild type mice|strain;;C57BL/6	GEO Accession;;GSM1711970		GSM1711970	Mouse islet polyA RNA-Seq biological replicate 1 CT020	5926118028	21567597	2015-11-10 17:09:03	2943124080	5926118028	21567597	2	21567597	index:0,count:21567597,average:136.73,stdev:19.03|index:1,count:21567597,average:138.04,stdev:18.43	GSM1711970_r1				in_mesa	26542580	4.14	3.1	0.05	2998519373	2985324827	2834600395	2832605787	99.56	99.93	18988696	16471208	193.093	1041.593	127	138347	87.63	92.89	20610378	16640169	20610378	16640169	88.82	89.18	20610378	16865857	20610378	15977154	173150244	5.77	0.21	0	4.98	0	0.20	0	0.07	0	0.00	0	11.69	0	18988890	0	274	0	268.09	0	1.79	0	0.01	0	1.24	0	0.01	0	60.10	0	0.77	0	44607	0	21567597	0	1074247	0	43072	0	15134	0	0	0	2520501	0	6276	0	0	0	67048	0	13495962	0	21423	0	13590709	0	83.06	0	17914643	0	189937	8577559	45.160021480807	21567597.0	18988890.0	44607.0	1074247.0	43072.0	15134.0	0.0	2520501.0	17914643.0	88.0	0.2	5.0	0.2	0.1	0.0	11.7	83.1	35	151	136.73	7	2948891533	25.6	24.4	25.3	24.6	0.0	32.9	20.8	bulk
1911052	SRR2063290	SRP059509	SRS961424	SRX1059063	SRA272961	GEO		Genome-wide Circadian Control of Transcription at Active Enhancers Regulates Insulin Secretion and Diabetes Risk	The molecular clock is a transcriptional oscillator present in brain and peripheral cells that coordinates behavior and physiology with the solar cycle. Here we reveal that the clock gates insulin secretion through genome-wide transcriptional control of the pancreatic exocyst across species. Clock transcription factors bind to unique enhancer sites in cycling genes in beta cells that diverge from those in liver, revealing the dynamics of inter-tissue clock control of genomic and physiologic processes important in glucose homeostasis. Overall design: Transcriptome profiling in mouse and human islets at serial 4-hour time intervals by polyA RNA-Seq		GSM1711971: Mouse islet polyA RNA-Seq biological replicate 1 CT24; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Mouse islets were isolated by perfusing the pancreatic bile duct with collagenase Illumina stranded LT kit for RNA-Seq	NextSeq 500	cell type;;Pancreatic islet cells|genotype;;wild type|source_name;;C57BL/6 wild type mice|strain;;C57BL/6	GEO Accession;;GSM1711971		GSM1711971	Mouse islet polyA RNA-Seq biological replicate 1 CT24	11676381709	42404469	2015-11-10 17:09:03	5820912191	11676381709	42404469	2	42404469	index:0,count:42404469,average:137.03,stdev:18.66|index:1,count:42404469,average:138.33,stdev:18.06	GSM1711971_r1				in_mesa	26542580	4.86	2.99	0.04	5771022097	5765919703	5402919554	5420034377	99.91	100.32	36924409	32238208	192.467	974.065	127	275706	89.06	95.33	40524312	32885439	40524312	32885439	91.04	91.49	40524312	33615249	40524312	31560003	203630006	3.53	0.28	0	5.73	0	0.20	0	0.05	0	0.00	0	12.67	0	36924776	0	275	0	268.41	0	1.82	0	0.01	0	1.23	0	0.01	0	122.32	0	0.78	0	118460	0	42404469	0	2429920	0	82743	0	23138	0	0	0	5373812	0	11671	0	0	0	121996	0	26506425	0	41210	0	26681302	0	81.35	0	34494856	0	216889	16734556	77.157237112071	42404469.0	36924776.0	118460.0	2429920.0	82743.0	23138.0	0.0	5373812.0	34494856.0	87.1	0.3	5.7	0.2	0.1	0.0	12.7	81.3	35	151	137.03	7	5810620418	25.7	24.4	25.5	24.3	0.0	32.7	20.6	bulk
1911068	SRR2063291	SRP059509	SRS961423	SRX1059064	SRA272961	GEO		Genome-wide Circadian Control of Transcription at Active Enhancers Regulates Insulin Secretion and Diabetes Risk	The molecular clock is a transcriptional oscillator present in brain and peripheral cells that coordinates behavior and physiology with the solar cycle. Here we reveal that the clock gates insulin secretion through genome-wide transcriptional control of the pancreatic exocyst across species. Clock transcription factors bind to unique enhancer sites in cycling genes in beta cells that diverge from those in liver, revealing the dynamics of inter-tissue clock control of genomic and physiologic processes important in glucose homeostasis. Overall design: Transcriptome profiling in mouse and human islets at serial 4-hour time intervals by polyA RNA-Seq		GSM1711972: Mouse islet polyA RNA-Seq biological replicate 1 CT28; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Mouse islets were isolated by perfusing the pancreatic bile duct with collagenase Illumina stranded LT kit for RNA-Seq	NextSeq 500	cell type;;Pancreatic islet cells|genotype;;wild type|source_name;;C57BL/6 wild type mice|strain;;C57BL/6	GEO Accession;;GSM1711972		GSM1711972	Mouse islet polyA RNA-Seq biological replicate 1 CT28	8797308220	32005649	2015-11-10 17:09:03	4380285960	8797308220	32005649	2	32005649	index:0,count:32005649,average:136.75,stdev:19.09|index:1,count:32005649,average:138.12,stdev:18.44	GSM1711972_r1				in_mesa	26542580	4.56	3.19	0.05	4462178156	4452428275	4188404612	4196862935	99.78	100.2	28134414	24478313	193.965	989.677	127	203221	88.27	94.26	30835776	24833382	30835776	24833382	89.91	90.37	30835776	25294733	30835776	23808005	200748039	4.50	0.14	0	5.59	0	0.20	0	0.06	0	0.00	0	11.83	0	28134674	0	274	0	268.21	0	1.86	0	0.01	0	1.26	0	0.01	0	120.52	0	0.78	0	45298	0	32005649	0	1788912	0	63910	0	20217	0	0	0	3786848	0	9065	0	0	0	95390	0	19829353	0	30285	0	19964093	0	82.32	0	26345762	0	206425	12700622	61.526568971782	32005649.0	28134674.0	45298.0	1788912.0	63910.0	20217.0	0.0	3786848.0	26345762.0	87.9	0.1	5.6	0.2	0.1	0.0	11.8	82.3	35	151	136.75	7	4376657350	25.7	24.4	25.2	24.7	0.0	32.8	20.7	bulk
1911086	SRR2063292	SRP059509	SRS961422	SRX1059065	SRA272961	GEO		Genome-wide Circadian Control of Transcription at Active Enhancers Regulates Insulin Secretion and Diabetes Risk	The molecular clock is a transcriptional oscillator present in brain and peripheral cells that coordinates behavior and physiology with the solar cycle. Here we reveal that the clock gates insulin secretion through genome-wide transcriptional control of the pancreatic exocyst across species. Clock transcription factors bind to unique enhancer sites in cycling genes in beta cells that diverge from those in liver, revealing the dynamics of inter-tissue clock control of genomic and physiologic processes important in glucose homeostasis. Overall design: Transcriptome profiling in mouse and human islets at serial 4-hour time intervals by polyA RNA-Seq		GSM1711973: Mouse islet polyA RNA-Seq biological replicate 1 CT32; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Mouse islets were isolated by perfusing the pancreatic bile duct with collagenase Illumina stranded LT kit for RNA-Seq	NextSeq 500	cell type;;Pancreatic islet cells|genotype;;wild type|source_name;;C57BL/6 wild type mice|strain;;C57BL/6	GEO Accession;;GSM1711973		GSM1711973	Mouse islet polyA RNA-Seq biological replicate 1 CT32	4922015640	17869953	2015-11-10 17:09:03	2453053994	4922015640	17869953	2	17869953	index:0,count:17869953,average:137.07,stdev:18.85|index:1,count:17869953,average:138.36,stdev:18.23	GSM1711973_r1				in_mesa	26542580	3.94	3.09	0.06	2484527058	2469948420	2357362317	2351988172	99.41	99.77	15641358	13657952	192.196	1004.892	127	115123	85.93	90.72	16890538	13440654	16890538	13440654	86.78	87.05	16890538	13573582	16890538	12895704	196308239	7.90	0.15	0	4.63	0	0.21	0	0.08	0	0.00	0	12.18	0	15641497	0	275	0	268.73	0	1.75	0	0.01	0	1.20	0	0.01	0	103.26	0	0.77	0	27160	0	17869953	0	826576	0	36928	0	14146	0	0	0	2177382	0	4902	0	0	0	54276	0	10681597	0	17087	0	10757862	0	82.90	0	14814921	0	181243	6817960	37.617783859239	17869953.0	15641497.0	27160.0	826576.0	36928.0	14146.0	0.0	2177382.0	14814921.0	87.5	0.2	4.6	0.2	0.1	0.0	12.2	82.9	35	151	137.07	7	2449511423	26.0	24.3	25.2	24.6	0.0	32.8	20.7	bulk
1911101	SRR2063293	SRP059509	SRS961421	SRX1059066	SRA272961	GEO		Genome-wide Circadian Control of Transcription at Active Enhancers Regulates Insulin Secretion and Diabetes Risk	The molecular clock is a transcriptional oscillator present in brain and peripheral cells that coordinates behavior and physiology with the solar cycle. Here we reveal that the clock gates insulin secretion through genome-wide transcriptional control of the pancreatic exocyst across species. Clock transcription factors bind to unique enhancer sites in cycling genes in beta cells that diverge from those in liver, revealing the dynamics of inter-tissue clock control of genomic and physiologic processes important in glucose homeostasis. Overall design: Transcriptome profiling in mouse and human islets at serial 4-hour time intervals by polyA RNA-Seq		GSM1711974: Mouse islet polyA RNA-Seq biological replicate 1 CT36; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Mouse islets were isolated by perfusing the pancreatic bile duct with collagenase Illumina stranded LT kit for RNA-Seq	NextSeq 500	cell type;;Pancreatic islet cells|genotype;;wild type|source_name;;C57BL/6 wild type mice|strain;;C57BL/6	GEO Accession;;GSM1711974		GSM1711974	Mouse islet polyA RNA-Seq biological replicate 1 CT36	6699706719	24344916	2015-11-10 17:09:03	3346832127	6699706719	24344916	2	24344916	index:0,count:24344916,average:137.07,stdev:18.81|index:1,count:24344916,average:138.13,stdev:18.28	GSM1711974_r1				in_mesa	26542580	3.45	3.28	0.06	3349206067	3332153501	3169074172	3166246931	99.49	99.91	21317169	18411326	190.898	1045.053	127	157237	86.27	91.35	23181130	18391220	23181130	18391220	87.15	87.53	23181130	18579096	23181130	17622632	247152942	7.38	0.14	0	4.87	0	0.24	0	0.08	0	0.00	0	12.11	0	21317365	0	275	0	268.17	0	1.72	0	0.01	0	1.19	0	0.01	0	117.32	0	0.80	0	35160	0	24344916	0	1184630	0	59186	0	19614	0	0	0	2948751	0	7024	0	0	0	75829	0	14702151	0	21224	0	14806228	0	82.70	0	20132735	0	202369	9322406	46.066373802312	24344916.0	21317365.0	35160.0	1184630.0	59186.0	19614.0	0.0	2948751.0	20132735.0	87.6	0.1	4.9	0.2	0.1	0.0	12.1	82.7	35	151	137.07	7	3336918857	25.9	24.3	24.9	24.9	0.0	32.7	20.6	bulk
1911116	SRR2063294	SRP059509	SRS961420	SRX1059067	SRA272961	GEO		Genome-wide Circadian Control of Transcription at Active Enhancers Regulates Insulin Secretion and Diabetes Risk	The molecular clock is a transcriptional oscillator present in brain and peripheral cells that coordinates behavior and physiology with the solar cycle. Here we reveal that the clock gates insulin secretion through genome-wide transcriptional control of the pancreatic exocyst across species. Clock transcription factors bind to unique enhancer sites in cycling genes in beta cells that diverge from those in liver, revealing the dynamics of inter-tissue clock control of genomic and physiologic processes important in glucose homeostasis. Overall design: Transcriptome profiling in mouse and human islets at serial 4-hour time intervals by polyA RNA-Seq		GSM1711975: Mouse islet polyA RNA-Seq biological replicate 1 CT40; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Mouse islets were isolated by perfusing the pancreatic bile duct with collagenase Illumina stranded LT kit for RNA-Seq	NextSeq 500	cell type;;Pancreatic islet cells|genotype;;wild type|source_name;;C57BL/6 wild type mice|strain;;C57BL/6	GEO Accession;;GSM1711975		GSM1711975	Mouse islet polyA RNA-Seq biological replicate 1 CT40	6047314974	22149672	2015-11-10 17:09:03	3024445491	6047314974	22149672	2	22149672	index:0,count:22149672,average:135.68,stdev:19.45|index:1,count:22149672,average:137.35,stdev:18.76	GSM1711975_r1				in_mesa	26542580	4.56	3.16	0.06	2944427609	2930335447	2763627485	2762707895	99.52	99.97	19249938	16767611	186.435	988.818	128	151642	86.77	92.57	21069819	16703144	21069819	16703144	88.35	88.73	21069819	17007697	21069819	16011298	180558380	6.13	0.15	0	5.44	0	0.21	0	0.07	0	0.00	0	12.80	0	19250142	0	273	0	265.85	0	1.80	0	0.01	0	1.21	0	0.01	0	123.63	0	0.80	0	32596	0	22149672	0	1205586	0	47515	0	15996	0	0	0	2836019	0	5969	0	0	0	64672	0	13015894	0	20165	0	13106700	0	81.47	0	18044556	0	186211	8073185	43.355038101938	22149672.0	19250142.0	32596.0	1205586.0	47515.0	15996.0	0.0	2836019.0	18044556.0	86.9	0.1	5.4	0.2	0.1	0.0	12.8	81.5	35	151	135.68	7	3005162944	26.0	24.0	25.0	24.9	0.0	32.8	20.7	bulk
1911133	SRR2063295	SRP059509	SRS961419	SRX1059068	SRA272961	GEO		Genome-wide Circadian Control of Transcription at Active Enhancers Regulates Insulin Secretion and Diabetes Risk	The molecular clock is a transcriptional oscillator present in brain and peripheral cells that coordinates behavior and physiology with the solar cycle. Here we reveal that the clock gates insulin secretion through genome-wide transcriptional control of the pancreatic exocyst across species. Clock transcription factors bind to unique enhancer sites in cycling genes in beta cells that diverge from those in liver, revealing the dynamics of inter-tissue clock control of genomic and physiologic processes important in glucose homeostasis. Overall design: Transcriptome profiling in mouse and human islets at serial 4-hour time intervals by polyA RNA-Seq		GSM1711976: Mouse islet polyA RNA-Seq biological replicate 1 CT44; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Mouse islets were isolated by perfusing the pancreatic bile duct with collagenase Illumina stranded LT kit for RNA-Seq	NextSeq 500	cell type;;Pancreatic islet cells|genotype;;wild type|source_name;;C57BL/6 wild type mice|strain;;C57BL/6	GEO Accession;;GSM1711976		GSM1711976	Mouse islet polyA RNA-Seq biological replicate 1 CT44	8058438218	29287888	2015-11-10 17:09:03	4019721223	8058438218	29287888	2	29287888	index:0,count:29287888,average:136.90,stdev:18.93|index:1,count:29287888,average:138.24,stdev:18.31	GSM1711976_r1				in_mesa	26542580	5.12	3.12	0.05	4051296272	4030676543	3812853553	3808312592	99.49	99.88	25546633	22286674	191.354	1002.069	127	185731	86.83	92.42	27793245	22181939	27793245	22181939	88.37	88.68	27793245	22574714	27793245	21284434	249293889	6.15	0.15	0	5.27	0	0.17	0	0.07	0	0.00	0	12.53	0	25546877	0	275	0	268.28	0	1.85	0	0.01	0	1.24	0	0.01	0	107.15	0	0.78	0	43662	0	29287888	0	1544807	0	49608	0	20314	0	0	0	3671089	0	7913	0	0	0	88093	0	17682752	0	28006	0	17806764	0	81.95	0	24002070	0	198602	11267852	56.735843546389	29287888.0	25546877.0	43662.0	1544807.0	49608.0	20314.0	0.0	3671089.0	24002070.0	87.2	0.1	5.3	0.2	0.1	0.0	12.5	82.0	35	151	136.90	7	4009646144	26.2	24.0	25.0	24.8	0.0	32.8	20.6	bulk
1911148	SRR2063296	SRP059509	SRS961418	SRX1059069	SRA272961	GEO		Genome-wide Circadian Control of Transcription at Active Enhancers Regulates Insulin Secretion and Diabetes Risk	The molecular clock is a transcriptional oscillator present in brain and peripheral cells that coordinates behavior and physiology with the solar cycle. Here we reveal that the clock gates insulin secretion through genome-wide transcriptional control of the pancreatic exocyst across species. Clock transcription factors bind to unique enhancer sites in cycling genes in beta cells that diverge from those in liver, revealing the dynamics of inter-tissue clock control of genomic and physiologic processes important in glucose homeostasis. Overall design: Transcriptome profiling in mouse and human islets at serial 4-hour time intervals by polyA RNA-Seq		GSM1711977: Mouse islet polyA RNA-Seq biological replicate 2 CT0; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Mouse islets were isolated by perfusing the pancreatic bile duct with collagenase Illumina stranded LT kit for RNA-Seq	NextSeq 500	cell type;;Pancreatic islet cells|genotype;;wild type|source_name;;C57BL/6 wild type mice|strain;;C57BL/6	GEO Accession;;GSM1711977		GSM1711977	Mouse islet polyA RNA-Seq biological replicate 2 CT0	4233181872	28055847	2015-11-10 17:09:03	1781188127	4233181872	28055847	2	28055847	index:0,count:28055847,average:75.44,stdev:1.40|index:1,count:28055847,average:75.44,stdev:1.42	GSM1711977_r1				in_mesa	26542580	5.01	3.11	0.05	3543903315	3531613124	3292968931	3299909960	99.65	100.21	27170599	25830356	158.043	432.807	126	344507	87.31	94.05	30168470	23724353	30168470	23724353	90.26	90.76	30168470	24525777	30168470	22895184	161845483	4.57	0.20	0	6.93	0	0.25	0	0.09	0	0.00	0	2.81	0	27171444	0	150	0	149.65	0	1.90	0	0.01	0	1.25	0	0.01	0	306.06	0	0.37	0	55677	0	28055847	0	1945492	0	70004	0	26378	0	0	0	788021	0	4130	0	0	0	42727	0	9193166	0	15253	0	9255276	0	89.91	0	25225952	0	183008	8796152	48.064303199860	28055847.0	27171444.0	55677.0	1945492.0	70004.0	26378.0	0.0	788021.0	25225952.0	96.8	0.2	6.9	0.2	0.1	0.0	2.8	89.9	35	76	75.44	7	2116624699	25.0	24.3	25.4	25.3	0.0	34.9	24.3	bulk
1911165	SRR2063297	SRP059509	SRS961417	SRX1059070	SRA272961	GEO		Genome-wide Circadian Control of Transcription at Active Enhancers Regulates Insulin Secretion and Diabetes Risk	The molecular clock is a transcriptional oscillator present in brain and peripheral cells that coordinates behavior and physiology with the solar cycle. Here we reveal that the clock gates insulin secretion through genome-wide transcriptional control of the pancreatic exocyst across species. Clock transcription factors bind to unique enhancer sites in cycling genes in beta cells that diverge from those in liver, revealing the dynamics of inter-tissue clock control of genomic and physiologic processes important in glucose homeostasis. Overall design: Transcriptome profiling in mouse and human islets at serial 4-hour time intervals by polyA RNA-Seq		GSM1711978: Mouse islet polyA RNA-Seq biological replicate 2 CT4; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Mouse islets were isolated by perfusing the pancreatic bile duct with collagenase Illumina stranded LT kit for RNA-Seq	NextSeq 500	cell type;;Pancreatic islet cells|genotype;;wild type|source_name;;C57BL/6 wild type mice|strain;;C57BL/6	GEO Accession;;GSM1711978		GSM1711978	Mouse islet polyA RNA-Seq biological replicate 2 CT4	4337349933	28733958	2015-11-10 17:09:03	1823589804	4337349933	28733958	2	28733958	index:0,count:28733958,average:75.48,stdev:1.16|index:1,count:28733958,average:75.47,stdev:1.20	GSM1711978_r1				in_mesa	26542580	4.45	3.29	0.06	3649266672	3630078212	3396879742	3398312931	99.47	100.04	27620384	26159037	161.226	460.991	127	336506	87.19	93.74	30673013	24083259	30673013	24083259	89.98	90.53	30673013	24853537	30673013	23257881	176660358	4.84	0.23	0	6.71	0	0.28	0	0.09	0	0.00	0	3.50	0	27621227	0	150	0	149.71	0	1.80	0	0.01	0	1.29	0	0.01	0	161.88	0	0.37	0	67041	0	28733958	0	1929102	0	79853	0	27146	0	0	0	1005732	0	4364	0	0	0	45559	0	9215909	0	14976	0	9280808	0	89.41	0	25692125	0	190436	8887958	46.671627213342	28733958.0	27621227.0	67041.0	1929102.0	79853.0	27146.0	0.0	1005732.0	25692125.0	96.1	0.2	6.7	0.3	0.1	0.0	3.5	89.4	35	76	75.48	7	2168814851	25.1	24.3	25.1	25.5	0.0	34.9	24.3	bulk
1911180	SRR2063298	SRP059509	SRS961416	SRX1059071	SRA272961	GEO		Genome-wide Circadian Control of Transcription at Active Enhancers Regulates Insulin Secretion and Diabetes Risk	The molecular clock is a transcriptional oscillator present in brain and peripheral cells that coordinates behavior and physiology with the solar cycle. Here we reveal that the clock gates insulin secretion through genome-wide transcriptional control of the pancreatic exocyst across species. Clock transcription factors bind to unique enhancer sites in cycling genes in beta cells that diverge from those in liver, revealing the dynamics of inter-tissue clock control of genomic and physiologic processes important in glucose homeostasis. Overall design: Transcriptome profiling in mouse and human islets at serial 4-hour time intervals by polyA RNA-Seq		GSM1711979: Mouse islet polyA RNA-Seq biological replicate 2 CT8; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Mouse islets were isolated by perfusing the pancreatic bile duct with collagenase Illumina stranded LT kit for RNA-Seq	NextSeq 500	cell type;;Pancreatic islet cells|genotype;;wild type|source_name;;C57BL/6 wild type mice|strain;;C57BL/6	GEO Accession;;GSM1711979		GSM1711979	Mouse islet polyA RNA-Seq biological replicate 2 CT8	4234615036	28047849	2015-11-10 17:09:03	1777691434	4234615036	28047849	2	28047849	index:0,count:28047849,average:75.49,stdev:1.04|index:1,count:28047849,average:75.49,stdev:1.08	GSM1711979_r1				in_mesa	26542580	4.28	3.23	0.06	3644548807	3620202906	3423880231	3417003314	99.33	99.8	27098082	25657701	164.146	465.274	127	331008	86.25	91.84	29654847	23372184	29654847	23372184	88.57	88.91	29654847	24002835	29654847	22626086	246266731	6.76	0.21	0	5.89	0	0.24	0	0.11	0	0.00	0	3.03	0	27099001	0	150	0	149.78	0	1.69	0	0.01	0	1.19	0	0.00	0	282.84	0	0.37	0	57675	0	28047849	0	1650949	0	68214	0	30067	0	0	0	850567	0	4203	0	0	0	45525	0	8884871	0	13947	0	8948546	0	90.73	0	25448052	0	189177	8674366	45.853174540245	28047849.0	27099001.0	57675.0	1650949.0	68214.0	30067.0	0.0	850567.0	25448052.0	96.6	0.2	5.9	0.2	0.1	0.0	3.0	90.7	35	76	75.49	7	2117380331	25.3	24.1	25.0	25.6	0.0	34.9	24.4	bulk
1911195	SRR2063299	SRP059509	SRS961415	SRX1059072	SRA272961	GEO		Genome-wide Circadian Control of Transcription at Active Enhancers Regulates Insulin Secretion and Diabetes Risk	The molecular clock is a transcriptional oscillator present in brain and peripheral cells that coordinates behavior and physiology with the solar cycle. Here we reveal that the clock gates insulin secretion through genome-wide transcriptional control of the pancreatic exocyst across species. Clock transcription factors bind to unique enhancer sites in cycling genes in beta cells that diverge from those in liver, revealing the dynamics of inter-tissue clock control of genomic and physiologic processes important in glucose homeostasis. Overall design: Transcriptome profiling in mouse and human islets at serial 4-hour time intervals by polyA RNA-Seq		GSM1711980: Mouse islet polyA RNA-Seq biological replicate 2 CT12; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Mouse islets were isolated by perfusing the pancreatic bile duct with collagenase Illumina stranded LT kit for RNA-Seq	NextSeq 500	cell type;;Pancreatic islet cells|genotype;;wild type|source_name;;C57BL/6 wild type mice|strain;;C57BL/6	GEO Accession;;GSM1711980		GSM1711980	Mouse islet polyA RNA-Seq biological replicate 2 CT12	2521334596	16695716	2015-11-10 17:09:03	1069042036	2521334596	16695716	2	16695716	index:0,count:16695716,average:75.51,stdev:0.94|index:1,count:16695716,average:75.51,stdev:0.99	GSM1711980_r1				in_mesa	26542580	4.07	3.09	0.06	2245428833	2231939182	2122969172	2118895895	99.4	99.81	16023124	14748224	194.552	664.455	138	144049	85.65	90.63	17369465	13724639	17369465	13724639	87.41	87.66	17369465	14006047	17369465	13274416	178663328	7.96	0.33	0	5.27	0	0.22	0	0.11	0	0.00	0	3.70	0	16023628	0	151	0	149.78	0	1.82	0	0.01	0	1.26	0	0.01	0	264.78	0	0.38	0	54456	0	16695716	0	880627	0	36742	0	17759	0	0	0	617587	0	2529	0	0	0	27433	0	5277479	0	9265	0	5316706	0	90.70	0	15143001	0	169743	5257579	30.973760331796	16695716.0	16023628.0	54456.0	880627.0	36742.0	17759.0	0.0	617587.0	15143001.0	96.0	0.3	5.3	0.2	0.1	0.0	3.7	90.7	35	76	75.51	7	1260673277	24.8	24.7	25.4	25.2	0.0	34.9	24.2	bulk
1912843	SRR2063300	SRP059509	SRS961414	SRX1059073	SRA272961	GEO		Genome-wide Circadian Control of Transcription at Active Enhancers Regulates Insulin Secretion and Diabetes Risk	The molecular clock is a transcriptional oscillator present in brain and peripheral cells that coordinates behavior and physiology with the solar cycle. Here we reveal that the clock gates insulin secretion through genome-wide transcriptional control of the pancreatic exocyst across species. Clock transcription factors bind to unique enhancer sites in cycling genes in beta cells that diverge from those in liver, revealing the dynamics of inter-tissue clock control of genomic and physiologic processes important in glucose homeostasis. Overall design: Transcriptome profiling in mouse and human islets at serial 4-hour time intervals by polyA RNA-Seq		GSM1711981: Mouse islet polyA RNA-Seq biological replicate 2 CT16; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Mouse islets were isolated by perfusing the pancreatic bile duct with collagenase Illumina stranded LT kit for RNA-Seq	NextSeq 500	cell type;;Pancreatic islet cells|genotype;;wild type|source_name;;C57BL/6 wild type mice|strain;;C57BL/6	GEO Accession;;GSM1711981		GSM1711981	Mouse islet polyA RNA-Seq biological replicate 2 CT16	4467615624	29594219	2015-11-10 17:09:03	1885583645	4467615624	29594219	2	29594219	index:0,count:29594219,average:75.48,stdev:1.10|index:1,count:29594219,average:75.48,stdev:1.14	GSM1711981_r1				in_mesa	26542580	4.83	3.26	0.05	3784769031	3764697210	3533044675	3532717183	99.47	99.99	28444994	26983662	160.136	452.810	127	363467	87.26	93.52	31374196	24821437	31374196	24821437	90.0	90.44	31374196	25601564	31374196	24004807	193342875	5.11	0.21	0	6.43	0	0.24	0	0.09	0	0.00	0	3.54	0	28445912	0	150	0	149.73	0	1.73	0	0.01	0	1.22	0	0.00	0	287.94	0	0.37	0	63176	0	29594219	0	1903239	0	72123	0	28114	0	0	0	1048070	0	4394	0	0	0	47413	0	9489399	0	15338	0	9556544	0	89.69	0	26542673	0	192377	9205233	47.849966472083	29594219.0	28445912.0	63176.0	1903239.0	72123.0	28114.0	0.0	1048070.0	26542673.0	96.1	0.2	6.4	0.2	0.1	0.0	3.5	89.7	35	76	75.48	7	2233917103	25.3	24.0	25.0	25.6	0.0	34.8	24.1	bulk
1912862	SRR2063301	SRP059509	SRS961413	SRX1059074	SRA272961	GEO		Genome-wide Circadian Control of Transcription at Active Enhancers Regulates Insulin Secretion and Diabetes Risk	The molecular clock is a transcriptional oscillator present in brain and peripheral cells that coordinates behavior and physiology with the solar cycle. Here we reveal that the clock gates insulin secretion through genome-wide transcriptional control of the pancreatic exocyst across species. Clock transcription factors bind to unique enhancer sites in cycling genes in beta cells that diverge from those in liver, revealing the dynamics of inter-tissue clock control of genomic and physiologic processes important in glucose homeostasis. Overall design: Transcriptome profiling in mouse and human islets at serial 4-hour time intervals by polyA RNA-Seq		GSM1711982: Mouse islet polyA RNA-Seq biological replicate 2 CT020; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Mouse islets were isolated by perfusing the pancreatic bile duct with collagenase Illumina stranded LT kit for RNA-Seq	NextSeq 500	cell type;;Pancreatic islet cells|genotype;;wild type|source_name;;C57BL/6 wild type mice|strain;;C57BL/6	GEO Accession;;GSM1711982		GSM1711982	Mouse islet polyA RNA-Seq biological replicate 2 CT020	3398514794	22513371	2015-11-10 17:09:03	1426244971	3398514794	22513371	2	22513371	index:0,count:22513371,average:75.48,stdev:1.11|index:1,count:22513371,average:75.48,stdev:1.15	GSM1711982_r1				in_mesa	26542580	5.28	3.23	0.06	2856570296	2830666589	2670762711	2660202154	99.09	99.6	21717824	20727015	155.074	420.911	127	293302	85.54	91.52	23843526	18578219	23843526	18578219	88.29	88.59	23843526	19174731	23843526	17984771	195474303	6.84	0.18	0	6.30	0	0.22	0	0.11	0	0.00	0	3.20	0	21718575	0	150	0	149.77	0	1.67	0	0.01	0	1.21	0	0.01	0	290.50	0	0.36	0	41319	0	22513371	0	1418178	0	50113	0	25277	0	0	0	719406	0	3264	0	0	0	36029	0	7005579	0	11250	0	7056122	0	90.17	0	20300397	0	176208	6748725	38.299765050395	22513371.0	21718575.0	41319.0	1418178.0	50113.0	25277.0	0.0	719406.0	20300397.0	96.5	0.2	6.3	0.2	0.1	0.0	3.2	90.2	35	76	75.48	7	1699259917	25.6	23.7	25.0	25.7	0.0	34.9	24.3	bulk
1912879	SRR2063302	SRP059509	SRS961412	SRX1059075	SRA272961	GEO		Genome-wide Circadian Control of Transcription at Active Enhancers Regulates Insulin Secretion and Diabetes Risk	The molecular clock is a transcriptional oscillator present in brain and peripheral cells that coordinates behavior and physiology with the solar cycle. Here we reveal that the clock gates insulin secretion through genome-wide transcriptional control of the pancreatic exocyst across species. Clock transcription factors bind to unique enhancer sites in cycling genes in beta cells that diverge from those in liver, revealing the dynamics of inter-tissue clock control of genomic and physiologic processes important in glucose homeostasis. Overall design: Transcriptome profiling in mouse and human islets at serial 4-hour time intervals by polyA RNA-Seq		GSM1711983: Mouse islet polyA RNA-Seq biological replicate 2 CT24; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Mouse islets were isolated by perfusing the pancreatic bile duct with collagenase Illumina stranded LT kit for RNA-Seq	NextSeq 500	cell type;;Pancreatic islet cells|genotype;;wild type|source_name;;C57BL/6 wild type mice|strain;;C57BL/6	GEO Accession;;GSM1711983		GSM1711983	Mouse islet polyA RNA-Seq biological replicate 2 CT24	4453853469	29512396	2015-11-10 17:09:03	1873158341	4453853469	29512396	2	29512396	index:0,count:29512396,average:75.46,stdev:1.26|index:1,count:29512396,average:75.45,stdev:1.30	GSM1711983_r1				in_mesa	26542580	5.52	3.2	0.05	3652955817	3632373362	3384062229	3383953725	99.44	100.0	28349887	27162764	150.711	387.130	127	396140	86.26	93.19	31574250	24456181	31574250	24456181	89.5	89.94	31574250	25372724	31574250	23602228	192005569	5.26	0.18	0	7.14	0	0.22	0	0.10	0	0.00	0	3.61	0	28350869	0	150	0	149.69	0	1.82	0	0.01	0	1.27	0	0.01	0	256.01	0	0.37	0	53352	0	29512396	0	2108621	0	66187	0	29155	0	0	0	1066185	0	4174	0	0	0	44759	0	9316478	0	15545	0	9380956	0	88.92	0	26242248	0	184821	8871705	48.001606960248	29512396.0	28350869.0	53352.0	2108621.0	66187.0	29155.0	0.0	1066185.0	26242248.0	96.1	0.2	7.1	0.2	0.1	0.0	3.6	88.9	35	76	75.46	7	2227003227	25.4	24.1	25.1	25.5	0.0	34.8	24.0	bulk
1912975	SRR2063308	SRP059509	SRS961406	SRX1059081	SRA272961	GEO		Genome-wide Circadian Control of Transcription at Active Enhancers Regulates Insulin Secretion and Diabetes Risk	The molecular clock is a transcriptional oscillator present in brain and peripheral cells that coordinates behavior and physiology with the solar cycle. Here we reveal that the clock gates insulin secretion through genome-wide transcriptional control of the pancreatic exocyst across species. Clock transcription factors bind to unique enhancer sites in cycling genes in beta cells that diverge from those in liver, revealing the dynamics of inter-tissue clock control of genomic and physiologic processes important in glucose homeostasis. Overall design: Transcriptome profiling in mouse and human islets at serial 4-hour time intervals by polyA RNA-Seq		GSM1711989: Mouse islet polyA RNA-Seq biological replicate 3 CT0; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Mouse islets were isolated by perfusing the pancreatic bile duct with collagenase Illumina stranded LT kit for RNA-Seq	NextSeq 500	cell type;;Pancreatic islet cells|genotype;;wild type|source_name;;C57BL/6 wild type mice|strain;;C57BL/6	GEO Accession;;GSM1711989		GSM1711989	Mouse islet polyA RNA-Seq biological replicate 3 CT0	5107768792	33851848	2015-11-10 17:09:03	2177743173	5107768792	33851848	2	33851848	index:0,count:33851848,average:75.45,stdev:1.34|index:1,count:33851848,average:75.43,stdev:1.40	GSM1711989_r1				in_mesa	26542580	3.85	3.46	0.07	4335276953	4304109294	3972563003	3974301138	99.28	100.04	32612789	31331338	153.794	355.818	130	483584	86.01	93.93	37199085	28050733	37199085	28050733	89.87	90.58	37199085	29310420	37199085	27052547	204120178	4.71	0.16	0	8.12	0	0.44	0	0.10	0	0.00	0	3.12	0	32614288	0	150	0	149.60	0	1.73	0	0.01	0	1.25	0	0.01	0	144.05	0	0.41	0	53512	0	33851848	0	2749698	0	149910	0	32673	0	0	0	1054977	0	4910	0	0	0	46524	0	9764913	0	14445	0	9830792	0	88.22	0	29864590	0	185664	9645547	51.951627671493	33851848.0	32614288.0	53512.0	2749698.0	149910.0	32673.0	0.0	1054977.0	29864590.0	96.3	0.2	8.1	0.4	0.1	0.0	3.1	88.2	35	76	75.45	7	2554255737	25.8	23.7	23.9	26.7	0.0	34.8	24.2	bulk
1912991	SRR2063309	SRP059509	SRS961405	SRX1059082	SRA272961	GEO		Genome-wide Circadian Control of Transcription at Active Enhancers Regulates Insulin Secretion and Diabetes Risk	The molecular clock is a transcriptional oscillator present in brain and peripheral cells that coordinates behavior and physiology with the solar cycle. Here we reveal that the clock gates insulin secretion through genome-wide transcriptional control of the pancreatic exocyst across species. Clock transcription factors bind to unique enhancer sites in cycling genes in beta cells that diverge from those in liver, revealing the dynamics of inter-tissue clock control of genomic and physiologic processes important in glucose homeostasis. Overall design: Transcriptome profiling in mouse and human islets at serial 4-hour time intervals by polyA RNA-Seq		GSM1711990: Mouse islet polyA RNA-Seq biological replicate 3 CT4; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Mouse islets were isolated by perfusing the pancreatic bile duct with collagenase Illumina stranded LT kit for RNA-Seq	NextSeq 500	cell type;;Pancreatic islet cells|genotype;;wild type|source_name;;C57BL/6 wild type mice|strain;;C57BL/6	GEO Accession;;GSM1711990		GSM1711990	Mouse islet polyA RNA-Seq biological replicate 3 CT4	6038121880	40129162	2015-11-10 17:09:03	2580385156	6038121880	40129162	2	40129162	index:0,count:40129162,average:75.24,stdev:2.45|index:1,count:40129162,average:75.23,stdev:2.47	GSM1711990_r1				in_mesa	26542580	5.07	3.52	0.07	4862087685	4819609359	4426832181	4422239871	99.13	99.9	38566775	37338870	143.001	314.051	127	577245	85.84	94.44	44155586	33106748	44155586	33106748	90.42	91.16	44155586	34875124	44155586	31957247	198470187	4.08	0.17	0	8.75	0	0.30	0	0.11	0	0.00	0	3.47	0	38568573	0	150	0	149.27	0	1.66	0	0.01	0	1.26	0	0.01	0	274.65	0	0.41	0	66435	0	40129162	0	3511594	0	122058	0	45319	0	0	0	1393212	0	5032	0	0	0	47640	0	10788010	0	17846	0	10858528	0	87.36	0	35056979	0	172318	10185021	59.105961071972	40129162.0	38568573.0	66435.0	3511594.0	122058.0	45319.0	0.0	1393212.0	35056979.0	96.1	0.2	8.8	0.3	0.1	0.0	3.5	87.4	35	76	75.24	7	3019353589	26.2	23.4	23.8	26.6	0.0	34.8	24.1	bulk
1913119	SRR2063311	SRP059509	SRS961403	SRX1059084	SRA272961	GEO		Genome-wide Circadian Control of Transcription at Active Enhancers Regulates Insulin Secretion and Diabetes Risk	The molecular clock is a transcriptional oscillator present in brain and peripheral cells that coordinates behavior and physiology with the solar cycle. Here we reveal that the clock gates insulin secretion through genome-wide transcriptional control of the pancreatic exocyst across species. Clock transcription factors bind to unique enhancer sites in cycling genes in beta cells that diverge from those in liver, revealing the dynamics of inter-tissue clock control of genomic and physiologic processes important in glucose homeostasis. Overall design: Transcriptome profiling in mouse and human islets at serial 4-hour time intervals by polyA RNA-Seq		GSM1711992: Mouse islet polyA RNA-Seq biological replicate 3 CT12; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Mouse islets were isolated by perfusing the pancreatic bile duct with collagenase Illumina stranded LT kit for RNA-Seq	NextSeq 500	cell type;;Pancreatic islet cells|genotype;;wild type|source_name;;C57BL/6 wild type mice|strain;;C57BL/6	GEO Accession;;GSM1711992		GSM1711992	Mouse islet polyA RNA-Seq biological replicate 3 CT12	4308911976	28539005	2015-11-10 17:09:03	1837369238	4308911976	28539005	2	28539005	index:0,count:28539005,average:75.50,stdev:1.04|index:1,count:28539005,average:75.48,stdev:1.11	GSM1711992_r1				in_mesa	26542580	4.96	3.15	0.06	3771478704	3739732695	3515128973	3502157371	99.16	99.63	27497449	25860027	168.748	506.220	132	361558	85.46	91.67	30467317	23499909	30467317	23499909	88.61	88.85	30467317	24366351	30467317	22776716	261052381	6.92	0.17	0	6.53	0	0.34	0	0.11	0	0.00	0	3.19	0	27498702	0	150	0	149.66	0	1.72	0	0.00	0	1.24	0	0.00	0	127.00	0	0.40	0	49234	0	28539005	0	1863683	0	97927	0	32754	0	0	0	909622	0	4443	0	0	0	48250	0	9610833	0	15348	0	9678874	0	89.82	0	25635019	0	195656	9608496	49.109130310341	28539005.0	27498702.0	49234.0	1863683.0	97927.0	32754.0	0.0	909622.0	25635019.0	96.4	0.2	6.5	0.3	0.1	0.0	3.2	89.8	35	76	75.50	7	2154670639	24.7	24.0	25.4	25.9	0.0	34.8	24.3	bulk
1913134	SRR2063312	SRP059509	SRS961402	SRX1059085	SRA272961	GEO		Genome-wide Circadian Control of Transcription at Active Enhancers Regulates Insulin Secretion and Diabetes Risk	The molecular clock is a transcriptional oscillator present in brain and peripheral cells that coordinates behavior and physiology with the solar cycle. Here we reveal that the clock gates insulin secretion through genome-wide transcriptional control of the pancreatic exocyst across species. Clock transcription factors bind to unique enhancer sites in cycling genes in beta cells that diverge from those in liver, revealing the dynamics of inter-tissue clock control of genomic and physiologic processes important in glucose homeostasis. Overall design: Transcriptome profiling in mouse and human islets at serial 4-hour time intervals by polyA RNA-Seq		GSM1711993: Mouse islet polyA RNA-Seq biological replicate 3 CT16; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Mouse islets were isolated by perfusing the pancreatic bile duct with collagenase Illumina stranded LT kit for RNA-Seq	NextSeq 500	cell type;;Pancreatic islet cells|genotype;;wild type|source_name;;C57BL/6 wild type mice|strain;;C57BL/6	GEO Accession;;GSM1711993		GSM1711993	Mouse islet polyA RNA-Seq biological replicate 3 CT16	4714633643	31294639	2015-11-10 17:09:03	2019578628	4714633643	31294639	2	31294639	index:0,count:31294639,average:75.33,stdev:1.97|index:1,count:31294639,average:75.32,stdev:1.99	GSM1711993_r1				in_mesa	26542580	9.02	3.28	0.05	3687400169	3640407559	3300975605	3287347144	98.73	99.59	30001126	28992127	137.603	329.921	116	474001	82.71	92.43	34587678	24815460	34587678	24815460	88.92	89.26	34587678	26678742	34587678	23962926	206739296	5.61	0.16	0	10.08	0	0.27	0	0.12	0	0.00	0	3.74	0	30002466	0	150	0	149.36	0	1.73	0	0.01	0	1.27	0	0.01	0	277.49	0	0.41	0	49761	0	31294639	0	3155298	0	84617	0	37528	0	0	0	1170028	0	4049	0	0	0	42551	0	9149625	0	14229	0	9210454	0	85.79	0	26847168	0	174340	8485522	48.672261099002	31294639.0	30002466.0	49761.0	3155298.0	84617.0	37528.0	0.0	1170028.0	26847168.0	95.9	0.2	10.1	0.3	0.1	0.0	3.7	85.8	35	76	75.33	7	2357481456	26.1	22.6	24.4	26.8	0.0	34.7	24.0	bulk
1913150	SRR2063313	SRP059509	SRS961401	SRX1059086	SRA272961	GEO		Genome-wide Circadian Control of Transcription at Active Enhancers Regulates Insulin Secretion and Diabetes Risk	The molecular clock is a transcriptional oscillator present in brain and peripheral cells that coordinates behavior and physiology with the solar cycle. Here we reveal that the clock gates insulin secretion through genome-wide transcriptional control of the pancreatic exocyst across species. Clock transcription factors bind to unique enhancer sites in cycling genes in beta cells that diverge from those in liver, revealing the dynamics of inter-tissue clock control of genomic and physiologic processes important in glucose homeostasis. Overall design: Transcriptome profiling in mouse and human islets at serial 4-hour time intervals by polyA RNA-Seq		GSM1711994: Mouse islet polyA RNA-Seq biological replicate 3 CT020; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Mouse islets were isolated by perfusing the pancreatic bile duct with collagenase Illumina stranded LT kit for RNA-Seq	NextSeq 500	cell type;;Pancreatic islet cells|genotype;;wild type|source_name;;C57BL/6 wild type mice|strain;;C57BL/6	GEO Accession;;GSM1711994		GSM1711994	Mouse islet polyA RNA-Seq biological replicate 3 CT020	4789385318	31748668	2015-11-10 17:09:03	2042588926	4789385318	31748668	2	31748668	index:0,count:31748668,average:75.43,stdev:1.42|index:1,count:31748668,average:75.42,stdev:1.47	GSM1711994_r1				in_mesa	26542580	5.37	3.46	0.06	3937359452	3890598679	3655608889	3634198904	98.81	99.41	30567126	29429591	145.685	359.250	127	471893	84.91	91.49	33956146	25955432	33956146	25955432	88.31	88.67	33956146	26996318	33956146	25156376	268089562	6.81	0.18	0	6.92	0	0.29	0	0.12	0	0.00	0	3.30	0	30568521	0	150	0	149.60	0	1.56	0	0.01	0	1.20	0	0.00	0	335.18	0	0.40	0	56318	0	31748668	0	2197730	0	92479	0	39343	0	0	0	1048325	0	4507	0	0	0	49273	0	9368547	0	14686	0	9437013	0	89.36	0	28370791	0	184919	8994231	48.638760754709	31748668.0	30568521.0	56318.0	2197730.0	92479.0	39343.0	0.0	1048325.0	28370791.0	96.3	0.2	6.9	0.3	0.1	0.0	3.3	89.4	35	76	75.43	7	2394896008	26.2	23.1	24.0	26.7	0.0	34.8	24.1	bulk
1913165	SRR2063314	SRP059509	SRS961400	SRX1059087	SRA272961	GEO		Genome-wide Circadian Control of Transcription at Active Enhancers Regulates Insulin Secretion and Diabetes Risk	The molecular clock is a transcriptional oscillator present in brain and peripheral cells that coordinates behavior and physiology with the solar cycle. Here we reveal that the clock gates insulin secretion through genome-wide transcriptional control of the pancreatic exocyst across species. Clock transcription factors bind to unique enhancer sites in cycling genes in beta cells that diverge from those in liver, revealing the dynamics of inter-tissue clock control of genomic and physiologic processes important in glucose homeostasis. Overall design: Transcriptome profiling in mouse and human islets at serial 4-hour time intervals by polyA RNA-Seq		GSM1711995: Mouse islet polyA RNA-Seq biological replicate 3 CT24; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Mouse islets were isolated by perfusing the pancreatic bile duct with collagenase Illumina stranded LT kit for RNA-Seq	NextSeq 500	cell type;;Pancreatic islet cells|genotype;;wild type|source_name;;C57BL/6 wild type mice|strain;;C57BL/6	GEO Accession;;GSM1711995		GSM1711995	Mouse islet polyA RNA-Seq biological replicate 3 CT24	4666983322	30919604	2015-11-10 17:09:03	1993856964	4666983322	30919604	2	30919604	index:0,count:30919604,average:75.48,stdev:1.16|index:1,count:30919604,average:75.46,stdev:1.22	GSM1711995_r1				in_mesa	26542580	4.19	3.27	0.08	3921522001	3893262493	3649525934	3645125661	99.28	99.88	29651417	28181777	157.021	429.871	128	400245	86.38	92.85	33006544	25613521	33006544	25613521	89.36	89.85	33006544	26498191	33006544	24786938	230603724	5.88	0.16	0	6.68	0	0.36	0	0.11	0	0.00	0	3.64	0	29652791	0	150	0	149.62	0	1.64	0	0.00	0	1.21	0	0.00	0	131.11	0	0.40	0	48248	0	30919604	0	2066486	0	109822	0	32871	0	0	0	1124120	0	4831	0	0	0	50587	0	10018643	0	14661	0	10088722	0	89.22	0	27586305	0	199190	9753141	48.964009237412	30919604.0	29652791.0	48248.0	2066486.0	109822.0	32871.0	0.0	1124120.0	27586305.0	95.9	0.2	6.7	0.4	0.1	0.0	3.6	89.2	35	76	75.48	7	2333738470	25.1	24.1	24.8	26.0	0.0	34.7	23.9	bulk
1913180	SRR2063315	SRP059509	SRS961399	SRX1059088	SRA272961	GEO		Genome-wide Circadian Control of Transcription at Active Enhancers Regulates Insulin Secretion and Diabetes Risk	The molecular clock is a transcriptional oscillator present in brain and peripheral cells that coordinates behavior and physiology with the solar cycle. Here we reveal that the clock gates insulin secretion through genome-wide transcriptional control of the pancreatic exocyst across species. Clock transcription factors bind to unique enhancer sites in cycling genes in beta cells that diverge from those in liver, revealing the dynamics of inter-tissue clock control of genomic and physiologic processes important in glucose homeostasis. Overall design: Transcriptome profiling in mouse and human islets at serial 4-hour time intervals by polyA RNA-Seq		GSM1711996: Mouse islet polyA RNA-Seq biological replicate 3 CT28; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Mouse islets were isolated by perfusing the pancreatic bile duct with collagenase Illumina stranded LT kit for RNA-Seq	NextSeq 500	cell type;;Pancreatic islet cells|genotype;;wild type|source_name;;C57BL/6 wild type mice|strain;;C57BL/6	GEO Accession;;GSM1711996		GSM1711996	Mouse islet polyA RNA-Seq biological replicate 3 CT28	4607668443	30574869	2015-11-10 17:09:03	1973278857	4607668443	30574869	2	30574869	index:0,count:30574869,average:75.36,stdev:1.81|index:1,count:30574869,average:75.34,stdev:1.84	GSM1711996_r1				in_mesa	26542580	5.92	3.48	0.06	3616037094	3586391056	3300159839	3297602515	99.18	99.92	29298497	28270715	138.521	335.472	118	452236	86.04	94.37	33367775	25209134	33367775	25209134	90.52	91.18	33367775	26521297	33367775	24355903	150381824	4.16	0.23	0	8.46	0	0.34	0	0.10	0	0.00	0	3.73	0	29299895	0	150	0	149.45	0	1.64	0	0.01	0	1.26	0	0.00	0	310.06	0	0.41	0	69248	0	30574869	0	2587437	0	103993	0	31835	0	0	0	1139146	0	4532	0	0	0	44875	0	8982924	0	14019	0	9046350	0	87.37	0	26712458	0	180761	8361502	46.257223626778	30574869.0	29299895.0	69248.0	2587437.0	103993.0	31835.0	0.0	1139146.0	26712458.0	95.8	0.2	8.5	0.3	0.1	0.0	3.7	87.4	35	76	75.36	7	2304110422	26.2	23.1	24.0	26.7	0.0	34.7	23.9	bulk
1913196	SRR2063316	SRP059509	SRS961398	SRX1059089	SRA272961	GEO		Genome-wide Circadian Control of Transcription at Active Enhancers Regulates Insulin Secretion and Diabetes Risk	The molecular clock is a transcriptional oscillator present in brain and peripheral cells that coordinates behavior and physiology with the solar cycle. Here we reveal that the clock gates insulin secretion through genome-wide transcriptional control of the pancreatic exocyst across species. Clock transcription factors bind to unique enhancer sites in cycling genes in beta cells that diverge from those in liver, revealing the dynamics of inter-tissue clock control of genomic and physiologic processes important in glucose homeostasis. Overall design: Transcriptome profiling in mouse and human islets at serial 4-hour time intervals by polyA RNA-Seq		GSM1711997: Mouse islet polyA RNA-Seq biological replicate 3 CT32; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Mouse islets were isolated by perfusing the pancreatic bile duct with collagenase Illumina stranded LT kit for RNA-Seq	NextSeq 500	cell type;;Pancreatic islet cells|genotype;;wild type|source_name;;C57BL/6 wild type mice|strain;;C57BL/6	GEO Accession;;GSM1711997		GSM1711997	Mouse islet polyA RNA-Seq biological replicate 3 CT32	3597395283	23845515	2015-11-10 17:09:03	1537263465	3597395283	23845515	2	23845515	index:0,count:23845515,average:75.44,stdev:1.39|index:1,count:23845515,average:75.42,stdev:1.44	GSM1711997_r1				in_mesa	26542580	4.47	3.33	0.07	2934761759	2910357295	2737399017	2730386415	99.17	99.74	22915821	21949966	147.768	386.555	127	322839	85.35	91.56	25407709	19560295	25407709	19560295	88.28	88.67	25407709	20230883	25407709	18942001	209111784	7.13	0.16	0	6.52	0	0.32	0	0.12	0	0.00	0	3.45	0	22916857	0	150	0	149.59	0	1.54	0	0.01	0	1.18	0	0.00	0	337.97	0	0.40	0	38417	0	23845515	0	1553566	0	77350	0	27779	0	0	0	823529	0	3742	0	0	0	38656	0	7338183	0	11236	0	7391817	0	89.59	0	21363291	0	185238	6997144	37.773804510953	23845515.0	22916857.0	38417.0	1553566.0	77350.0	27779.0	0.0	823529.0	21363291.0	96.1	0.2	6.5	0.3	0.1	0.0	3.5	89.6	35	76	75.44	7	1798918855	25.5	23.8	24.5	26.2	0.0	34.7	24.0	bulk
1913211	SRR2063317	SRP059509	SRS961397	SRX1059090	SRA272961	GEO		Genome-wide Circadian Control of Transcription at Active Enhancers Regulates Insulin Secretion and Diabetes Risk	The molecular clock is a transcriptional oscillator present in brain and peripheral cells that coordinates behavior and physiology with the solar cycle. Here we reveal that the clock gates insulin secretion through genome-wide transcriptional control of the pancreatic exocyst across species. Clock transcription factors bind to unique enhancer sites in cycling genes in beta cells that diverge from those in liver, revealing the dynamics of inter-tissue clock control of genomic and physiologic processes important in glucose homeostasis. Overall design: Transcriptome profiling in mouse and human islets at serial 4-hour time intervals by polyA RNA-Seq		GSM1711998: Mouse islet polyA RNA-Seq biological replicate 3 CT36; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Mouse islets were isolated by perfusing the pancreatic bile duct with collagenase Illumina stranded LT kit for RNA-Seq	NextSeq 500	cell type;;Pancreatic islet cells|genotype;;wild type|source_name;;C57BL/6 wild type mice|strain;;C57BL/6	GEO Accession;;GSM1711998		GSM1711998	Mouse islet polyA RNA-Seq biological replicate 3 CT36	3986260269	26673548	2015-11-10 17:09:03	1725031696	3986260269	26673548	2	26673548	index:0,count:26673548,average:74.73,stdev:3.89|index:1,count:26673548,average:74.72,stdev:3.89	GSM1711998_r1				in_mesa	26542580	7.36	3.51	0.07	2874999007	2824942622	2626046995	2600808030	98.26	99.04	25536342	24647041	126.095	332.399	107	394309	81.97	89.85	28935068	20933103	28935068	20933103	86.82	87.1	28935068	22171451	28935068	20291156	232789062	8.10	0.14	0	8.40	0	0.31	0	0.20	0	0.00	0	3.75	0	25537427	0	149	0	148.24	0	1.44	0	0.01	0	1.17	0	0.01	0	297.29	0	0.42	0	38055	0	26673548	0	2240622	0	82421	0	54152	0	0	0	999548	0	3466	0	0	0	36431	0	7215694	0	10919	0	7266510	0	87.34	0	23296805	0	166107	6171061	37.151119459144	26673548.0	25537427.0	38055.0	2240622.0	82421.0	54152.0	0.0	999548.0	23296805.0	95.7	0.1	8.4	0.3	0.2	0.0	3.7	87.3	35	76	74.73	7	1993333403	26.9	22.1	23.3	27.6	0.0	34.7	23.7	bulk
1913227	SRR2063318	SRP059509	SRS961396	SRX1059091	SRA272961	GEO		Genome-wide Circadian Control of Transcription at Active Enhancers Regulates Insulin Secretion and Diabetes Risk	The molecular clock is a transcriptional oscillator present in brain and peripheral cells that coordinates behavior and physiology with the solar cycle. Here we reveal that the clock gates insulin secretion through genome-wide transcriptional control of the pancreatic exocyst across species. Clock transcription factors bind to unique enhancer sites in cycling genes in beta cells that diverge from those in liver, revealing the dynamics of inter-tissue clock control of genomic and physiologic processes important in glucose homeostasis. Overall design: Transcriptome profiling in mouse and human islets at serial 4-hour time intervals by polyA RNA-Seq		GSM1711999: Mouse islet polyA RNA-Seq biological replicate 3 CT40; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Mouse islets were isolated by perfusing the pancreatic bile duct with collagenase Illumina stranded LT kit for RNA-Seq	NextSeq 500	cell type;;Pancreatic islet cells|genotype;;wild type|source_name;;C57BL/6 wild type mice|strain;;C57BL/6	GEO Accession;;GSM1711999		GSM1711999	Mouse islet polyA RNA-Seq biological replicate 3 CT40	4787216970	31768588	2015-11-10 17:09:03	2058991369	4787216970	31768588	2	31768588	index:0,count:31768588,average:75.35,stdev:1.80|index:1,count:31768588,average:75.34,stdev:1.83	GSM1711999_r1				in_mesa	26542580	6.95	3.59	0.06	3723977087	3681477769	3398294543	3383895277	98.86	99.58	30522581	29504580	135.394	329.767	118	496678	85.05	93.25	34582036	25961283	34582036	25961283	89.87	90.36	34582036	27430583	34582036	25157107	193107661	5.19	0.19	0	8.45	0	0.27	0	0.12	0	0.00	0	3.53	0	30524002	0	150	0	149.43	0	1.47	0	0.01	0	1.21	0	0.00	0	133.45	0	0.42	0	60262	0	31768588	0	2683440	0	86200	0	36874	0	0	0	1121512	0	4481	0	0	0	46651	0	9052567	0	13698	0	9117397	0	87.64	0	27840562	0	185183	8303568	44.839796309596	31768588.0	30524002.0	60262.0	2683440.0	86200.0	36874.0	0.0	1121512.0	27840562.0	96.1	0.2	8.4	0.3	0.1	0.0	3.5	87.6	35	76	75.35	7	2393911534	26.5	22.7	23.8	27.0	0.0	34.7	24.0	bulk
1913243	SRR2063319	SRP059509	SRS961395	SRX1059092	SRA272961	GEO		Genome-wide Circadian Control of Transcription at Active Enhancers Regulates Insulin Secretion and Diabetes Risk	The molecular clock is a transcriptional oscillator present in brain and peripheral cells that coordinates behavior and physiology with the solar cycle. Here we reveal that the clock gates insulin secretion through genome-wide transcriptional control of the pancreatic exocyst across species. Clock transcription factors bind to unique enhancer sites in cycling genes in beta cells that diverge from those in liver, revealing the dynamics of inter-tissue clock control of genomic and physiologic processes important in glucose homeostasis. Overall design: Transcriptome profiling in mouse and human islets at serial 4-hour time intervals by polyA RNA-Seq		GSM1712000: Mouse islet polyA RNA-Seq biological replicate 3 CT44; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Mouse islets were isolated by perfusing the pancreatic bile duct with collagenase Illumina stranded LT kit for RNA-Seq	NextSeq 500	cell type;;Pancreatic islet cells|genotype;;wild type|source_name;;C57BL/6 wild type mice|strain;;C57BL/6	GEO Accession;;GSM1712000		GSM1712000	Mouse islet polyA RNA-Seq biological replicate 3 CT44	5153464722	34275946	2015-11-10 17:09:03	2213605582	5153464722	34275946	2	34275946	index:0,count:34275946,average:75.19,stdev:2.48|index:1,count:34275946,average:75.17,stdev:2.49	GSM1712000_r1				in_mesa	26542580	6.46	3.68	0.09	3856676577	3796027417	3545444041	3518049807	98.43	99.23	32795097	31677936	130.232	335.069	116	538189	82.99	90.33	36877369	27218120	36877369	27218120	87.11	87.52	36877369	28569420	36877369	26371103	301757543	7.82	0.15	0	7.78	0	0.29	0	0.16	0	0.00	0	3.86	0	32796602	0	150	0	149.13	0	1.44	0	0.01	0	1.17	0	0.01	0	127.87	0	0.41	0	51302	0	34275946	0	2666224	0	100071	0	55338	0	0	0	1323935	0	4902	0	0	0	51411	0	9316629	0	13569	0	9386511	0	87.91	0	30130378	0	184400	8240457	44.687944685466	34275946.0	32796602.0	51302.0	2666224.0	100071.0	55338.0	0.0	1323935.0	30130378.0	95.7	0.1	7.8	0.3	0.2	0.0	3.9	87.9	35	76	75.19	7	2577082145	27.0	22.2	23.1	27.7	0.0	34.7	23.8	bulk
3825777	SRR2063303	SRP059509	SRS961411	SRX1059076	SRA272961	GEO		Genome-wide Circadian Control of Transcription at Active Enhancers Regulates Insulin Secretion and Diabetes Risk	The molecular clock is a transcriptional oscillator present in brain and peripheral cells that coordinates behavior and physiology with the solar cycle. Here we reveal that the clock gates insulin secretion through genome-wide transcriptional control of the pancreatic exocyst across species. Clock transcription factors bind to unique enhancer sites in cycling genes in beta cells that diverge from those in liver, revealing the dynamics of inter-tissue clock control of genomic and physiologic processes important in glucose homeostasis. Overall design: Transcriptome profiling in mouse and human islets at serial 4-hour time intervals by polyA RNA-Seq		GSM1711984: Mouse islet polyA RNA-Seq biological replicate 2 CT28; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Mouse islets were isolated by perfusing the pancreatic bile duct with collagenase Illumina stranded LT kit for RNA-Seq	NextSeq 500	cell type;;Pancreatic islet cells|genotype;;wild type|source_name;;C57BL/6 wild type mice|strain;;C57BL/6	GEO Accession;;GSM1711984		GSM1711984	Mouse islet polyA RNA-Seq biological replicate 2 CT28	4206745560	27878607	2015-11-10 17:09:03	1767641967	4206745560	27878607	2	27878607	index:0,count:27878607,average:75.45,stdev:1.30|index:1,count:27878607,average:75.44,stdev:1.33	GSM1711984_r1				in_mesa	26542580	5.14	3.35	0.06	3423890939	3401459824	3167809341	3168016236	99.34	100.01	26827550	25693115	147.624	386.071	127	371307	85.78	92.79	29983684	23014211	29983684	23014211	88.67	89.25	29983684	23789204	29983684	22136534	186338551	5.44	0.18	0	7.27	0	0.25	0	0.10	0	0.00	0	3.42	0	26828406	0	150	0	149.65	0	1.93	0	0.01	0	1.33	0	0.01	0	406.33	0	0.38	0	50951	0	27878607	0	2026497	0	68501	0	28831	0	0	0	952869	0	4122	0	0	0	42789	0	8599401	0	13131	0	8659443	0	88.96	0	24801909	0	185395	8113315	43.762318293374	27878607.0	26828406.0	50951.0	2026497.0	68501.0	28831.0	0.0	952869.0	24801909.0	96.2	0.2	7.3	0.2	0.1	0.0	3.4	89.0	35	76	75.45	7	2103540130	25.5	23.9	24.8	25.9	0.0	34.9	24.2	bulk
3825810	SRR2063304	SRP059509	SRS961410	SRX1059077	SRA272961	GEO		Genome-wide Circadian Control of Transcription at Active Enhancers Regulates Insulin Secretion and Diabetes Risk	The molecular clock is a transcriptional oscillator present in brain and peripheral cells that coordinates behavior and physiology with the solar cycle. Here we reveal that the clock gates insulin secretion through genome-wide transcriptional control of the pancreatic exocyst across species. Clock transcription factors bind to unique enhancer sites in cycling genes in beta cells that diverge from those in liver, revealing the dynamics of inter-tissue clock control of genomic and physiologic processes important in glucose homeostasis. Overall design: Transcriptome profiling in mouse and human islets at serial 4-hour time intervals by polyA RNA-Seq		GSM1711985: Mouse islet polyA RNA-Seq biological replicate 2 CT32; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Mouse islets were isolated by perfusing the pancreatic bile duct with collagenase Illumina stranded LT kit for RNA-Seq	NextSeq 500	cell type;;Pancreatic islet cells|genotype;;wild type|source_name;;C57BL/6 wild type mice|strain;;C57BL/6	GEO Accession;;GSM1711985		GSM1711985	Mouse islet polyA RNA-Seq biological replicate 2 CT32	4280413706	28367981	2015-11-10 17:09:03	1802621961	4280413706	28367981	2	28367981	index:0,count:28367981,average:75.45,stdev:1.31|index:1,count:28367981,average:75.44,stdev:1.34	GSM1711985_r1				in_mesa	26542580	5.0	3.24	0.06	3471589089	3441272508	3240800025	3229757127	99.13	99.66	27222124	26158477	145.870	374.281	126	400206	85.07	91.18	30028391	23157561	30028391	23157561	87.81	88.15	30028391	23903701	30028391	22390299	250503400	7.22	0.19	0	6.43	0	0.25	0	0.12	0	0.00	0	3.68	0	27223012	0	150	0	149.70	0	1.66	0	0.01	0	1.21	0	0.01	0	297.74	0	0.37	0	53373	0	28367981	0	1824014	0	69638	0	32667	0	0	0	1042664	0	4108	0	0	0	43939	0	8671025	0	13764	0	8732836	0	89.53	0	25398998	0	184294	8196007	44.472457052319	28367981.0	27223012.0	53373.0	1824014.0	69638.0	32667.0	0.0	1042664.0	25398998.0	96.0	0.2	6.4	0.2	0.1	0.0	3.7	89.5	35	76	75.45	7	2140230191	25.8	23.6	24.9	25.7	0.0	34.8	24.0	bulk
3825840	SRR2063305	SRP059509	SRS961409	SRX1059078	SRA272961	GEO		Genome-wide Circadian Control of Transcription at Active Enhancers Regulates Insulin Secretion and Diabetes Risk	The molecular clock is a transcriptional oscillator present in brain and peripheral cells that coordinates behavior and physiology with the solar cycle. Here we reveal that the clock gates insulin secretion through genome-wide transcriptional control of the pancreatic exocyst across species. Clock transcription factors bind to unique enhancer sites in cycling genes in beta cells that diverge from those in liver, revealing the dynamics of inter-tissue clock control of genomic and physiologic processes important in glucose homeostasis. Overall design: Transcriptome profiling in mouse and human islets at serial 4-hour time intervals by polyA RNA-Seq		GSM1711986: Mouse islet polyA RNA-Seq biological replicate 2 CT36; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Mouse islets were isolated by perfusing the pancreatic bile duct with collagenase Illumina stranded LT kit for RNA-Seq	NextSeq 500	cell type;;Pancreatic islet cells|genotype;;wild type|source_name;;C57BL/6 wild type mice|strain;;C57BL/6	GEO Accession;;GSM1711986		GSM1711986	Mouse islet polyA RNA-Seq biological replicate 2 CT36	4353981958	28849959	2015-11-10 17:09:03	1842088500	4353981958	28849959	2	28849959	index:0,count:28849959,average:75.46,stdev:1.23|index:1,count:28849959,average:75.46,stdev:1.26	GSM1711986_r1				in_mesa	26542580	4.9	3.33	0.07	3627271351	3597545220	3383406723	3374026267	99.18	99.72	27812302	26549041	153.013	408.125	127	369621	85.09	91.28	30731801	23667471	30731801	23667471	87.9	88.25	30731801	24446587	30731801	22881901	260705464	7.19	0.19	0	6.53	0	0.25	0	0.12	0	0.00	0	3.22	0	27813155	0	150	0	149.70	0	1.66	0	0.01	0	1.21	0	0.01	0	130.64	0	0.39	0	53826	0	28849959	0	1883374	0	73352	0	34020	0	0	0	929432	0	4242	0	0	0	44579	0	8847455	0	13683	0	8909959	0	89.88	0	25929781	0	191654	8474834	44.219447546099	28849959.0	27813155.0	53826.0	1883374.0	73352.0	34020.0	0.0	929432.0	25929781.0	96.4	0.2	6.5	0.3	0.1	0.0	3.2	89.9	35	76	75.46	7	2177099015	25.6	23.8	24.8	25.8	0.0	34.8	24.1	bulk
3825873	SRR2063306	SRP059509	SRS961408	SRX1059079	SRA272961	GEO		Genome-wide Circadian Control of Transcription at Active Enhancers Regulates Insulin Secretion and Diabetes Risk	The molecular clock is a transcriptional oscillator present in brain and peripheral cells that coordinates behavior and physiology with the solar cycle. Here we reveal that the clock gates insulin secretion through genome-wide transcriptional control of the pancreatic exocyst across species. Clock transcription factors bind to unique enhancer sites in cycling genes in beta cells that diverge from those in liver, revealing the dynamics of inter-tissue clock control of genomic and physiologic processes important in glucose homeostasis. Overall design: Transcriptome profiling in mouse and human islets at serial 4-hour time intervals by polyA RNA-Seq		GSM1711987: Mouse islet polyA RNA-Seq biological replicate 2 CT40; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Mouse islets were isolated by perfusing the pancreatic bile duct with collagenase Illumina stranded LT kit for RNA-Seq	NextSeq 500	cell type;;Pancreatic islet cells|genotype;;wild type|source_name;;C57BL/6 wild type mice|strain;;C57BL/6	GEO Accession;;GSM1711987		GSM1711987	Mouse islet polyA RNA-Seq biological replicate 2 CT40	4567446302	30296644	2015-11-10 17:09:03	1931620584	4567446302	30296644	2	30296644	index:0,count:30296644,average:75.39,stdev:1.65|index:1,count:30296644,average:75.37,stdev:1.66	GSM1711987_r1				in_mesa	26542580	5.39	3.34	0.06	3511088473	3486880590	3238717746	3237587972	99.31	99.97	29062873	28045836	135.409	343.204	115	471530	86.31	93.66	32616680	25085400	32616680	25085400	89.78	90.36	32616680	26093197	32616680	24203199	169675341	4.83	0.16	0	7.52	0	0.26	0	0.11	0	0.00	0	3.70	0	29063815	0	150	0	149.55	0	1.68	0	0.01	0	1.22	0	0.01	0	315.23	0	0.38	0	49865	0	30296644	0	2279123	0	80234	0	32047	0	0	0	1120548	0	4544	0	0	0	45377	0	9279194	0	14115	0	9343230	0	88.41	0	26784692	0	183222	8417634	45.942266758359	30296644.0	29063815.0	49865.0	2279123.0	80234.0	32047.0	0.0	1120548.0	26784692.0	95.9	0.2	7.5	0.3	0.1	0.0	3.7	88.4	35	76	75.39	7	2283913603	25.9	23.5	24.6	26.0	0.0	34.8	24.1	bulk
3825905	SRR2063307	SRP059509	SRS961407	SRX1059080	SRA272961	GEO		Genome-wide Circadian Control of Transcription at Active Enhancers Regulates Insulin Secretion and Diabetes Risk	The molecular clock is a transcriptional oscillator present in brain and peripheral cells that coordinates behavior and physiology with the solar cycle. Here we reveal that the clock gates insulin secretion through genome-wide transcriptional control of the pancreatic exocyst across species. Clock transcription factors bind to unique enhancer sites in cycling genes in beta cells that diverge from those in liver, revealing the dynamics of inter-tissue clock control of genomic and physiologic processes important in glucose homeostasis. Overall design: Transcriptome profiling in mouse and human islets at serial 4-hour time intervals by polyA RNA-Seq		GSM1711988: Mouse islet polyA RNA-Seq biological replicate 2 CT44; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Mouse islets were isolated by perfusing the pancreatic bile duct with collagenase Illumina stranded LT kit for RNA-Seq	NextSeq 500	cell type;;Pancreatic islet cells|genotype;;wild type|source_name;;C57BL/6 wild type mice|strain;;C57BL/6	GEO Accession;;GSM1711988		GSM1711988	Mouse islet polyA RNA-Seq biological replicate 2 CT44	5667819381	37548701	2015-11-10 17:09:03	2387283806	5667819381	37548701	2	37548701	index:0,count:37548701,average:75.47,stdev:1.14|index:1,count:37548701,average:75.47,stdev:1.17	GSM1711988_r1				in_mesa	26542580	5.08	3.31	0.06	4718344367	4681451719	4398945842	4389403270	99.22	99.78	36107634	34506877	152.701	407.196	126	495761	85.76	92.02	39864935	30965941	39864935	30965941	88.52	88.92	39864935	31961901	39864935	29923295	301427792	6.39	0.18	0	6.54	0	0.25	0	0.11	0	0.00	0	3.48	0	36108781	0	150	0	149.74	0	1.72	0	0.01	0	1.24	0	0.01	0	136.96	0	0.37	0	68628	0	37548701	0	2456835	0	93863	0	41080	0	0	0	1304977	0	5567	0	0	0	59797	0	11675402	0	17963	0	11758729	0	89.62	0	33651946	0	199272	11202268	56.215966116665	37548701.0	36108781.0	68628.0	2456835.0	93863.0	41080.0	0.0	1304977.0	33651946.0	96.2	0.2	6.5	0.2	0.1	0.0	3.5	89.6	35	76	75.47	7	2833980536	25.7	23.7	24.7	25.8	0.0	34.8	24.1	bulk
3826193	SRR2063310	SRP059509	SRS961404	SRX1059083	SRA272961	GEO		Genome-wide Circadian Control of Transcription at Active Enhancers Regulates Insulin Secretion and Diabetes Risk	The molecular clock is a transcriptional oscillator present in brain and peripheral cells that coordinates behavior and physiology with the solar cycle. Here we reveal that the clock gates insulin secretion through genome-wide transcriptional control of the pancreatic exocyst across species. Clock transcription factors bind to unique enhancer sites in cycling genes in beta cells that diverge from those in liver, revealing the dynamics of inter-tissue clock control of genomic and physiologic processes important in glucose homeostasis. Overall design: Transcriptome profiling in mouse and human islets at serial 4-hour time intervals by polyA RNA-Seq		GSM1711991: Mouse islet polyA RNA-Seq biological replicate 3 CT8; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Mouse islets were isolated by perfusing the pancreatic bile duct with collagenase Illumina stranded LT kit for RNA-Seq	NextSeq 500	cell type;;Pancreatic islet cells|genotype;;wild type|source_name;;C57BL/6 wild type mice|strain;;C57BL/6	GEO Accession;;GSM1711991		GSM1711991	Mouse islet polyA RNA-Seq biological replicate 3 CT8	4557780805	30218062	2015-11-10 17:09:03	1942677387	4557780805	30218062	2	30218062	index:0,count:30218062,average:75.42,stdev:1.51|index:1,count:30218062,average:75.41,stdev:1.55	GSM1711991_r1				in_mesa	26542580	5.35	3.51	0.07	3864540275	3817546797	3593229532	3571126957	98.78	99.38	29137563	28015341	150.920	368.431	132	437591	84.13	90.51	32284004	24514922	32284004	24514922	87.43	87.72	32284004	25476222	32284004	23761155	303665162	7.86	0.17	0	6.79	0	0.28	0	0.13	0	0.00	0	3.17	0	29138874	0	150	0	149.58	0	1.55	0	0.01	0	1.20	0	0.00	0	142.02	0	0.40	0	51803	0	30218062	0	2052140	0	84694	0	37821	0	0	0	956673	0	4558	0	0	0	47030	0	8628877	0	13499	0	8693964	0	89.64	0	27086734	0	189603	8435040	44.487903672410	30218062.0	29138874.0	51803.0	2052140.0	84694.0	37821.0	0.0	956673.0	27086734.0	96.4	0.2	6.8	0.3	0.1	0.0	3.2	89.6	35	76	75.42	7	2279092880	26.4	23.0	23.8	26.9	0.0	34.8	24.2	bulk
1463593	SRR2075552	SRP059792	SRS969747	SRX1070581	SRA273724	Yale University	Kaech Lab	The transcription factors ZEB2 and T-bet cooperate to program cytotoxic T cell terminal differentiation	T-bet is critical for cytotoxic T lymphocyte (CTL) differentiation, but it is unclear how it operates in a graded manner in the formation of both terminal effector and memory precursor cells during infection. We find that at high concentrations T-bet induced expression of Zeb2 mRNA, which then triggered CTLs to adopt terminally differentiated states. ZEB2 and T-bet cooperate to switch on a terminal CTL differentiation program, while simultaneously repressing genes necessary for central memory CTL development. Chromatin Immunoprecipitation sequencing (ChIP-seq) showed that a large proportion of these genes were bound by T-bet, and this binding was altered by ZEB2 deficiency. Furthermore, T-bet overexpression could not fully bypass ZEB2 function. Thus, the coordinated actions of T-bet and ZEB2 outline a novel genetic pathway that forces commitment of CTLs to terminal differentiation, thereby restricting their memory cell potential.		RNA-seq of WT P14 CTLs isolated 8 d.p.i. with LCMV replicate 1		RNA-seq of WT P14 CTLs isolated 8 d.p.i. with LCMV replicate 1	CD8_WT.1	RNA-Seq	TRANSCRIPTOMIC	other	paired				Illumina HiSeq 2500	age;;6-8 weeks|BioSampleModel;;Model organism or animal|breed;;C57BL/6|cell_type;;P14 CD8+ T cells|genotype;;WT|ID;;1|sex;;female|tissue;;Splenocytes	alignment_software;;STAR	150	CD8_WT.1	RNA-seq of WT P14 CTLs isolated 8 d.p.i. with LCMV replicate 1	4655386153	31018381	2015-09-15 00:00:00	2231170851	4655386153	31018381	2	31018381	index:0,count:31014676,average:75.23,stdev:3.99|index:1,count:31017303,average:74.86,stdev:5.14	SAMN03785068.bam						2.42	3.35	0.14	4374784779	4310726165	4114335361	4071342837	98.54	98.96	30649914	27960651	201.811	992.545	154	253653	79.44	84.5	33813634	24349357	33813634	24349357	81.45	81.43	33813634	24963440	33813634	23467110	620916172	14.19	0.29	0.00	5.91	18.54	0.17	1.19	0.00	0.04	0.00	0.00	1.00	0.02	30650545	4723	150	75	149.28	75.86	1.51	0.00	0.00	0.00	1.18	0.00	0.00	0.00	487.55	17.22	0.11	0.01	88408	0	31013598	4783	1833137	887	52737	57	207	2	0	0	310109	1	6453	1	0	0	59220	0	8420297	298	14096	0	8500066	299	92.92	80.20	28817408	3836	158869	8598895	54.125694754798	31018381.0	30655268.0	88408.0	1834024.0	52794.0	209.0	0.0	310110.0	28821244.0	98.8	0.3	5.9	0.2	0.0	0.0	1.0	92.9	67	76	75.94	38	363240	27.3	22.7	22.9	27.0	0.0	37.2	30.4	bulk
1463610	SRR2075553	SRP059792	SRS969738	SRX1070582	SRA273724	Yale University	Kaech Lab	The transcription factors ZEB2 and T-bet cooperate to program cytotoxic T cell terminal differentiation	T-bet is critical for cytotoxic T lymphocyte (CTL) differentiation, but it is unclear how it operates in a graded manner in the formation of both terminal effector and memory precursor cells during infection. We find that at high concentrations T-bet induced expression of Zeb2 mRNA, which then triggered CTLs to adopt terminally differentiated states. ZEB2 and T-bet cooperate to switch on a terminal CTL differentiation program, while simultaneously repressing genes necessary for central memory CTL development. Chromatin Immunoprecipitation sequencing (ChIP-seq) showed that a large proportion of these genes were bound by T-bet, and this binding was altered by ZEB2 deficiency. Furthermore, T-bet overexpression could not fully bypass ZEB2 function. Thus, the coordinated actions of T-bet and ZEB2 outline a novel genetic pathway that forces commitment of CTLs to terminal differentiation, thereby restricting their memory cell potential.		RNA-seq of WT P14 CTLs isolated 8 d.p.i. with LCMV replicate 2		RNA-seq of WT P14 CTLs isolated 8 d.p.i. with LCMV replicate 2	CD8_WT.2	RNA-Seq	TRANSCRIPTOMIC	other	paired				Illumina HiSeq 2500	age;;6-8 weeks|BioSampleModel;;Model organism or animal|breed;;C57BL/6|cell_type;;P14 CD8+ T cells|genotype;;WT|ID;;2|sex;;female|tissue;;Splenocytes	alignment_software;;STAR	150	CD8_WT.2	RNA-seq of WT P14 CTLs isolated 8 d.p.i. with LCMV replicate 2	3389132120	22582964	2015-09-15 00:00:00	1625308492	3389132120	22582964	2	22582964	index:0,count:22581444,average:75.22,stdev:4.03|index:1,count:22582199,average:74.86,stdev:5.14	SAMN03785069.bam						2.71	3.25	0.15	3170701583	3130341354	2971749863	2946502615	98.73	99.15	22297796	20354612	201.996	996.942	155	175559	79.02	84.34	24693483	17619240	24693483	17619240	81.29	81.21	24693483	18125308	24693483	16966551	458867583	14.47	0.30	0.00	6.23	15.97	0.17	0.66	0.00	0.00	0.00	0.00	1.08	0.04	22298295	2269	150	75	149.27	75.83	1.66	0.00	0.00	0.00	1.22	0.00	0.00	0.00	298.86	4.11	0.11	0.01	67312	0	22580679	2285	1407221	365	37566	15	133	0	0	0	244685	1	4592	0	0	0	41907	0	6002752	113	9939	0	6059190	113	92.52	83.33	20891074	1904	144553	6105512	42.237186360712	22582964.0	22300564.0	67312.0	1407586.0	37581.0	133.0	0.0	244686.0	20892978.0	98.7	0.3	6.2	0.2	0.0	0.0	1.1	92.5	69	76	75.95	37	173539	27.6	22.6	22.7	27.1	0.0	37.0	29.9	bulk
1463626	SRR2075554	SRP059792	SRS969737	SRX1070583	SRA273724	Yale University	Kaech Lab	The transcription factors ZEB2 and T-bet cooperate to program cytotoxic T cell terminal differentiation	T-bet is critical for cytotoxic T lymphocyte (CTL) differentiation, but it is unclear how it operates in a graded manner in the formation of both terminal effector and memory precursor cells during infection. We find that at high concentrations T-bet induced expression of Zeb2 mRNA, which then triggered CTLs to adopt terminally differentiated states. ZEB2 and T-bet cooperate to switch on a terminal CTL differentiation program, while simultaneously repressing genes necessary for central memory CTL development. Chromatin Immunoprecipitation sequencing (ChIP-seq) showed that a large proportion of these genes were bound by T-bet, and this binding was altered by ZEB2 deficiency. Furthermore, T-bet overexpression could not fully bypass ZEB2 function. Thus, the coordinated actions of T-bet and ZEB2 outline a novel genetic pathway that forces commitment of CTLs to terminal differentiation, thereby restricting their memory cell potential.		RNA-seq of WT P14 CTLs isolated 8 d.p.i. with LCMV replicate 3		RNA-seq of WT P14 CTLs isolated 8 d.p.i. with LCMV replicate 3	CD8_WT.3	RNA-Seq	TRANSCRIPTOMIC	other	paired				Illumina HiSeq 2500	age;;6-8 weeks|BioSampleModel;;Model organism or animal|breed;;C57BL/6|cell_type;;P14 CD8+ T cells|genotype;;WT|ID;;3|sex;;female|tissue;;Splenocytes	alignment_software;;STAR	150	CD8_WT.3	RNA-seq of WT P14 CTLs isolated 8 d.p.i. with LCMV replicate 3	3271395288	21799477	2015-09-15 00:00:00	1565180083	3271395288	21799477	2	21799477	index:0,count:21797567,average:75.22,stdev:4.04|index:1,count:21798586,average:74.86,stdev:5.14	SAMN03785070.bam						2.55	3.27	0.16	3059571786	3016778223	2866054641	2838556398	98.6	99.04	21525754	19745785	200.061	990.741	148	176141	77.66	82.93	23890740	16716960	23890740	16716960	79.94	79.82	23890740	17207667	23890740	16089249	486104887	15.89	0.27	0.00	6.28	19.31	0.18	0.96	0.00	0.00	0.00	0.00	1.06	0.00	21526225	2774	150	75	149.31	75.87	1.57	0.00	0.00	0.00	1.20	0.00	0.00	0.00	516.24	10.08	0.10	0.01	58563	0	21796676	2801	1369406	541	39441	27	116	0	0	0	230894	0	4390	0	0	0	40097	0	5697633	160	9490	0	5751610	160	92.48	79.72	20156819	2233	146367	5797760	39.611114527182	21799477.0	21528999.0	58563.0	1369947.0	39468.0	116.0	0.0	230894.0	20159052.0	98.8	0.3	6.3	0.2	0.0	0.0	1.1	92.5	68	76	75.94	37	212712	27.7	22.8	22.8	26.6	0.0	37.1	30.1	bulk
1463896	SRR2075565	SRP059792	SRS969728	SRX1070594	SRA273724	Yale University	Kaech Lab	The transcription factors ZEB2 and T-bet cooperate to program cytotoxic T cell terminal differentiation	T-bet is critical for cytotoxic T lymphocyte (CTL) differentiation, but it is unclear how it operates in a graded manner in the formation of both terminal effector and memory precursor cells during infection. We find that at high concentrations T-bet induced expression of Zeb2 mRNA, which then triggered CTLs to adopt terminally differentiated states. ZEB2 and T-bet cooperate to switch on a terminal CTL differentiation program, while simultaneously repressing genes necessary for central memory CTL development. Chromatin Immunoprecipitation sequencing (ChIP-seq) showed that a large proportion of these genes were bound by T-bet, and this binding was altered by ZEB2 deficiency. Furthermore, T-bet overexpression could not fully bypass ZEB2 function. Thus, the coordinated actions of T-bet and ZEB2 outline a novel genetic pathway that forces commitment of CTLs to terminal differentiation, thereby restricting their memory cell potential.		RNA-seq of TE (KLRGhi IL7Rlo) P14 CTLs isolated 8 d.p.i. with LCMV replicate 2		RNA-seq of TE (KLRGhi IL7Rlo) P14 CTLs isolated 8 d.p.i. with LCMV replicate 2	CD8_TE.2	RNA-Seq	TRANSCRIPTOMIC	other	paired				Illumina HiSeq 2500	age;;6-8 weeks|BioSampleModel;;Model organism or animal|breed;;C57BL/6|cell_type;;P14 CD8+ KLRG1hi IL7Rlo T cells|genotype;;WT|ID;;14|sex;;female|tissue;;Splenocytes	alignment_software;;STAR	150	CD8_TE.2	RNA-seq of TE (KLRGhi IL7Rlo) P14 CTLs isolated 8 d.p.i. with LCMV replicate 2	4118172833	27555039	2015-09-15 00:00:00	2017844767	4118172833	27555039	2	27555039	index:0,count:27553292,average:74.83,stdev:4.75|index:1,count:27554000,average:74.63,stdev:5.52	SAMN03785081.bam						1.73	3.22	0.08	3693599548	3664883363	3491323028	3479530643	99.22	99.66	27242730	24935938	185.083	998.548	127	236223	81.48	86.25	29922170	22199061	29922170	22199061	82.86	82.99	29922170	22574975	29922170	21357678	477451117	12.93	0.26	0.00	5.47	13.10	0.18	0.83	0.00	0.07	0.00	0.00	0.94	0.00	27243415	2761	149	75	148.66	75.80	1.62	0.00	0.00	0.00	1.26	0.00	0.00	0.00	495.94	10.03	0.11	0.01	71350	0	27552253	2786	1506752	365	50207	23	131	2	0	0	258500	0	6756	0	0	0	57223	0	7986557	165	11387	0	8061923	165	93.41	86.00	25736663	2396	158303	7901725	49.915194279325	27555039.0	27246176.0	71350.0	1507117.0	50230.0	133.0	0.0	258500.0	25739059.0	98.9	0.3	5.5	0.2	0.0	0.0	0.9	93.4	67	76	75.92	37	211501	27.6	22.2	22.2	28.0	0.0	37.2	30.1	bulk
1463912	SRR2075566	SRP059792	SRS969727	SRX1070595	SRA273724	Yale University	Kaech Lab	The transcription factors ZEB2 and T-bet cooperate to program cytotoxic T cell terminal differentiation	T-bet is critical for cytotoxic T lymphocyte (CTL) differentiation, but it is unclear how it operates in a graded manner in the formation of both terminal effector and memory precursor cells during infection. We find that at high concentrations T-bet induced expression of Zeb2 mRNA, which then triggered CTLs to adopt terminally differentiated states. ZEB2 and T-bet cooperate to switch on a terminal CTL differentiation program, while simultaneously repressing genes necessary for central memory CTL development. Chromatin Immunoprecipitation sequencing (ChIP-seq) showed that a large proportion of these genes were bound by T-bet, and this binding was altered by ZEB2 deficiency. Furthermore, T-bet overexpression could not fully bypass ZEB2 function. Thus, the coordinated actions of T-bet and ZEB2 outline a novel genetic pathway that forces commitment of CTLs to terminal differentiation, thereby restricting their memory cell potential.		RNA-seq of TE (KLRGhi IL7Rlo) P14 CTLs isolated 8 d.p.i. with LCMV replicate 3		RNA-seq of TE (KLRGhi IL7Rlo) P14 CTLs isolated 8 d.p.i. with LCMV replicate 3	CD8_TE.3	RNA-Seq	TRANSCRIPTOMIC	other	paired				Illumina HiSeq 2500	age;;6-8 weeks|BioSampleModel;;Model organism or animal|breed;;C57BL/6|cell_type;;P14 CD8+ KLRG1hi IL7Rlo T cells|genotype;;WT|ID;;15|sex;;female|tissue;;Splenocytes	alignment_software;;STAR	150	CD8_TE.3	RNA-seq of TE (KLRGhi IL7Rlo) P14 CTLs isolated 8 d.p.i. with LCMV replicate 3	4785349480	32017867	2015-09-15 00:00:00	2345609463	4785349480	32017867	2	32017867	index:0,count:32010795,average:74.84,stdev:4.73|index:1,count:32016521,average:74.64,stdev:5.50	SAMN03785082.bam						1.74	3.25	0.07	4324288748	4284823699	4093830223	4074907678	99.09	99.54	31650321	28813391	189.228	1095.777	130	261998	83.17	87.89	34679513	26323158	34679513	26323158	84.48	84.69	34679513	26739824	34679513	25363180	485029597	11.22	0.27	0.01	5.32	18.78	0.18	0.87	0.00	0.05	0.00	0.00	0.94	0.00	31651064	8341	149	75	148.67	75.86	1.56	0.00	0.00	0.00	1.25	0.00	0.00	0.00	533.49	30.30	0.11	0.02	87957	1	32009449	8418	1702323	1581	58078	73	140	4	0	0	300167	0	7775	0	0	0	66330	1	9399453	487	13228	0	9486786	488	93.56	80.30	29948741	6760	158929	9341574	58.778284642828	32017867.0	31659405.0	87958.0	1703904.0	58151.0	144.0	0.0	300167.0	29955501.0	98.9	0.3	5.3	0.2	0.0	0.0	0.9	93.6	68	76	75.94	38	639244	28.1	22.5	22.1	27.3	0.0	37.5	31.3	bulk
1464088	SRR2075571	SRP059792	SRS969722	SRX1070600	SRA273724	Yale University	Kaech Lab	The transcription factors ZEB2 and T-bet cooperate to program cytotoxic T cell terminal differentiation	T-bet is critical for cytotoxic T lymphocyte (CTL) differentiation, but it is unclear how it operates in a graded manner in the formation of both terminal effector and memory precursor cells during infection. We find that at high concentrations T-bet induced expression of Zeb2 mRNA, which then triggered CTLs to adopt terminally differentiated states. ZEB2 and T-bet cooperate to switch on a terminal CTL differentiation program, while simultaneously repressing genes necessary for central memory CTL development. Chromatin Immunoprecipitation sequencing (ChIP-seq) showed that a large proportion of these genes were bound by T-bet, and this binding was altered by ZEB2 deficiency. Furthermore, T-bet overexpression could not fully bypass ZEB2 function. Thus, the coordinated actions of T-bet and ZEB2 outline a novel genetic pathway that forces commitment of CTLs to terminal differentiation, thereby restricting their memory cell potential.		RNA-seq of WT KLRG1hi P14 CTLs isolated 8 d.p.i. with LCMV replicate 1		RNA-seq of WT KLRG1hi P14 CTLs isolated 8 d.p.i. with LCMV replicate 1	CD8_Klrg1hi_WT.1	RNA-Seq	TRANSCRIPTOMIC	other	paired				Illumina HiSeq 2500	age;;6-8 weeks|BioSampleModel;;Model organism or animal|breed;;C57BL/6|cell_type;;P14 CD8+ KLRG1hi T cells|genotype;;WT|ID;;20|sex;;female|tissue;;Splenocytes	alignment_software;;STAR	150	CD8_Klrg1hi_WT.1	RNA-seq of WT KLRG1hi P14 CTLs isolated 8 d.p.i. with LCMV replicate 1	3712894099	24779744	2015-09-15 00:00:00	1848546765	3712894099	24779744	2	24779744	index:0,count:24779372,average:75.30,stdev:3.90|index:1,count:24778820,average:74.54,stdev:5.72	SAMN03785087.bam						8.34	3.9	0.04	3215330897	3207536906	2737021492	2752610468	99.76	100.57	24180687	22026811	184.939	1008.035	124	202900	82.68	97.32	29674814	19992855	29674814	19992855	92.66	93.01	29674814	22406215	29674814	19106762	61448375	1.91	0.41	0.00	14.69	17.13	0.18	0.85	0.00	0.08	0.00	0.00	2.22	0.00	24182276	1284	149	75	148.80	75.58	1.99	0.00	0.01	0.00	1.31	0.00	0.00	0.00	474.48	4.67	0.13	0.03	102699	0	24778448	1296	3639896	222	45207	11	131	1	0	0	550834	0	6285	0	0	0	43620	1	7364714	203	10512	0	7425131	204	82.90	81.94	20542380	1062	125464	7270533	57.949156730217	24779744.0	24183560.0	102699.0	3640118.0	45218.0	132.0	0.0	550834.0	20543442.0	97.6	0.4	14.7	0.2	0.0	0.0	2.2	82.9	67	76	75.87	37	98325	24.8	24.6	24.0	26.6	0.0	35.2	27.1	bulk
1464104	SRR2075572	SRP059792	SRS969721	SRX1070601	SRA273724	Yale University	Kaech Lab	The transcription factors ZEB2 and T-bet cooperate to program cytotoxic T cell terminal differentiation	T-bet is critical for cytotoxic T lymphocyte (CTL) differentiation, but it is unclear how it operates in a graded manner in the formation of both terminal effector and memory precursor cells during infection. We find that at high concentrations T-bet induced expression of Zeb2 mRNA, which then triggered CTLs to adopt terminally differentiated states. ZEB2 and T-bet cooperate to switch on a terminal CTL differentiation program, while simultaneously repressing genes necessary for central memory CTL development. Chromatin Immunoprecipitation sequencing (ChIP-seq) showed that a large proportion of these genes were bound by T-bet, and this binding was altered by ZEB2 deficiency. Furthermore, T-bet overexpression could not fully bypass ZEB2 function. Thus, the coordinated actions of T-bet and ZEB2 outline a novel genetic pathway that forces commitment of CTLs to terminal differentiation, thereby restricting their memory cell potential.		RNA-seq of WT KLRG1hi P14 CTLs isolated 8 d.p.i. with LCMV replicate 2		RNA-seq of WT KLRG1hi P14 CTLs isolated 8 d.p.i. with LCMV replicate 2	CD8_Klrg1hi_WT.2	RNA-Seq	TRANSCRIPTOMIC	other	paired				Illumina HiSeq 2500	age;;6-8 weeks|BioSampleModel;;Model organism or animal|breed;;C57BL/6|cell_type;;P14 CD8+ KLRG1hi T cells|genotype;;WT|ID;;21|sex;;female|tissue;;Splenocytes	alignment_software;;STAR	150	CD8_Klrg1hi_WT.2	RNA-seq of WT KLRG1hi P14 CTLs isolated 8 d.p.i. with LCMV replicate 2	3759476667	25068707	2015-09-15 00:00:00	1831394615	3759476667	25068707	2	25068707	index:0,count:25068228,average:75.31,stdev:3.88|index:1,count:25067783,average:74.66,stdev:5.48	SAMN03785088.bam						2.68	3.38	0.09	3342942530	3320290730	3129804029	3123916188	99.32	99.81	24722956	22255420	193.214	1084.719	124	191152	82.63	88.34	27474055	20430454	27474055	20430454	84.96	85.08	27474055	21006355	27474055	19677171	359712549	10.76	0.26	0.00	6.37	8.77	0.21	0.86	0.00	0.50	0.00	0.00	1.16	0.00	24723854	1384	149	75	149.11	75.65	1.58	0.00	0.01	0.00	1.24	0.00	0.00	0.00	379.17	5.05	0.11	0.03	66353	0	25067304	1403	1596250	123	51430	12	108	7	0	0	291912	0	6534	0	0	0	51485	2	7604293	184	12239	0	7674551	186	92.26	89.88	23127604	1261	167967	7449908	44.353402751731	25068707.0	24725238.0	66353.0	1596373.0	51442.0	115.0	0.0	291912.0	23128865.0	98.6	0.3	6.4	0.2	0.0	0.0	1.2	92.3	67	76	75.89	37	106478	25.7	23.7	22.9	27.7	0.0	35.7	27.6	bulk
1464120	SRR2075573	SRP059792	SRS969720	SRX1070602	SRA273724	Yale University	Kaech Lab	The transcription factors ZEB2 and T-bet cooperate to program cytotoxic T cell terminal differentiation	T-bet is critical for cytotoxic T lymphocyte (CTL) differentiation, but it is unclear how it operates in a graded manner in the formation of both terminal effector and memory precursor cells during infection. We find that at high concentrations T-bet induced expression of Zeb2 mRNA, which then triggered CTLs to adopt terminally differentiated states. ZEB2 and T-bet cooperate to switch on a terminal CTL differentiation program, while simultaneously repressing genes necessary for central memory CTL development. Chromatin Immunoprecipitation sequencing (ChIP-seq) showed that a large proportion of these genes were bound by T-bet, and this binding was altered by ZEB2 deficiency. Furthermore, T-bet overexpression could not fully bypass ZEB2 function. Thus, the coordinated actions of T-bet and ZEB2 outline a novel genetic pathway that forces commitment of CTLs to terminal differentiation, thereby restricting their memory cell potential.		RNA-seq of WT KLRG1hi P14 CTLs isolated 8 d.p.i. with LCMV replicate 3		RNA-seq of WT KLRG1hi P14 CTLs isolated 8 d.p.i. with LCMV replicate 3	CD8_Klrg1hi_WT.3	RNA-Seq	TRANSCRIPTOMIC	other	paired				Illumina HiSeq 2500	age;;6-8 weeks|BioSampleModel;;Model organism or animal|breed;;C57BL/6|cell_type;;P14 CD8+ KLRG1hi T cells|genotype;;WT|ID;;22|sex;;female|tissue;;Splenocytes	alignment_software;;STAR	150	CD8_Klrg1hi_WT.3	RNA-seq of WT KLRG1hi P14 CTLs isolated 8 d.p.i. with LCMV replicate 3	3338654728	22265761	2015-09-15 00:00:00	1628060615	3338654728	22265761	2	22265761	index:0,count:22265306,average:75.32,stdev:3.85|index:1,count:22264829,average:74.63,stdev:5.55	SAMN03785089.bam						2.49	3.32	0.09	2925083450	2905982801	2745831693	2740629614	99.35	99.81	21962559	20039055	184.559	992.765	124	180303	79.65	84.94	24336435	17494659	24336435	17494659	81.58	81.56	24336435	17917023	24336435	16797507	409110777	13.99	0.27	0.00	6.14	9.23	0.19	0.65	0.00	0.22	0.00	0.00	1.16	0.00	21963389	1375	149	75	149.10	75.60	1.83	0.00	0.01	0.00	1.31	0.00	0.00	0.00	568.45	4.99	0.11	0.01	60093	0	22264374	1387	1366955	128	42766	9	84	3	0	0	258135	0	5563	0	0	0	43945	4	6349550	164	10515	0	6409573	168	92.51	89.91	20596434	1247	164225	6147522	37.433533262293	22265761.0	21964764.0	60093.0	1367083.0	42775.0	87.0	0.0	258135.0	20597681.0	98.6	0.3	6.1	0.2	0.0	0.0	1.2	92.5	67	76	75.89	37	105255	25.0	24.3	22.9	27.7	0.0	35.5	27.2	bulk
731918	SRR2075561	SRP059792	SRS969732	SRX1070590	SRA273724	Yale University	Kaech Lab	The transcription factors ZEB2 and T-bet cooperate to program cytotoxic T cell terminal differentiation	T-bet is critical for cytotoxic T lymphocyte (CTL) differentiation, but it is unclear how it operates in a graded manner in the formation of both terminal effector and memory precursor cells during infection. We find that at high concentrations T-bet induced expression of Zeb2 mRNA, which then triggered CTLs to adopt terminally differentiated states. ZEB2 and T-bet cooperate to switch on a terminal CTL differentiation program, while simultaneously repressing genes necessary for central memory CTL development. Chromatin Immunoprecipitation sequencing (ChIP-seq) showed that a large proportion of these genes were bound by T-bet, and this binding was altered by ZEB2 deficiency. Furthermore, T-bet overexpression could not fully bypass ZEB2 function. Thus, the coordinated actions of T-bet and ZEB2 outline a novel genetic pathway that forces commitment of CTLs to terminal differentiation, thereby restricting their memory cell potential.		RNA-seq of MP (KLRG1lo IL7Rhi) P14 CTLs isolated 8 d.p.i. with LCMV replicate 1		RNA-seq of MP (KLRG1lo IL7Rhi) P14 CTLs isolated 8 d.p.i. with LCMV replicate 1	CD8_MP.1	RNA-Seq	TRANSCRIPTOMIC	other	paired				Illumina HiSeq 2500	age;;6-8 weeks|BioSampleModel;;Model organism or animal|breed;;C57BL/6|cell_type;;P14 CD8+ KLRG1lo IL7Rhi T cells|genotype;;WT|ID;;10|sex;;female|tissue;;Splenocytes	alignment_software;;STAR	150	CD8_MP.1	RNA-seq of MP (KLRG1lo IL7Rhi) P14 CTLs isolated 8 d.p.i. with LCMV replicate 1	4937775836	33043797	2015-09-15 00:00:00	2437119860	4937775836	33043797	2	33043797	index:0,count:33042378,average:74.74,stdev:5.00|index:1,count:33042754,average:74.70,stdev:5.40	SAMN03785077.bam						1.85	3.34	0.09	4356412648	4306930215	4099746803	4074110498	98.86	99.37	32635444	30123306	178.677	1030.218	126	286900	80.75	85.87	36100781	26354845	36100781	26354845	82.48	82.64	36100781	26917019	36100781	25363518	567329328	13.02	0.26	0.04	5.89	10.07	0.21	0.89	0.00	0.20	0.00	0.00	1.02	0.00	32636251	2435	149	75	148.66	75.80	1.61	0.00	0.00	0.00	1.23	0.00	0.00	0.00	466.47	4.43	0.10	0.01	84890	1	33041335	2462	1945247	248	68115	22	178	5	0	0	336791	0	7302	0	0	0	65953	2	9289153	140	13336	0	9375744	142	92.89	88.83	30691004	2187	160329	9102012	56.770839960332	33043797.0	32638686.0	84891.0	1945495.0	68137.0	183.0	0.0	336791.0	30693191.0	98.8	0.3	5.9	0.2	0.0	0.0	1.0	92.9	67	76	75.91	37	186891	27.0	22.2	21.9	28.9	0.0	36.7	29.0	bulk
731926	SRR2075562	SRP059792	SRS969731	SRX1070591	SRA273724	Yale University	Kaech Lab	The transcription factors ZEB2 and T-bet cooperate to program cytotoxic T cell terminal differentiation	T-bet is critical for cytotoxic T lymphocyte (CTL) differentiation, but it is unclear how it operates in a graded manner in the formation of both terminal effector and memory precursor cells during infection. We find that at high concentrations T-bet induced expression of Zeb2 mRNA, which then triggered CTLs to adopt terminally differentiated states. ZEB2 and T-bet cooperate to switch on a terminal CTL differentiation program, while simultaneously repressing genes necessary for central memory CTL development. Chromatin Immunoprecipitation sequencing (ChIP-seq) showed that a large proportion of these genes were bound by T-bet, and this binding was altered by ZEB2 deficiency. Furthermore, T-bet overexpression could not fully bypass ZEB2 function. Thus, the coordinated actions of T-bet and ZEB2 outline a novel genetic pathway that forces commitment of CTLs to terminal differentiation, thereby restricting their memory cell potential.		RNA-seq of MP (KLRG1lo IL7Rhi) P14 CTLs isolated 8 d.p.i. with LCMV replicate 2		RNA-seq of MP (KLRG1lo IL7Rhi) P14 CTLs isolated 8 d.p.i. with LCMV replicate 2	CD8_MP.2	RNA-Seq	TRANSCRIPTOMIC	other	paired				Illumina HiSeq 2500	age;;6-8 weeks|BioSampleModel;;Model organism or animal|breed;;C57BL/6|cell_type;;P14 CD8+ KLRG1lo IL7Rhi T cells|genotype;;WT|ID;;11|sex;;female|tissue;;Splenocytes	alignment_software;;STAR	150	CD8_MP.2	RNA-seq of MP (KLRG1lo IL7Rhi) P14 CTLs isolated 8 d.p.i. with LCMV replicate 2	4175098150	27939785	2015-09-15 00:00:00	2055957673	4175098150	27939785	2	27939785	index:0,count:27938614,average:74.74,stdev:4.99|index:1,count:27938912,average:74.69,stdev:5.41	SAMN03785078.bam						2.19	3.34	0.09	3685121842	3651606676	3441412905	3428190498	99.09	99.62	27561502	25371576	179.538	1012.047	126	244964	81.18	87.0	30817948	22374066	30817948	22374066	83.48	83.61	30817948	23007651	30817948	21502855	439672170	11.93	0.28	0.00	6.60	13.01	0.22	0.44	0.00	0.10	0.00	0.00	1.13	0.00	27562259	2033	149	75	148.63	75.81	1.68	0.00	0.00	0.00	1.25	0.00	0.00	0.00	523.83	7.36	0.10	0.01	76953	0	27937741	2044	1843574	266	60095	9	166	2	0	0	315221	0	6468	0	0	0	57643	1	8082322	134	11363	0	8157796	135	92.06	86.45	25718685	1767	153718	7943054	51.672894521136	27939785.0	27564292.0	76953.0	1843840.0	60104.0	168.0	0.0	315221.0	25720452.0	98.7	0.3	6.6	0.2	0.0	0.0	1.1	92.1	67	76	75.90	37	155132	27.0	22.5	22.5	28.0	0.0	36.7	29.0	bulk
731934	SRR2075563	SRP059792	SRS969730	SRX1070592	SRA273724	Yale University	Kaech Lab	The transcription factors ZEB2 and T-bet cooperate to program cytotoxic T cell terminal differentiation	T-bet is critical for cytotoxic T lymphocyte (CTL) differentiation, but it is unclear how it operates in a graded manner in the formation of both terminal effector and memory precursor cells during infection. We find that at high concentrations T-bet induced expression of Zeb2 mRNA, which then triggered CTLs to adopt terminally differentiated states. ZEB2 and T-bet cooperate to switch on a terminal CTL differentiation program, while simultaneously repressing genes necessary for central memory CTL development. Chromatin Immunoprecipitation sequencing (ChIP-seq) showed that a large proportion of these genes were bound by T-bet, and this binding was altered by ZEB2 deficiency. Furthermore, T-bet overexpression could not fully bypass ZEB2 function. Thus, the coordinated actions of T-bet and ZEB2 outline a novel genetic pathway that forces commitment of CTLs to terminal differentiation, thereby restricting their memory cell potential.		RNA-seq of MP (KLRG1lo IL7Rhi) P14 CTLs isolated 8 d.p.i. with LCMV replicate 3		RNA-seq of MP (KLRG1lo IL7Rhi) P14 CTLs isolated 8 d.p.i. with LCMV replicate 3	CD8_MP.3	RNA-Seq	TRANSCRIPTOMIC	other	paired				Illumina HiSeq 2500	age;;6-8 weeks|BioSampleModel;;Model organism or animal|breed;;C57BL/6|cell_type;;P14 CD8+ KLRG1lo IL7Rhi T cells|genotype;;WT|ID;;12|sex;;female|tissue;;Splenocytes	alignment_software;;STAR	150	CD8_MP.3	RNA-seq of MP (KLRG1lo IL7Rhi) P14 CTLs isolated 8 d.p.i. with LCMV replicate 3	3712913814	24838555	2015-09-15 00:00:00	1826755768	3712913814	24838555	2	24838555	index:0,count:24836929,average:74.77,stdev:4.95|index:1,count:24837798,average:74.72,stdev:5.35	SAMN03785079.bam						1.88	3.35	0.09	3278983220	3240735076	3084434257	3064299784	98.83	99.35	24526299	22611406	179.862	1031.295	125	215273	80.78	85.94	27154430	19812780	27154430	19812780	82.5	82.67	27154430	20233966	27154430	19057426	423663994	12.92	0.27	0.00	5.93	15.65	0.21	1.01	0.00	0.04	0.00	0.00	1.04	0.00	24526924	2358	149	75	148.71	75.81	1.64	0.00	0.00	0.00	1.25	0.00	0.00	0.00	516.82	8.58	0.10	0.02	66078	0	24836172	2383	1473219	373	52054	24	131	1	0	0	257063	0	5769	0	0	0	49683	0	6985485	129	10117	0	7051054	129	92.82	83.30	23053705	1985	150860	6853476	45.429378231473	24838555.0	24529282.0	66078.0	1473592.0	52078.0	132.0	0.0	257063.0	23055690.0	98.8	0.3	5.9	0.2	0.0	0.0	1.0	92.8	68	76	75.92	37	180911	27.1	22.5	22.0	28.4	0.0	37.0	29.6	bulk
731942	SRR2075564	SRP059792	SRS969729	SRX1070593	SRA273724	Yale University	Kaech Lab	The transcription factors ZEB2 and T-bet cooperate to program cytotoxic T cell terminal differentiation	T-bet is critical for cytotoxic T lymphocyte (CTL) differentiation, but it is unclear how it operates in a graded manner in the formation of both terminal effector and memory precursor cells during infection. We find that at high concentrations T-bet induced expression of Zeb2 mRNA, which then triggered CTLs to adopt terminally differentiated states. ZEB2 and T-bet cooperate to switch on a terminal CTL differentiation program, while simultaneously repressing genes necessary for central memory CTL development. Chromatin Immunoprecipitation sequencing (ChIP-seq) showed that a large proportion of these genes were bound by T-bet, and this binding was altered by ZEB2 deficiency. Furthermore, T-bet overexpression could not fully bypass ZEB2 function. Thus, the coordinated actions of T-bet and ZEB2 outline a novel genetic pathway that forces commitment of CTLs to terminal differentiation, thereby restricting their memory cell potential.		RNA-seq of TE (KLRGhi IL7Rlo) P14 CTLs isolated 8 d.p.i. with LCMV replicate 1		RNA-seq of TE (KLRGhi IL7Rlo) P14 CTLs isolated 8 d.p.i. with LCMV replicate 1	CD8_TE.1	RNA-Seq	TRANSCRIPTOMIC	other	paired				Illumina HiSeq 2500	age;;6-8 weeks|BioSampleModel;;Model organism or animal|breed;;C57BL/6|cell_type;;P14 CD8+ KLRG1hi IL7Rlo T cells|genotype;;WT|ID;;13|sex;;female|tissue;;Splenocytes	alignment_software;;STAR	150	CD8_TE.1	RNA-seq of TE (KLRGhi IL7Rlo) P14 CTLs isolated 8 d.p.i. with LCMV replicate 1	4799024730	32097932	2015-09-15 00:00:00	2348757290	4799024730	32097932	2	32097932	index:0,count:32095565,average:74.86,stdev:4.69|index:1,count:32096782,average:74.66,stdev:5.46	SAMN03785080.bam						1.74	3.27	0.07	4270701167	4232975307	4039610576	4021017208	99.12	99.54	31736713	29093409	182.587	1041.994	125	276378	82.35	87.12	34812375	26136255	34812375	26136255	83.72	83.88	34812375	26569571	34812375	25164618	511985710	11.99	0.27	0.00	5.41	14.96	0.18	0.97	0.00	0.09	0.00	0.00	0.93	0.00	31737407	3480	149	75	148.71	75.79	1.54	0.00	0.00	0.00	1.23	0.00	0.00	0.00	552.82	12.66	0.11	0.01	87206	0	32094415	3517	1735425	526	57016	34	140	3	0	0	299852	0	7834	0	0	0	65891	2	9309732	214	13598	0	9397055	216	93.48	83.99	30001982	2954	156936	9154851	58.334932711424	32097932.0	31740887.0	87206.0	1735951.0	57050.0	143.0	0.0	299852.0	30004936.0	98.9	0.3	5.4	0.2	0.0	0.0	0.9	93.5	69	76	75.92	38	266994	27.3	22.6	22.5	27.6	0.0	37.2	30.2	bulk
329159	SRR2098171	SRP060340	SRS988675	SRX1093183	SRA275699	Dana-Farber Cancer Institute		Overcoming Therapeutic Resistance in  HER2-Positive Breast Cancers With CDK4/6 Inhibitors	Resistance to anti-HER2 therapy leads to relapse and progression of HER2-positive breast cancers. Here, we show that tumor cells that resist HER2 pathway blockade retain expression of cyclin D1, and in a new transgenic mouse model ultimately give rise to cyclin D1/CDK4-dependent recurrences. Furthermore, the cyclin D1/CDK4 axis functionally mediates de novo and acquired resistance to anti-HER2 therapies, and a CDK4/6 inhibitor overcomes this. When combined, HER2 and CDK4/6 inhibitors synergistically reduce tumor cell viability by enhancing cell cycle arrest at the G1/S checkpoint, in association with reduced phosphorylation of both RB and S6RP. In vivo, CDK4/6 inhibition improves the efficacy of HER2 targeted therapy in both sensitive and resistant xenografts, and importantly also delays spontaneous tumor recurrence.		Overcoming Therapeutic Resistance in  HER2-Positive Breast Cancers With CDK4/6 Inhibitors		normal mammary gland,1		RNA-Seq	TRANSCRIPTOMIC	PolyA	paired		0.0E0		Illumina HiSeq 3000	age;;not applicable|BioSampleModel;;Model organism or animal|breed;;MM1|dev_stage;;normal|phenotype;;normal|sex;;not applicable|tissue;;mammary gland		100	TW49_QW48_MTB	TW49_QW48_MTB-Her2-Mg-1_03_11_2013	6349158800	63491588	2016-02-12 14:01:38	3817768672	6349158800	63491588	2	63491588	index:0,count:63491588,average:50,stdev:0|index:1,count:63491588,average:50,stdev:0	TW49_QW48_MTB_Her2				in_mesa	26977878	2.87	3.03	0.24	5684873426	5640340549	5165867094	5209153167	99.22	100.84	57703063	45181948	266.220	1795.875	148	275511	78.71	86.6	67995977	45418220	67995977	45418220	82.08	82.92	67995977	47360300	67995977	43486922	705933231	12.42	3.78	0	8.28	0	0.82	0	0.29	0	0.00	0	8.01	0	57703063	0	100	0	98.69	0	2.48	0	0.01	0	1.50	0	0.01	0	500.15	0	0.27	0	2400062	0	63491588	0	5256106	0	518648	0	183316	0	0	0	5086561	0	6085	0	0	0	62145	0	8463285	0	34221	0	8565736	0	82.60	0	52446957	0	205093	8759258	42.708712632806	63491588.0	57703063.0	2400062.0	5256106.0	518648.0	183316.0	0.0	5086561.0	52446957.0	90.9	3.8	8.3	0.8	0.3	0.0	8.0	82.6	50	50	50.00	38	3174579400	25.0	24.9	25.0	25.2	0.0	38.3	26.3	bulk
329163	SRR2098172	SRP060340	SRS988676	SRX1093184	SRA275699	Dana-Farber Cancer Institute		Overcoming Therapeutic Resistance in  HER2-Positive Breast Cancers With CDK4/6 Inhibitors	Resistance to anti-HER2 therapy leads to relapse and progression of HER2-positive breast cancers. Here, we show that tumor cells that resist HER2 pathway blockade retain expression of cyclin D1, and in a new transgenic mouse model ultimately give rise to cyclin D1/CDK4-dependent recurrences. Furthermore, the cyclin D1/CDK4 axis functionally mediates de novo and acquired resistance to anti-HER2 therapies, and a CDK4/6 inhibitor overcomes this. When combined, HER2 and CDK4/6 inhibitors synergistically reduce tumor cell viability by enhancing cell cycle arrest at the G1/S checkpoint, in association with reduced phosphorylation of both RB and S6RP. In vivo, CDK4/6 inhibition improves the efficacy of HER2 targeted therapy in both sensitive and resistant xenografts, and importantly also delays spontaneous tumor recurrence.		Overcoming Therapeutic Resistance in  HER2-Positive Breast Cancers With CDK4/6 Inhibitors		normal mammary gland,2		RNA-Seq	TRANSCRIPTOMIC	PolyA	paired		0.0E0		Illumina HiSeq 3000	age;;not applicable|BioSampleModel;;Model organism or animal|breed;;MM2|dev_stage;;normal|phenotype;;normal|sex;;not applicable|tissue;;mammary gland		100	TW50_QW49_MTB	TW50_QW49_MTB-Her2-Mg-2_03_11_2013	6601815100	66018151	2016-02-12 14:01:32	3931549362	6601815100	66018151	2	66018151	index:0,count:66018151,average:50,stdev:0|index:1,count:66018151,average:50,stdev:0	TW50_QW49_MTB_Her2_Mg				in_mesa	26977878	2.36	2.99	0.25	5942616982	5856829767	5443438661	5451881698	98.56	100.16	60236190	47856376	256.503	1581.918	146	314152	77.83	84.95	70430657	46884530	70430657	46884530	80.69	81.6	70430657	48604980	70430657	45032750	815432681	13.72	3.33	0	7.64	0	0.84	0	0.34	0	0.00	0	7.57	0	60236190	0	100	0	98.81	0	2.24	0	0.01	0	1.46	0	0.01	0	508.92	0	0.26	0	2201025	0	66018151	0	5046957	0	557485	0	225611	0	0	0	4998865	0	5683	0	0	0	63239	0	9146651	0	29757	0	9245330	0	83.60	0	55189233	0	204572	9492170	46.400142737031	66018151.0	60236190.0	2201025.0	5046957.0	557485.0	225611.0	0.0	4998865.0	55189233.0	91.2	3.3	7.6	0.8	0.3	0.0	7.6	83.6	50	50	50.00	38	3300907550	25.3	24.6	24.5	25.6	0.0	38.4	26.3	bulk
329170	SRR2098174	SRP060340	SRS988677	SRX1093185	SRA275699	Dana-Farber Cancer Institute		Overcoming Therapeutic Resistance in  HER2-Positive Breast Cancers With CDK4/6 Inhibitors	Resistance to anti-HER2 therapy leads to relapse and progression of HER2-positive breast cancers. Here, we show that tumor cells that resist HER2 pathway blockade retain expression of cyclin D1, and in a new transgenic mouse model ultimately give rise to cyclin D1/CDK4-dependent recurrences. Furthermore, the cyclin D1/CDK4 axis functionally mediates de novo and acquired resistance to anti-HER2 therapies, and a CDK4/6 inhibitor overcomes this. When combined, HER2 and CDK4/6 inhibitors synergistically reduce tumor cell viability by enhancing cell cycle arrest at the G1/S checkpoint, in association with reduced phosphorylation of both RB and S6RP. In vivo, CDK4/6 inhibition improves the efficacy of HER2 targeted therapy in both sensitive and resistant xenografts, and importantly also delays spontaneous tumor recurrence.		Overcoming Therapeutic Resistance in  HER2-Positive Breast Cancers With CDK4/6 Inhibitors		normal mammary gland,3		RNA-Seq	TRANSCRIPTOMIC	PolyA	paired		0.0E0		Illumina HiSeq 3000	age;;not applicable|BioSampleModel;;Model organism or animal|breed;;MM3|dev_stage;;normal|phenotype;;normal|sex;;not applicable|tissue;;mammary gland		100	TW1_QW45	TW1_QW45_10ML/L_MG_c_1	5783633800	57836338	2016-02-12 14:01:24	3349966289	5783633800	57836338	2	57836338	index:0,count:57836338,average:50,stdev:0|index:1,count:57836338,average:50,stdev:0	TW1_QW45				in_mesa	26977878	14.39	2.89	0.06	5279846446	5207785544	4382690031	4374773252	98.64	99.82	53472904	47035648	211.508	916.581	136	446542	75.35	90.69	66548277	40294267	66548277	40294267	87.59	87.25	66548277	46834355	66548277	38766101	372561645	7.06	2.74	0	15.63	0	0.40	0	0.19	0	0.00	0	6.96	0	53472904	0	100	0	98.87	0	1.81	0	0.01	0	1.39	0	0.01	0	428.42	0	0.36	0	1584097	0	57836338	0	9040983	0	230637	0	107037	0	0	0	4025760	0	4652	0	0	0	34329	0	6776570	0	19259	0	6834810	0	76.82	0	44431921	0	157333	7054236	44.836340754959	57836338.0	53472904.0	1584097.0	9040983.0	230637.0	107037.0	0.0	4025760.0	44431921.0	92.5	2.7	15.6	0.4	0.2	0.0	7.0	76.8	50	50	50.00	38	2891816900	25.6	24.3	24.3	25.7	0.2	38.5	26.1	bulk
329174	SRR2098175	SRP060340	SRS988678	SRX1093186	SRA275699	Dana-Farber Cancer Institute		Overcoming Therapeutic Resistance in  HER2-Positive Breast Cancers With CDK4/6 Inhibitors	Resistance to anti-HER2 therapy leads to relapse and progression of HER2-positive breast cancers. Here, we show that tumor cells that resist HER2 pathway blockade retain expression of cyclin D1, and in a new transgenic mouse model ultimately give rise to cyclin D1/CDK4-dependent recurrences. Furthermore, the cyclin D1/CDK4 axis functionally mediates de novo and acquired resistance to anti-HER2 therapies, and a CDK4/6 inhibitor overcomes this. When combined, HER2 and CDK4/6 inhibitors synergistically reduce tumor cell viability by enhancing cell cycle arrest at the G1/S checkpoint, in association with reduced phosphorylation of both RB and S6RP. In vivo, CDK4/6 inhibition improves the efficacy of HER2 targeted therapy in both sensitive and resistant xenografts, and importantly also delays spontaneous tumor recurrence.		Overcoming Therapeutic Resistance in  HER2-Positive Breast Cancers With CDK4/6 Inhibitors		normal mammary gland,4		RNA-Seq	TRANSCRIPTOMIC	PolyA	paired		0.0E0		Illumina HiSeq 3000	age;;not applicable|BioSampleModel;;Model organism or animal|breed;;MM4|dev_stage;;normal|phenotype;;normal|sex;;not applicable|tissue;;mammary gland		100	TW2_QW46	TW2_QW46_10ML/L_MG_c_2	5755894500	57558945	2016-02-12 14:01:16	3303641881	5755894500	57558945	2	57558945	index:0,count:57558945,average:50,stdev:0|index:1,count:57558945,average:50,stdev:0	TW2_QW46				in_mesa	26977878	2.43	3.03	0.17	5347769061	5250116144	4859352994	4840050121	98.17	99.6	54151459	46267061	210.719	1035.491	134	443905	80.63	88.7	64178154	43662980	64178154	43662980	85.15	86.19	64178154	46111445	64178154	42424996	543900142	10.17	2.38	0	8.56	0	1.05	0	0.32	0	0.00	0	4.55	0	54151459	0	100	0	98.95	0	1.66	0	0.01	0	1.42	0	0.01	0	409.51	0	0.33	0	1369030	0	57558945	0	4928491	0	605603	0	181813	0	0	0	2620070	0	5067	0	0	0	61441	0	8096818	0	20845	0	8184171	0	85.52	0	49222968	0	201355	8384579	41.640778724144	57558945.0	54151459.0	1369030.0	4928491.0	605603.0	181813.0	0.0	2620070.0	49222968.0	94.1	2.4	8.6	1.1	0.3	0.0	4.6	85.5	50	50	50.00	38	2877947250	25.2	24.9	24.6	25.2	0.2	38.5	26.4	bulk
329178	SRR2098176	SRP060340	SRS988679	SRX1093187	SRA275699	Dana-Farber Cancer Institute		Overcoming Therapeutic Resistance in  HER2-Positive Breast Cancers With CDK4/6 Inhibitors	Resistance to anti-HER2 therapy leads to relapse and progression of HER2-positive breast cancers. Here, we show that tumor cells that resist HER2 pathway blockade retain expression of cyclin D1, and in a new transgenic mouse model ultimately give rise to cyclin D1/CDK4-dependent recurrences. Furthermore, the cyclin D1/CDK4 axis functionally mediates de novo and acquired resistance to anti-HER2 therapies, and a CDK4/6 inhibitor overcomes this. When combined, HER2 and CDK4/6 inhibitors synergistically reduce tumor cell viability by enhancing cell cycle arrest at the G1/S checkpoint, in association with reduced phosphorylation of both RB and S6RP. In vivo, CDK4/6 inhibition improves the efficacy of HER2 targeted therapy in both sensitive and resistant xenografts, and importantly also delays spontaneous tumor recurrence.		Overcoming Therapeutic Resistance in  HER2-Positive Breast Cancers With CDK4/6 Inhibitors		normal mammary gland,5		RNA-Seq	TRANSCRIPTOMIC	PolyA	paired		0.0E0		Illumina HiSeq 3000	age;;not applicable|BioSampleModel;;Model organism or animal|breed;;MM5|dev_stage;;normal|phenotype;;normal|sex;;not applicable|tissue;;mammary gland		100	TW3_QW47	TW3_QW47_10ML/L_MG_c_3	8435492100	84354921	2016-02-12 14:00:25	5223698856	8435492100	84354921	2	84354921	index:0,count:84354921,average:50,stdev:0|index:1,count:84354921,average:50,stdev:0	TW3_QW47				in_mesa	26977878	2.43	3.12	0.15	7830812593	7723323834	7127587020	7123704247	98.63	99.95	79201290	67222366	216.996	1109.006	136	624512	80.67	88.6	93418123	63889760	93418123	63889760	85.19	86.05	93418123	67474156	93418123	62055901	827547621	10.57	2.60	0	8.40	0	0.92	0	0.32	0	0.00	0	4.86	0	79201290	0	100	0	98.99	0	1.70	0	0.01	0	1.40	0	0.01	0	586.25	0	0.21	0	2194867	0	84354921	0	7087931	0	780241	0	273486	0	0	0	4099904	0	8503	0	0	0	88420	0	12094541	0	31615	0	12223079	0	85.49	0	72113359	0	221183	12442370	56.253735594508	84354921.0	79201290.0	2194867.0	7087931.0	780241.0	273486.0	0.0	4099904.0	72113359.0	93.9	2.6	8.4	0.9	0.3	0.0	4.9	85.5	50	50	50.00	38	4217746050	25.1	25.0	24.7	25.2	0.0	38.1	27.1	bulk
1648942	SRR2120292	SRP061355	SRS1007827	SRX1113437	SRA278928	GEO		Injury-induced enhancer remodelling in spinal microglia - a novel mechanism for pain chronification? [RNA-Seq]	Chronic pain is common and devastating. Yet, its precise molecular origins remain unclear. The condition induces well-characterised changes in neurons and microglia, but it is unknown why they persist long after the precipitating injury has healed. We posit a role for enhancers - regions of open chromatin that define a cell’s transcription factor binding profile. Enhancer profiles can alter upon environmental stimulation, functioning as a kind of molecular memory. Here, a mouse model of persistent neuropathic pain was used to examine microglial enhancers with flow cytometry and sequencing. We observed injury-specific alterations of enhancers in close proximity to transcriptionally regulated genes. Our data also shine light on details relating to the spinal cord immune response and provide the first genome-wide gene expression profile of isolated microglia in a pain state. We hypothesise that enhancer deposition may constitute a novel mechanism by which painful experiences are encoded on a molecular level. Overall design: ChIP-seq and RNA-seq of isolated spinal cord microglia after peripheral spinal nerve ligation or sham surgery in mice (day 7)		GSM1827980: RNA_SNL1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Spinal cord microglia were isolated via a Percoll gradient Sequencing was performed by the High Throughput Genomics Group at the Wellcome Trust Centre for Human Genetics (Oxford University). RNA libraries were prepared using a SMARTer Ultra Low Input HV kit (634820, Clontech). Custom adaptor and barcode tags were used (5'- P-GATCGGAAGAGCGGTTCAGCAGGAATGCCGAG, 5’-ACACTCTTTCCCTACACGACGCTCTTCCGATCT). Samples were amplified (13 cycles for RNA) and multiplexed in replicate flow cells on an Illumina HiSeq2500 platform to yield 50bp paired-end reads at a depth of at least 20M. All libraries were prepared together to avoid batch effects.	Illumina HiSeq 2500	age;;6-8 weeks old|gender;;male|injury condition;;SNL|source_name;;mouse spinal cord microglia|strain;;C57BL/6	GEO Accession;;GSM1827980		GSM1827980	RNA_SNL1	2155589052	21133226	2016-05-12 16:05:14	1259224359	2155589052	21133226	2	21133226	index:0,count:21133226,average:51,stdev:0|index:1,count:21133226,average:51,stdev:0	GSM1827980_r1				in_mesa	27184839	3.63	2.78	0.12	1901663143	1866635403	1781280828	1756346438	98.16	98.6	19469084	17108154	223.293	1210.631	173	145492	58.88	63.01	21721593	11462777	21721593	11462777	61.75	60.44	21721593	12023036	21721593	10995918	665610828	35.00	2.76	0	6.04	0	0.50	0	0.27	0	0.00	0	7.10	0	19469084	0	102	0	97.94	0	1.24	0	0.01	0	1.16	0	0.00	0	322.37	0	0.18	0	583137	0	21133226	0	1276624	0	105166	0	57810	0	0	0	1501166	0	862	0	0	0	9564	0	1793502	0	64991	0	1868919	0	86.08	0	18192460	0	112061	1922289	17.153951865502	21133226.0	19469084.0	583137.0	1276624.0	105166.0	57810.0	0.0	1501166.0	18192460.0	92.1	2.8	6.0	0.5	0.3	0.0	7.1	86.1	51	51	51.00	38	1077794526	26.5	23.7	23.4	26.4	0.0	38.5	32.0	bulk
1648956	SRR2120293	SRP061355	SRS1007827	SRX1113437	SRA278928	GEO		Injury-induced enhancer remodelling in spinal microglia - a novel mechanism for pain chronification? [RNA-Seq]	Chronic pain is common and devastating. Yet, its precise molecular origins remain unclear. The condition induces well-characterised changes in neurons and microglia, but it is unknown why they persist long after the precipitating injury has healed. We posit a role for enhancers - regions of open chromatin that define a cell’s transcription factor binding profile. Enhancer profiles can alter upon environmental stimulation, functioning as a kind of molecular memory. Here, a mouse model of persistent neuropathic pain was used to examine microglial enhancers with flow cytometry and sequencing. We observed injury-specific alterations of enhancers in close proximity to transcriptionally regulated genes. Our data also shine light on details relating to the spinal cord immune response and provide the first genome-wide gene expression profile of isolated microglia in a pain state. We hypothesise that enhancer deposition may constitute a novel mechanism by which painful experiences are encoded on a molecular level. Overall design: ChIP-seq and RNA-seq of isolated spinal cord microglia after peripheral spinal nerve ligation or sham surgery in mice (day 7)		GSM1827980: RNA_SNL1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Spinal cord microglia were isolated via a Percoll gradient Sequencing was performed by the High Throughput Genomics Group at the Wellcome Trust Centre for Human Genetics (Oxford University). RNA libraries were prepared using a SMARTer Ultra Low Input HV kit (634820, Clontech). Custom adaptor and barcode tags were used (5'- P-GATCGGAAGAGCGGTTCAGCAGGAATGCCGAG, 5’-ACACTCTTTCCCTACACGACGCTCTTCCGATCT). Samples were amplified (13 cycles for RNA) and multiplexed in replicate flow cells on an Illumina HiSeq2500 platform to yield 50bp paired-end reads at a depth of at least 20M. All libraries were prepared together to avoid batch effects.	Illumina HiSeq 2500	age;;6-8 weeks old|gender;;male|injury condition;;SNL|source_name;;mouse spinal cord microglia|strain;;C57BL/6	GEO Accession;;GSM1827980		GSM1827980	RNA_SNL1	2135146926	20932813	2016-05-12 16:05:14	1247081744	2135146926	20932813	2	20932813	index:0,count:20932813,average:51,stdev:0|index:1,count:20932813,average:51,stdev:0	GSM1827980_r2				in_mesa	27184839	3.62	2.79	0.12	1888522419	1853862226	1768992842	1744348917	98.16	98.61	19332955	16988884	223.223	1200.015	177	144718	58.89	63.02	21570293	11384934	21570293	11384934	61.76	60.44	21570293	11939678	21570293	10919636	660922270	35.00	2.75	0	6.05	0	0.50	0	0.27	0	0.00	0	6.87	0	19332955	0	102	0	97.94	0	1.24	0	0.01	0	1.15	0	0.00	0	378.68	0	0.20	0	576669	0	20932813	0	1267211	0	104631	0	56286	0	0	0	1438941	0	854	0	0	0	9606	0	1775859	0	64039	0	1850358	0	86.30	0	18065744	0	112147	1903893	16.976762641890	20932813.0	19332955.0	576669.0	1267211.0	104631.0	56286.0	0.0	1438941.0	18065744.0	92.4	2.8	6.1	0.5	0.3	0.0	6.9	86.3	51	51	51.00	38	1067573463	26.5	23.7	23.4	26.4	0.0	38.5	31.7	bulk
1648972	SRR2120294	SRP061355	SRS1007826	SRX1113438	SRA278928	GEO		Injury-induced enhancer remodelling in spinal microglia - a novel mechanism for pain chronification? [RNA-Seq]	Chronic pain is common and devastating. Yet, its precise molecular origins remain unclear. The condition induces well-characterised changes in neurons and microglia, but it is unknown why they persist long after the precipitating injury has healed. We posit a role for enhancers - regions of open chromatin that define a cell’s transcription factor binding profile. Enhancer profiles can alter upon environmental stimulation, functioning as a kind of molecular memory. Here, a mouse model of persistent neuropathic pain was used to examine microglial enhancers with flow cytometry and sequencing. We observed injury-specific alterations of enhancers in close proximity to transcriptionally regulated genes. Our data also shine light on details relating to the spinal cord immune response and provide the first genome-wide gene expression profile of isolated microglia in a pain state. We hypothesise that enhancer deposition may constitute a novel mechanism by which painful experiences are encoded on a molecular level. Overall design: ChIP-seq and RNA-seq of isolated spinal cord microglia after peripheral spinal nerve ligation or sham surgery in mice (day 7)		GSM1827981: RNA_SNL2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Spinal cord microglia were isolated via a Percoll gradient Sequencing was performed by the High Throughput Genomics Group at the Wellcome Trust Centre for Human Genetics (Oxford University). RNA libraries were prepared using a SMARTer Ultra Low Input HV kit (634820, Clontech). Custom adaptor and barcode tags were used (5'- P-GATCGGAAGAGCGGTTCAGCAGGAATGCCGAG, 5’-ACACTCTTTCCCTACACGACGCTCTTCCGATCT). Samples were amplified (13 cycles for RNA) and multiplexed in replicate flow cells on an Illumina HiSeq2500 platform to yield 50bp paired-end reads at a depth of at least 20M. All libraries were prepared together to avoid batch effects.	Illumina HiSeq 2500	age;;6-8 weeks old|gender;;male|injury condition;;SNL|source_name;;mouse spinal cord microglia|strain;;C57BL/6	GEO Accession;;GSM1827981		GSM1827981	RNA_SNL2	1491269886	14620293	2016-05-12 16:05:14	879539267	1491269886	14620293	2	14620293	index:0,count:14620293,average:51,stdev:0|index:1,count:14620293,average:51,stdev:0	GSM1827981_r1				in_mesa	27184839	5.11	2.74	0.11	1309852088	1296361740	1214076938	1207981853	98.97	99.5	13451315	11407833	235.568	1318.623	180	95637	69.04	74.66	15175005	9286305	15175005	9286305	72.49	71.58	15175005	9750404	15175005	8902799	312811493	23.88	2.69	0	6.93	0	0.52	0	0.20	0	0.00	0	7.28	0	13451315	0	102	0	97.62	0	1.25	0	0.01	0	1.15	0	0.00	0	250.63	0	0.19	0	392856	0	14620293	0	1013369	0	75347	0	29604	0	0	0	1064027	0	668	0	0	0	7568	0	1545173	0	53283	0	1606692	0	85.07	0	12437946	0	104607	1616131	15.449549265346	14620293.0	13451315.0	392856.0	1013369.0	75347.0	29604.0	0.0	1064027.0	12437946.0	92.0	2.7	6.9	0.5	0.2	0.0	7.3	85.1	51	51	51.00	38	745634943	26.1	24.1	23.9	26.0	0.0	38.5	31.9	bulk
1648989	SRR2120295	SRP061355	SRS1007826	SRX1113438	SRA278928	GEO		Injury-induced enhancer remodelling in spinal microglia - a novel mechanism for pain chronification? [RNA-Seq]	Chronic pain is common and devastating. Yet, its precise molecular origins remain unclear. The condition induces well-characterised changes in neurons and microglia, but it is unknown why they persist long after the precipitating injury has healed. We posit a role for enhancers - regions of open chromatin that define a cell’s transcription factor binding profile. Enhancer profiles can alter upon environmental stimulation, functioning as a kind of molecular memory. Here, a mouse model of persistent neuropathic pain was used to examine microglial enhancers with flow cytometry and sequencing. We observed injury-specific alterations of enhancers in close proximity to transcriptionally regulated genes. Our data also shine light on details relating to the spinal cord immune response and provide the first genome-wide gene expression profile of isolated microglia in a pain state. We hypothesise that enhancer deposition may constitute a novel mechanism by which painful experiences are encoded on a molecular level. Overall design: ChIP-seq and RNA-seq of isolated spinal cord microglia after peripheral spinal nerve ligation or sham surgery in mice (day 7)		GSM1827981: RNA_SNL2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Spinal cord microglia were isolated via a Percoll gradient Sequencing was performed by the High Throughput Genomics Group at the Wellcome Trust Centre for Human Genetics (Oxford University). RNA libraries were prepared using a SMARTer Ultra Low Input HV kit (634820, Clontech). Custom adaptor and barcode tags were used (5'- P-GATCGGAAGAGCGGTTCAGCAGGAATGCCGAG, 5’-ACACTCTTTCCCTACACGACGCTCTTCCGATCT). Samples were amplified (13 cycles for RNA) and multiplexed in replicate flow cells on an Illumina HiSeq2500 platform to yield 50bp paired-end reads at a depth of at least 20M. All libraries were prepared together to avoid batch effects.	Illumina HiSeq 2500	age;;6-8 weeks old|gender;;male|injury condition;;SNL|source_name;;mouse spinal cord microglia|strain;;C57BL/6	GEO Accession;;GSM1827981		GSM1827981	RNA_SNL2	1469263896	14404548	2016-05-12 16:05:14	866494713	1469263896	14404548	2	14404548	index:0,count:14404548,average:51,stdev:0|index:1,count:14404548,average:51,stdev:0	GSM1827981_r2				in_mesa	27184839	5.1	2.75	0.11	1293480089	1280265596	1199058105	1193159011	98.98	99.51	13283593	11268939	235.635	1309.486	180	93991	69.04	74.66	14982931	9171012	14982931	9171012	72.47	71.56	14982931	9625997	14982931	8790557	308996362	23.89	2.69	0	6.94	0	0.52	0	0.20	0	0.00	0	7.07	0	13283593	0	102	0	97.62	0	1.24	0	0.01	0	1.15	0	0.00	0	367.78	0	0.21	0	388012	0	14404548	0	999428	0	74194	0	28832	0	0	0	1017929	0	656	0	0	0	7467	0	1521410	0	52373	0	1581906	0	85.28	0	12284165	0	104177	1591969	15.281386486461	14404548.0	13283593.0	388012.0	999428.0	74194.0	28832.0	0.0	1017929.0	12284165.0	92.2	2.7	6.9	0.5	0.2	0.0	7.1	85.3	51	51	51.00	38	734631948	26.1	24.1	23.9	26.0	0.0	38.5	31.6	bulk
1649004	SRR2120296	SRP061355	SRS1007825	SRX1113439	SRA278928	GEO		Injury-induced enhancer remodelling in spinal microglia - a novel mechanism for pain chronification? [RNA-Seq]	Chronic pain is common and devastating. Yet, its precise molecular origins remain unclear. The condition induces well-characterised changes in neurons and microglia, but it is unknown why they persist long after the precipitating injury has healed. We posit a role for enhancers - regions of open chromatin that define a cell’s transcription factor binding profile. Enhancer profiles can alter upon environmental stimulation, functioning as a kind of molecular memory. Here, a mouse model of persistent neuropathic pain was used to examine microglial enhancers with flow cytometry and sequencing. We observed injury-specific alterations of enhancers in close proximity to transcriptionally regulated genes. Our data also shine light on details relating to the spinal cord immune response and provide the first genome-wide gene expression profile of isolated microglia in a pain state. We hypothesise that enhancer deposition may constitute a novel mechanism by which painful experiences are encoded on a molecular level. Overall design: ChIP-seq and RNA-seq of isolated spinal cord microglia after peripheral spinal nerve ligation or sham surgery in mice (day 7)		GSM1827982: RNA_SNL3; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Spinal cord microglia were isolated via a Percoll gradient Sequencing was performed by the High Throughput Genomics Group at the Wellcome Trust Centre for Human Genetics (Oxford University). RNA libraries were prepared using a SMARTer Ultra Low Input HV kit (634820, Clontech). Custom adaptor and barcode tags were used (5'- P-GATCGGAAGAGCGGTTCAGCAGGAATGCCGAG, 5’-ACACTCTTTCCCTACACGACGCTCTTCCGATCT). Samples were amplified (13 cycles for RNA) and multiplexed in replicate flow cells on an Illumina HiSeq2500 platform to yield 50bp paired-end reads at a depth of at least 20M. All libraries were prepared together to avoid batch effects.	Illumina HiSeq 2500	age;;6-8 weeks old|gender;;male|injury condition;;SNL|source_name;;mouse spinal cord microglia|strain;;C57BL/6	GEO Accession;;GSM1827982		GSM1827982	RNA_SNL3	2308113936	22628568	2016-05-12 16:05:14	1355852333	2308113936	22628568	2	22628568	index:0,count:22628568,average:51,stdev:0|index:1,count:22628568,average:51,stdev:0	GSM1827982_r1				in_mesa	27184839	2.82	2.69	0.12	2018668022	2002653114	1893826363	1888178556	99.21	99.7	20665598	17249259	238.759	1375.960	178	139792	72.19	77.11	23067588	14918023	23067588	14918023	74.28	73.81	23067588	15349760	23067588	14279049	443303488	21.96	2.42	0	5.83	0	0.52	0	0.19	0	0.00	0	7.97	0	20665598	0	102	0	97.91	0	1.25	0	0.01	0	1.15	0	0.00	0	267.97	0	0.19	0	547220	0	22628568	0	1318873	0	117567	0	42088	0	0	0	1803315	0	1085	0	0	0	12171	0	2647503	0	79915	0	2740674	0	85.50	0	19346725	0	120017	2765080	23.039069465159	22628568.0	20665598.0	547220.0	1318873.0	117567.0	42088.0	0.0	1803315.0	19346725.0	91.3	2.4	5.8	0.5	0.2	0.0	8.0	85.5	51	51	51.00	38	1154056968	26.2	24.3	23.9	25.5	0.0	38.4	31.8	bulk
1649019	SRR2120297	SRP061355	SRS1007825	SRX1113439	SRA278928	GEO		Injury-induced enhancer remodelling in spinal microglia - a novel mechanism for pain chronification? [RNA-Seq]	Chronic pain is common and devastating. Yet, its precise molecular origins remain unclear. The condition induces well-characterised changes in neurons and microglia, but it is unknown why they persist long after the precipitating injury has healed. We posit a role for enhancers - regions of open chromatin that define a cell’s transcription factor binding profile. Enhancer profiles can alter upon environmental stimulation, functioning as a kind of molecular memory. Here, a mouse model of persistent neuropathic pain was used to examine microglial enhancers with flow cytometry and sequencing. We observed injury-specific alterations of enhancers in close proximity to transcriptionally regulated genes. Our data also shine light on details relating to the spinal cord immune response and provide the first genome-wide gene expression profile of isolated microglia in a pain state. We hypothesise that enhancer deposition may constitute a novel mechanism by which painful experiences are encoded on a molecular level. Overall design: ChIP-seq and RNA-seq of isolated spinal cord microglia after peripheral spinal nerve ligation or sham surgery in mice (day 7)		GSM1827982: RNA_SNL3; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Spinal cord microglia were isolated via a Percoll gradient Sequencing was performed by the High Throughput Genomics Group at the Wellcome Trust Centre for Human Genetics (Oxford University). RNA libraries were prepared using a SMARTer Ultra Low Input HV kit (634820, Clontech). Custom adaptor and barcode tags were used (5'- P-GATCGGAAGAGCGGTTCAGCAGGAATGCCGAG, 5’-ACACTCTTTCCCTACACGACGCTCTTCCGATCT). Samples were amplified (13 cycles for RNA) and multiplexed in replicate flow cells on an Illumina HiSeq2500 platform to yield 50bp paired-end reads at a depth of at least 20M. All libraries were prepared together to avoid batch effects.	Illumina HiSeq 2500	age;;6-8 weeks old|gender;;male|injury condition;;SNL|source_name;;mouse spinal cord microglia|strain;;C57BL/6	GEO Accession;;GSM1827982		GSM1827982	RNA_SNL3	2288226282	22433591	2016-05-12 16:05:14	1343964797	2288226282	22433591	2	22433591	index:0,count:22433591,average:51,stdev:0|index:1,count:22433591,average:51,stdev:0	GSM1827982_r2				in_mesa	27184839	2.83	2.69	0.12	2006004383	1990019229	1881985098	1876339441	99.2	99.7	20534972	17143577	238.871	1362.817	178	139052	72.2	77.12	22919676	14826868	22919676	14826868	74.28	73.81	22919676	15254347	22919676	14190571	440086514	21.94	2.42	0	5.84	0	0.52	0	0.18	0	0.00	0	7.76	0	20534972	0	102	0	97.91	0	1.25	0	0.01	0	1.15	0	0.00	0	281.40	0	0.20	0	542845	0	22433591	0	1310259	0	116310	0	41373	0	0	0	1740936	0	1107	0	0	0	12088	0	2627172	0	79790	0	2720157	0	85.70	0	19224713	0	119369	2743868	22.986437014635	22433591.0	20534972.0	542845.0	1310259.0	116310.0	41373.0	0.0	1740936.0	19224713.0	91.5	2.4	5.8	0.5	0.2	0.0	7.8	85.7	51	51	51.00	38	1144113141	26.2	24.3	24.0	25.5	0.0	38.4	31.6	bulk
1649034	SRR2120298	SRP061355	SRS1007824	SRX1113440	SRA278928	GEO		Injury-induced enhancer remodelling in spinal microglia - a novel mechanism for pain chronification? [RNA-Seq]	Chronic pain is common and devastating. Yet, its precise molecular origins remain unclear. The condition induces well-characterised changes in neurons and microglia, but it is unknown why they persist long after the precipitating injury has healed. We posit a role for enhancers - regions of open chromatin that define a cell’s transcription factor binding profile. Enhancer profiles can alter upon environmental stimulation, functioning as a kind of molecular memory. Here, a mouse model of persistent neuropathic pain was used to examine microglial enhancers with flow cytometry and sequencing. We observed injury-specific alterations of enhancers in close proximity to transcriptionally regulated genes. Our data also shine light on details relating to the spinal cord immune response and provide the first genome-wide gene expression profile of isolated microglia in a pain state. We hypothesise that enhancer deposition may constitute a novel mechanism by which painful experiences are encoded on a molecular level. Overall design: ChIP-seq and RNA-seq of isolated spinal cord microglia after peripheral spinal nerve ligation or sham surgery in mice (day 7)		GSM1827983: RNA_SNL4; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Spinal cord microglia were isolated via a Percoll gradient Sequencing was performed by the High Throughput Genomics Group at the Wellcome Trust Centre for Human Genetics (Oxford University). RNA libraries were prepared using a SMARTer Ultra Low Input HV kit (634820, Clontech). Custom adaptor and barcode tags were used (5'- P-GATCGGAAGAGCGGTTCAGCAGGAATGCCGAG, 5’-ACACTCTTTCCCTACACGACGCTCTTCCGATCT). Samples were amplified (13 cycles for RNA) and multiplexed in replicate flow cells on an Illumina HiSeq2500 platform to yield 50bp paired-end reads at a depth of at least 20M. All libraries were prepared together to avoid batch effects.	Illumina HiSeq 2500	age;;6-8 weeks old|gender;;male|injury condition;;SNL|source_name;;mouse spinal cord microglia|strain;;C57BL/6	GEO Accession;;GSM1827983		GSM1827983	RNA_SNL4	2254865346	22106523	2016-05-12 16:05:14	1337334877	2254865346	22106523	2	22106523	index:0,count:22106523,average:51,stdev:0|index:1,count:22106523,average:51,stdev:0	GSM1827983_r1				in_mesa	27184839	4.9	2.86	0.09	1991356247	1972875211	1840245804	1833261504	99.07	99.62	20470420	17078251	236.252	1380.124	179	139298	74.24	80.53	23149238	15197685	23149238	15197685	78.0	77.43	23149238	15967244	23149238	14613565	363164560	18.24	2.58	0	7.23	0	0.51	0	0.17	0	0.00	0	6.72	0	20470420	0	102	0	97.53	0	1.23	0	0.00	0	1.15	0	0.00	0	282.21	0	0.19	0	569457	0	22106523	0	1597786	0	113156	0	37314	0	0	0	1485633	0	1122	0	0	0	12497	0	2655415	0	74774	0	2743808	0	85.37	0	18872634	0	125199	2759910	22.044185656435	22106523.0	20470420.0	569457.0	1597786.0	113156.0	37314.0	0.0	1485633.0	18872634.0	92.6	2.6	7.2	0.5	0.2	0.0	6.7	85.4	51	51	51.00	38	1127432673	25.5	24.7	24.3	25.5	0.0	38.4	31.8	bulk
1649050	SRR2120299	SRP061355	SRS1007824	SRX1113440	SRA278928	GEO		Injury-induced enhancer remodelling in spinal microglia - a novel mechanism for pain chronification? [RNA-Seq]	Chronic pain is common and devastating. Yet, its precise molecular origins remain unclear. The condition induces well-characterised changes in neurons and microglia, but it is unknown why they persist long after the precipitating injury has healed. We posit a role for enhancers - regions of open chromatin that define a cell’s transcription factor binding profile. Enhancer profiles can alter upon environmental stimulation, functioning as a kind of molecular memory. Here, a mouse model of persistent neuropathic pain was used to examine microglial enhancers with flow cytometry and sequencing. We observed injury-specific alterations of enhancers in close proximity to transcriptionally regulated genes. Our data also shine light on details relating to the spinal cord immune response and provide the first genome-wide gene expression profile of isolated microglia in a pain state. We hypothesise that enhancer deposition may constitute a novel mechanism by which painful experiences are encoded on a molecular level. Overall design: ChIP-seq and RNA-seq of isolated spinal cord microglia after peripheral spinal nerve ligation or sham surgery in mice (day 7)		GSM1827983: RNA_SNL4; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Spinal cord microglia were isolated via a Percoll gradient Sequencing was performed by the High Throughput Genomics Group at the Wellcome Trust Centre for Human Genetics (Oxford University). RNA libraries were prepared using a SMARTer Ultra Low Input HV kit (634820, Clontech). Custom adaptor and barcode tags were used (5'- P-GATCGGAAGAGCGGTTCAGCAGGAATGCCGAG, 5’-ACACTCTTTCCCTACACGACGCTCTTCCGATCT). Samples were amplified (13 cycles for RNA) and multiplexed in replicate flow cells on an Illumina HiSeq2500 platform to yield 50bp paired-end reads at a depth of at least 20M. All libraries were prepared together to avoid batch effects.	Illumina HiSeq 2500	age;;6-8 weeks old|gender;;male|injury condition;;SNL|source_name;;mouse spinal cord microglia|strain;;C57BL/6	GEO Accession;;GSM1827983		GSM1827983	RNA_SNL4	2237804622	21939261	2016-05-12 16:05:14	1326865136	2237804622	21939261	2	21939261	index:0,count:21939261,average:51,stdev:0|index:1,count:21939261,average:51,stdev:0	GSM1827983_r2				in_mesa	27184839	4.9	2.86	0.09	1980363679	1961949169	1830040486	1823080189	99.07	99.62	20355797	16982976	236.268	1373.527	179	138701	74.25	80.54	23024436	15114633	23024436	15114633	78.02	77.45	23024436	15881099	23024436	14534548	360898987	18.22	2.57	0	7.24	0	0.51	0	0.17	0	0.00	0	6.54	0	20355797	0	102	0	97.54	0	1.23	0	0.00	0	1.15	0	0.00	0	276.16	0	0.21	0	564890	0	21939261	0	1589089	0	112500	0	36442	0	0	0	1434522	0	1212	0	0	0	12374	0	2638197	0	73718	0	2725501	0	85.54	0	18766708	0	125008	2744336	21.953282989889	21939261.0	20355797.0	564890.0	1589089.0	112500.0	36442.0	0.0	1434522.0	18766708.0	92.8	2.6	7.2	0.5	0.2	0.0	6.5	85.5	51	51	51.00	38	1118902311	25.5	24.7	24.3	25.5	0.0	38.4	31.6	bulk
1650698	SRR2120300	SRP061355	SRS1007823	SRX1113441	SRA278928	GEO		Injury-induced enhancer remodelling in spinal microglia - a novel mechanism for pain chronification? [RNA-Seq]	Chronic pain is common and devastating. Yet, its precise molecular origins remain unclear. The condition induces well-characterised changes in neurons and microglia, but it is unknown why they persist long after the precipitating injury has healed. We posit a role for enhancers - regions of open chromatin that define a cell’s transcription factor binding profile. Enhancer profiles can alter upon environmental stimulation, functioning as a kind of molecular memory. Here, a mouse model of persistent neuropathic pain was used to examine microglial enhancers with flow cytometry and sequencing. We observed injury-specific alterations of enhancers in close proximity to transcriptionally regulated genes. Our data also shine light on details relating to the spinal cord immune response and provide the first genome-wide gene expression profile of isolated microglia in a pain state. We hypothesise that enhancer deposition may constitute a novel mechanism by which painful experiences are encoded on a molecular level. Overall design: ChIP-seq and RNA-seq of isolated spinal cord microglia after peripheral spinal nerve ligation or sham surgery in mice (day 7)		GSM1827984: RNA_SHAM1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Spinal cord microglia were isolated via a Percoll gradient Sequencing was performed by the High Throughput Genomics Group at the Wellcome Trust Centre for Human Genetics (Oxford University). RNA libraries were prepared using a SMARTer Ultra Low Input HV kit (634820, Clontech). Custom adaptor and barcode tags were used (5'- P-GATCGGAAGAGCGGTTCAGCAGGAATGCCGAG, 5’-ACACTCTTTCCCTACACGACGCTCTTCCGATCT). Samples were amplified (13 cycles for RNA) and multiplexed in replicate flow cells on an Illumina HiSeq2500 platform to yield 50bp paired-end reads at a depth of at least 20M. All libraries were prepared together to avoid batch effects.	Illumina HiSeq 2500	age;;6-8 weeks old|gender;;male|injury condition;;SHAM|source_name;;mouse spinal cord microglia|strain;;C57BL/6	GEO Accession;;GSM1827984		GSM1827984	RNA_SHAM1	1929470148	18916374	2016-05-12 16:05:14	1143133604	1929470148	18916374	2	18916374	index:0,count:18916374,average:51,stdev:0|index:1,count:18916374,average:51,stdev:0	GSM1827984_r1				in_mesa	27184839	5.52	2.85	0.12	1435183735	1416114417	1330643150	1320056197	98.67	99.2	14746970	12790250	220.350	1300.997	171	110613	66.41	71.8	16574855	9792952	16574855	9792952	70.05	69.01	16574855	10330570	16574855	9412926	379156239	26.42	2.34	0	5.86	0	0.42	0	0.19	0	0.00	0	21.43	0	14746970	0	102	0	97.59	0	1.24	0	0.01	0	1.15	0	0.00	0	205.74	0	0.19	0	441704	0	18916374	0	1107969	0	80069	0	35497	0	0	0	4053838	0	778	0	0	0	8071	0	1569350	0	54913	0	1633112	0	72.10	0	13639001	0	108659	1639825	15.091478846667	18916374.0	14746970.0	441704.0	1107969.0	80069.0	35497.0	0.0	4053838.0	13639001.0	78.0	2.3	5.9	0.4	0.2	0.0	21.4	72.1	51	51	51.00	38	964735074	25.8	24.4	23.3	26.5	0.0	38.4	31.5	bulk
1650715	SRR2120301	SRP061355	SRS1007823	SRX1113441	SRA278928	GEO		Injury-induced enhancer remodelling in spinal microglia - a novel mechanism for pain chronification? [RNA-Seq]	Chronic pain is common and devastating. Yet, its precise molecular origins remain unclear. The condition induces well-characterised changes in neurons and microglia, but it is unknown why they persist long after the precipitating injury has healed. We posit a role for enhancers - regions of open chromatin that define a cell’s transcription factor binding profile. Enhancer profiles can alter upon environmental stimulation, functioning as a kind of molecular memory. Here, a mouse model of persistent neuropathic pain was used to examine microglial enhancers with flow cytometry and sequencing. We observed injury-specific alterations of enhancers in close proximity to transcriptionally regulated genes. Our data also shine light on details relating to the spinal cord immune response and provide the first genome-wide gene expression profile of isolated microglia in a pain state. We hypothesise that enhancer deposition may constitute a novel mechanism by which painful experiences are encoded on a molecular level. Overall design: ChIP-seq and RNA-seq of isolated spinal cord microglia after peripheral spinal nerve ligation or sham surgery in mice (day 7)		GSM1827984: RNA_SHAM1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Spinal cord microglia were isolated via a Percoll gradient Sequencing was performed by the High Throughput Genomics Group at the Wellcome Trust Centre for Human Genetics (Oxford University). RNA libraries were prepared using a SMARTer Ultra Low Input HV kit (634820, Clontech). Custom adaptor and barcode tags were used (5'- P-GATCGGAAGAGCGGTTCAGCAGGAATGCCGAG, 5’-ACACTCTTTCCCTACACGACGCTCTTCCGATCT). Samples were amplified (13 cycles for RNA) and multiplexed in replicate flow cells on an Illumina HiSeq2500 platform to yield 50bp paired-end reads at a depth of at least 20M. All libraries were prepared together to avoid batch effects.	Illumina HiSeq 2500	age;;6-8 weeks old|gender;;male|injury condition;;SHAM|source_name;;mouse spinal cord microglia|strain;;C57BL/6	GEO Accession;;GSM1827984		GSM1827984	RNA_SHAM1	1905008712	18676556	2016-05-12 16:05:14	1129518015	1905008712	18676556	2	18676556	index:0,count:18676556,average:51,stdev:0|index:1,count:18676556,average:51,stdev:0	GSM1827984_r2				in_mesa	27184839	5.52	2.85	0.13	1420397958	1401628076	1317085800	1306698843	98.68	99.21	14594082	12662794	220.282	1286.708	169	109949	66.4	71.79	16398625	9690718	16398625	9690718	70.04	69.0	16398625	10221660	16398625	9315075	375474015	26.43	2.33	0	5.86	0	0.42	0	0.18	0	0.00	0	21.25	0	14594082	0	102	0	97.60	0	1.24	0	0.01	0	1.15	0	0.00	0	210.11	0	0.20	0	436069	0	18676556	0	1094709	0	78940	0	34455	0	0	0	3969079	0	735	0	0	0	7981	0	1549726	0	54410	0	1612852	0	72.28	0	13499373	0	108434	1619447	14.934863603667	18676556.0	14594082.0	436069.0	1094709.0	78940.0	34455.0	0.0	3969079.0	13499373.0	78.1	2.3	5.9	0.4	0.2	0.0	21.3	72.3	51	51	51.00	38	952504356	25.8	24.4	23.3	26.5	0.0	38.4	31.2	bulk
1650731	SRR2120302	SRP061355	SRS1007822	SRX1113442	SRA278928	GEO		Injury-induced enhancer remodelling in spinal microglia - a novel mechanism for pain chronification? [RNA-Seq]	Chronic pain is common and devastating. Yet, its precise molecular origins remain unclear. The condition induces well-characterised changes in neurons and microglia, but it is unknown why they persist long after the precipitating injury has healed. We posit a role for enhancers - regions of open chromatin that define a cell’s transcription factor binding profile. Enhancer profiles can alter upon environmental stimulation, functioning as a kind of molecular memory. Here, a mouse model of persistent neuropathic pain was used to examine microglial enhancers with flow cytometry and sequencing. We observed injury-specific alterations of enhancers in close proximity to transcriptionally regulated genes. Our data also shine light on details relating to the spinal cord immune response and provide the first genome-wide gene expression profile of isolated microglia in a pain state. We hypothesise that enhancer deposition may constitute a novel mechanism by which painful experiences are encoded on a molecular level. Overall design: ChIP-seq and RNA-seq of isolated spinal cord microglia after peripheral spinal nerve ligation or sham surgery in mice (day 7)		GSM1827985: RNA_SHAM2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Spinal cord microglia were isolated via a Percoll gradient Sequencing was performed by the High Throughput Genomics Group at the Wellcome Trust Centre for Human Genetics (Oxford University). RNA libraries were prepared using a SMARTer Ultra Low Input HV kit (634820, Clontech). Custom adaptor and barcode tags were used (5'- P-GATCGGAAGAGCGGTTCAGCAGGAATGCCGAG, 5’-ACACTCTTTCCCTACACGACGCTCTTCCGATCT). Samples were amplified (13 cycles for RNA) and multiplexed in replicate flow cells on an Illumina HiSeq2500 platform to yield 50bp paired-end reads at a depth of at least 20M. All libraries were prepared together to avoid batch effects.	Illumina HiSeq 2500	age;;6-8 weeks old|gender;;male|injury condition;;SHAM|source_name;;mouse spinal cord microglia|strain;;C57BL/6	GEO Accession;;GSM1827985		GSM1827985	RNA_SHAM2	1572025224	15412012	2016-05-12 16:05:14	929011336	1572025224	15412012	2	15412012	index:0,count:15412012,average:51,stdev:0|index:1,count:15412012,average:51,stdev:0	GSM1827985_r1				in_mesa	27184839	5.04	2.75	0.12	1361963161	1346788030	1266084297	1259056622	98.89	99.44	13976166	11919331	231.755	1346.488	179	99263	68.38	73.73	15674080	9557209	15674080	9557209	71.57	70.76	15674080	10003132	15674080	9172961	337461806	24.78	2.62	0	6.57	0	0.48	0	0.21	0	0.00	0	8.63	0	13976166	0	102	0	97.69	0	1.25	0	0.01	0	1.15	0	0.00	0	276.04	0	0.19	0	403625	0	15412012	0	1013072	0	73420	0	33029	0	0	0	1329397	0	760	0	0	0	7929	0	1591104	0	55862	0	1655655	0	84.11	0	12963094	0	108557	1658248	15.275366857964	15412012.0	13976166.0	403625.0	1013072.0	73420.0	33029.0	0.0	1329397.0	12963094.0	90.7	2.6	6.6	0.5	0.2	0.0	8.6	84.1	51	51	51.00	38	786012612	26.4	23.9	23.8	25.9	0.0	38.4	31.8	bulk
1650746	SRR2120303	SRP061355	SRS1007822	SRX1113442	SRA278928	GEO		Injury-induced enhancer remodelling in spinal microglia - a novel mechanism for pain chronification? [RNA-Seq]	Chronic pain is common and devastating. Yet, its precise molecular origins remain unclear. The condition induces well-characterised changes in neurons and microglia, but it is unknown why they persist long after the precipitating injury has healed. We posit a role for enhancers - regions of open chromatin that define a cell’s transcription factor binding profile. Enhancer profiles can alter upon environmental stimulation, functioning as a kind of molecular memory. Here, a mouse model of persistent neuropathic pain was used to examine microglial enhancers with flow cytometry and sequencing. We observed injury-specific alterations of enhancers in close proximity to transcriptionally regulated genes. Our data also shine light on details relating to the spinal cord immune response and provide the first genome-wide gene expression profile of isolated microglia in a pain state. We hypothesise that enhancer deposition may constitute a novel mechanism by which painful experiences are encoded on a molecular level. Overall design: ChIP-seq and RNA-seq of isolated spinal cord microglia after peripheral spinal nerve ligation or sham surgery in mice (day 7)		GSM1827985: RNA_SHAM2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Spinal cord microglia were isolated via a Percoll gradient Sequencing was performed by the High Throughput Genomics Group at the Wellcome Trust Centre for Human Genetics (Oxford University). RNA libraries were prepared using a SMARTer Ultra Low Input HV kit (634820, Clontech). Custom adaptor and barcode tags were used (5'- P-GATCGGAAGAGCGGTTCAGCAGGAATGCCGAG, 5’-ACACTCTTTCCCTACACGACGCTCTTCCGATCT). Samples were amplified (13 cycles for RNA) and multiplexed in replicate flow cells on an Illumina HiSeq2500 platform to yield 50bp paired-end reads at a depth of at least 20M. All libraries were prepared together to avoid batch effects.	Illumina HiSeq 2500	age;;6-8 weeks old|gender;;male|injury condition;;SHAM|source_name;;mouse spinal cord microglia|strain;;C57BL/6	GEO Accession;;GSM1827985		GSM1827985	RNA_SHAM2	1552827498	15223799	2016-05-12 16:05:14	917719620	1552827498	15223799	2	15223799	index:0,count:15223799,average:51,stdev:0|index:1,count:15223799,average:51,stdev:0	GSM1827985_r2				in_mesa	27184839	5.03	2.75	0.13	1348251641	1333182094	1253488055	1246513189	98.88	99.44	13833691	11797864	231.761	1339.303	177	98265	68.4	73.73	15511002	9461861	15511002	9461861	71.57	70.76	15511002	9900441	15511002	9080784	333814170	24.76	2.61	0	6.58	0	0.48	0	0.21	0	0.00	0	8.44	0	13833691	0	102	0	97.70	0	1.25	0	0.01	0	1.14	0	0.00	0	360.56	0	0.21	0	397199	0	15223799	0	1001105	0	72865	0	32271	0	0	0	1284972	0	721	0	0	0	7999	0	1573588	0	54969	0	1637277	0	84.29	0	12832586	0	108310	1639305	15.135306065922	15223799.0	13833691.0	397199.0	1001105.0	72865.0	32271.0	0.0	1284972.0	12832586.0	90.9	2.6	6.6	0.5	0.2	0.0	8.4	84.3	51	51	51.00	38	776413749	26.4	23.9	23.8	25.9	0.0	38.4	31.6	bulk
1650762	SRR2120304	SRP061355	SRS1007821	SRX1113443	SRA278928	GEO		Injury-induced enhancer remodelling in spinal microglia - a novel mechanism for pain chronification? [RNA-Seq]	Chronic pain is common and devastating. Yet, its precise molecular origins remain unclear. The condition induces well-characterised changes in neurons and microglia, but it is unknown why they persist long after the precipitating injury has healed. We posit a role for enhancers - regions of open chromatin that define a cell’s transcription factor binding profile. Enhancer profiles can alter upon environmental stimulation, functioning as a kind of molecular memory. Here, a mouse model of persistent neuropathic pain was used to examine microglial enhancers with flow cytometry and sequencing. We observed injury-specific alterations of enhancers in close proximity to transcriptionally regulated genes. Our data also shine light on details relating to the spinal cord immune response and provide the first genome-wide gene expression profile of isolated microglia in a pain state. We hypothesise that enhancer deposition may constitute a novel mechanism by which painful experiences are encoded on a molecular level. Overall design: ChIP-seq and RNA-seq of isolated spinal cord microglia after peripheral spinal nerve ligation or sham surgery in mice (day 7)		GSM1827986: RNA_SHAM3; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Spinal cord microglia were isolated via a Percoll gradient Sequencing was performed by the High Throughput Genomics Group at the Wellcome Trust Centre for Human Genetics (Oxford University). RNA libraries were prepared using a SMARTer Ultra Low Input HV kit (634820, Clontech). Custom adaptor and barcode tags were used (5'- P-GATCGGAAGAGCGGTTCAGCAGGAATGCCGAG, 5’-ACACTCTTTCCCTACACGACGCTCTTCCGATCT). Samples were amplified (13 cycles for RNA) and multiplexed in replicate flow cells on an Illumina HiSeq2500 platform to yield 50bp paired-end reads at a depth of at least 20M. All libraries were prepared together to avoid batch effects.	Illumina HiSeq 2500	age;;6-8 weeks old|gender;;male|injury condition;;SHAM|source_name;;mouse spinal cord microglia|strain;;C57BL/6	GEO Accession;;GSM1827986		GSM1827986	RNA_SHAM3	2301351642	22562271	2016-05-12 16:05:14	1367243471	2301351642	22562271	2	22562271	index:0,count:22562271,average:51,stdev:0|index:1,count:22562271,average:51,stdev:0	GSM1827986_r1				in_mesa	27184839	5.15	2.74	0.14	1960429039	1942276259	1815014592	1809070983	99.07	99.67	20189964	17083334	237.265	1382.248	181	139431	70.15	75.96	22801235	14163197	22801235	14163197	73.51	72.75	22801235	14841704	22801235	13563731	440526642	22.47	2.78	0	6.85	0	0.47	0	0.20	0	0.00	0	9.85	0	20189964	0	102	0	97.36	0	1.26	0	0.01	0	1.15	0	0.00	0	319.78	0	0.20	0	626347	0	22562271	0	1545098	0	105236	0	44501	0	0	0	2222570	0	1143	0	0	0	11422	0	2332835	0	85294	0	2430694	0	82.64	0	18644866	0	115247	2457635	21.324936874713	22562271.0	20189964.0	626347.0	1545098.0	105236.0	44501.0	0.0	2222570.0	18644866.0	89.5	2.8	6.8	0.5	0.2	0.0	9.9	82.6	51	51	51.00	38	1150675821	26.8	23.8	23.4	25.9	0.0	38.4	31.7	bulk
1650778	SRR2120305	SRP061355	SRS1007821	SRX1113443	SRA278928	GEO		Injury-induced enhancer remodelling in spinal microglia - a novel mechanism for pain chronification? [RNA-Seq]	Chronic pain is common and devastating. Yet, its precise molecular origins remain unclear. The condition induces well-characterised changes in neurons and microglia, but it is unknown why they persist long after the precipitating injury has healed. We posit a role for enhancers - regions of open chromatin that define a cell’s transcription factor binding profile. Enhancer profiles can alter upon environmental stimulation, functioning as a kind of molecular memory. Here, a mouse model of persistent neuropathic pain was used to examine microglial enhancers with flow cytometry and sequencing. We observed injury-specific alterations of enhancers in close proximity to transcriptionally regulated genes. Our data also shine light on details relating to the spinal cord immune response and provide the first genome-wide gene expression profile of isolated microglia in a pain state. We hypothesise that enhancer deposition may constitute a novel mechanism by which painful experiences are encoded on a molecular level. Overall design: ChIP-seq and RNA-seq of isolated spinal cord microglia after peripheral spinal nerve ligation or sham surgery in mice (day 7)		GSM1827986: RNA_SHAM3; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Spinal cord microglia were isolated via a Percoll gradient Sequencing was performed by the High Throughput Genomics Group at the Wellcome Trust Centre for Human Genetics (Oxford University). RNA libraries were prepared using a SMARTer Ultra Low Input HV kit (634820, Clontech). Custom adaptor and barcode tags were used (5'- P-GATCGGAAGAGCGGTTCAGCAGGAATGCCGAG, 5’-ACACTCTTTCCCTACACGACGCTCTTCCGATCT). Samples were amplified (13 cycles for RNA) and multiplexed in replicate flow cells on an Illumina HiSeq2500 platform to yield 50bp paired-end reads at a depth of at least 20M. All libraries were prepared together to avoid batch effects.	Illumina HiSeq 2500	age;;6-8 weeks old|gender;;male|injury condition;;SHAM|source_name;;mouse spinal cord microglia|strain;;C57BL/6	GEO Accession;;GSM1827986		GSM1827986	RNA_SHAM3	2278549950	22338725	2016-05-12 16:05:14	1353668142	2278549950	22338725	2	22338725	index:0,count:22338725,average:51,stdev:0|index:1,count:22338725,average:51,stdev:0	GSM1827986_r2				in_mesa	27184839	5.16	2.74	0.13	1946793185	1928822458	1802253216	1796435436	99.08	99.68	20048521	16965113	237.258	1369.978	179	139234	70.14	75.96	22637622	14061473	22637622	14061473	73.5	72.74	22637622	14736516	22637622	13466166	437734094	22.48	2.78	0	6.87	0	0.47	0	0.20	0	0.00	0	9.59	0	20048521	0	102	0	97.37	0	1.26	0	0.01	0	1.15	0	0.00	0	237.23	0	0.21	0	620971	0	22338725	0	1535716	0	104808	0	43582	0	0	0	2141814	0	1170	0	0	0	11011	0	2315503	0	84931	0	2412615	0	82.87	0	18512805	0	115168	2438627	21.174518963601	22338725.0	20048521.0	620971.0	1535716.0	104808.0	43582.0	0.0	2141814.0	18512805.0	89.7	2.8	6.9	0.5	0.2	0.0	9.6	82.9	51	51	51.00	38	1139274975	26.8	23.8	23.4	25.9	0.0	38.4	31.5	bulk
1650794	SRR2120306	SRP061355	SRS1007820	SRX1113444	SRA278928	GEO		Injury-induced enhancer remodelling in spinal microglia - a novel mechanism for pain chronification? [RNA-Seq]	Chronic pain is common and devastating. Yet, its precise molecular origins remain unclear. The condition induces well-characterised changes in neurons and microglia, but it is unknown why they persist long after the precipitating injury has healed. We posit a role for enhancers - regions of open chromatin that define a cell’s transcription factor binding profile. Enhancer profiles can alter upon environmental stimulation, functioning as a kind of molecular memory. Here, a mouse model of persistent neuropathic pain was used to examine microglial enhancers with flow cytometry and sequencing. We observed injury-specific alterations of enhancers in close proximity to transcriptionally regulated genes. Our data also shine light on details relating to the spinal cord immune response and provide the first genome-wide gene expression profile of isolated microglia in a pain state. We hypothesise that enhancer deposition may constitute a novel mechanism by which painful experiences are encoded on a molecular level. Overall design: ChIP-seq and RNA-seq of isolated spinal cord microglia after peripheral spinal nerve ligation or sham surgery in mice (day 7)		GSM1827987: RNA_SHAM4; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Spinal cord microglia were isolated via a Percoll gradient Sequencing was performed by the High Throughput Genomics Group at the Wellcome Trust Centre for Human Genetics (Oxford University). RNA libraries were prepared using a SMARTer Ultra Low Input HV kit (634820, Clontech). Custom adaptor and barcode tags were used (5'- P-GATCGGAAGAGCGGTTCAGCAGGAATGCCGAG, 5’-ACACTCTTTCCCTACACGACGCTCTTCCGATCT). Samples were amplified (13 cycles for RNA) and multiplexed in replicate flow cells on an Illumina HiSeq2500 platform to yield 50bp paired-end reads at a depth of at least 20M. All libraries were prepared together to avoid batch effects.	Illumina HiSeq 2500	age;;6-8 weeks old|gender;;male|injury condition;;SHAM|source_name;;mouse spinal cord microglia|strain;;C57BL/6	GEO Accession;;GSM1827987		GSM1827987	RNA_SHAM4	2323769610	22782055	2016-05-12 16:05:14	1367902171	2323769610	22782055	2	22782055	index:0,count:22782055,average:51,stdev:0|index:1,count:22782055,average:51,stdev:0	GSM1827987_r1				in_mesa	27184839	3.77	2.74	0.12	2028871017	1993848784	1905385917	1881279504	98.27	98.73	20749601	17990274	229.871	1249.954	182	149220	62.99	67.21	23026729	13069444	23026729	13069444	65.49	64.51	23026729	13588712	23026729	12543815	629262135	31.02	2.56	0	5.73	0	0.47	0	0.24	0	0.00	0	8.21	0	20749601	0	102	0	98.01	0	1.24	0	0.01	0	1.15	0	0.00	0	344.60	0	0.18	0	583935	0	22782055	0	1305262	0	106518	0	55599	0	0	0	1870337	0	981	0	0	0	10586	0	2099352	0	70830	0	2181749	0	85.35	0	19444339	0	118248	2190054	18.520854475340	22782055.0	20749601.0	583935.0	1305262.0	106518.0	55599.0	0.0	1870337.0	19444339.0	91.1	2.6	5.7	0.5	0.2	0.0	8.2	85.3	51	51	51.00	38	1161884805	26.3	24.0	23.7	26.1	0.0	38.5	31.9	bulk
1650811	SRR2120307	SRP061355	SRS1007820	SRX1113444	SRA278928	GEO		Injury-induced enhancer remodelling in spinal microglia - a novel mechanism for pain chronification? [RNA-Seq]	Chronic pain is common and devastating. Yet, its precise molecular origins remain unclear. The condition induces well-characterised changes in neurons and microglia, but it is unknown why they persist long after the precipitating injury has healed. We posit a role for enhancers - regions of open chromatin that define a cell’s transcription factor binding profile. Enhancer profiles can alter upon environmental stimulation, functioning as a kind of molecular memory. Here, a mouse model of persistent neuropathic pain was used to examine microglial enhancers with flow cytometry and sequencing. We observed injury-specific alterations of enhancers in close proximity to transcriptionally regulated genes. Our data also shine light on details relating to the spinal cord immune response and provide the first genome-wide gene expression profile of isolated microglia in a pain state. We hypothesise that enhancer deposition may constitute a novel mechanism by which painful experiences are encoded on a molecular level. Overall design: ChIP-seq and RNA-seq of isolated spinal cord microglia after peripheral spinal nerve ligation or sham surgery in mice (day 7)		GSM1827987: RNA_SHAM4; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Spinal cord microglia were isolated via a Percoll gradient Sequencing was performed by the High Throughput Genomics Group at the Wellcome Trust Centre for Human Genetics (Oxford University). RNA libraries were prepared using a SMARTer Ultra Low Input HV kit (634820, Clontech). Custom adaptor and barcode tags were used (5'- P-GATCGGAAGAGCGGTTCAGCAGGAATGCCGAG, 5’-ACACTCTTTCCCTACACGACGCTCTTCCGATCT). Samples were amplified (13 cycles for RNA) and multiplexed in replicate flow cells on an Illumina HiSeq2500 platform to yield 50bp paired-end reads at a depth of at least 20M. All libraries were prepared together to avoid batch effects.	Illumina HiSeq 2500	age;;6-8 weeks old|gender;;male|injury condition;;SHAM|source_name;;mouse spinal cord microglia|strain;;C57BL/6	GEO Accession;;GSM1827987		GSM1827987	RNA_SHAM4	2303273424	22581112	2016-05-12 16:05:14	1355989887	2303273424	22581112	2	22581112	index:0,count:22581112,average:51,stdev:0|index:1,count:22581112,average:51,stdev:0	GSM1827987_r2				in_mesa	27184839	3.77	2.74	0.12	2015414137	1980628469	1892566147	1868700060	98.27	98.74	20610323	17873671	229.894	1237.567	180	148691	62.99	67.22	22878320	12982286	22878320	12982286	65.5	64.53	22878320	13500115	22878320	12461334	625046696	31.01	2.56	0	5.75	0	0.47	0	0.24	0	0.00	0	8.01	0	20610323	0	102	0	98.02	0	1.24	0	0.01	0	1.15	0	0.00	0	361.30	0	0.20	0	578682	0	22581112	0	1298234	0	106306	0	54642	0	0	0	1809841	0	1006	0	0	0	10722	0	2084251	0	70196	0	2166175	0	85.52	0	19312089	0	117748	2175443	18.475413595135	22581112.0	20610323.0	578682.0	1298234.0	106306.0	54642.0	0.0	1809841.0	19312089.0	91.3	2.6	5.7	0.5	0.2	0.0	8.0	85.5	51	51	51.00	38	1151636712	26.3	24.0	23.7	26.1	0.0	38.5	31.6	bulk
1478687	SRR2153901	SRP062242	SRS1028434	SRX1140952	SRA288475	GEO		Gene expression profiling of neurons with Rbfox1 and Rbfox3 knockdown and rescue with cytoplasmic or nuclear Rbfox1 isoform [RNA-seq]	Human genetic studies have identified the neuronal RNA binding protein, Rbfox1, as a candidate gene for autism spectrum disorders. While Rbfox1 functions as a splicing regulator in the nucleus, it is also alternatively spliced to produce cytoplasmic isoforms. To investigate cytoplasmic Rbfox1, we knocked down Rbfox proteins in mouse neurons and rescued with cytoplasmic or nuclear Rbfox1. Transcriptome profiling showed that nuclear Rbfox1 rescued splicing changes induced by knockdown, whereas cytoplasmic Rbfox1 rescued changes in mRNA levels. iCLIP-seq of subcellular fractions revealed that in nascent RNA Rbfox1 bound predominantly to introns, while cytoplasmic Rbox1 bound to 3'' UTRs. Cytoplasmic Rbfox1 binding increased target mRNA stability and translation, and overlapped significantly with miRNA binding sites. Cytoplasmic Rbfox1 target mRNAs were enriched in genes involved in cortical development and autism. Our results uncover a new Rbfox1 regulatory network and highlight the importance of cytoplasmic RNA metabolism to cortical development and disease. In this data set, we included the data from RNA-seq experiments. Overall design: We performed RNA-seq to profile gene expression and splicing changes. The expression levels of Rbfox1 and Rbfox3 in cultured mouse hippocampal neurons were reduced by siRNAs. The reduction of Rbfox1 and 3 was rescued by expression of cytoplasmic or nuclear Rbfox1 splice isoform. The gene expression and splicing profiles were compared between different treatments. Eight samples were analyzed.		GSM1847354: siNT_EGFP_Rep1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted by RNeasy Mini kit (Qiagen) according to manufacturer's instruction. Ribosomal RNA was removed using Ribo-Zero™ rRNA Removal Kits (Epicentre), and the cDNA libraries were prepared using TruSeq RNA Sample Preparation Kit (Illumina). RNA-Seq HiSeq2000 (Illumina) paired-end 50 nt, non-strand specific.	Illumina HiSeq 2000	age;;14 DIV|cell_type;;hippocampal neurons|sirna;;Non-targeting|source_name;;Hippocampal culture_Control siRNAs_EGFP|treated with;;AAV2/9-SynI-EGFP and Non-targeting siRNAs	GEO Accession;;GSM1847354		GSM1847354	siNT_EGFP_Rep1	10076426300	100764263	2015-12-10 18:37:12	8937200346	10076426300	100764263	2	100764263	index:0,count:100764263,average:50,stdev:0|index:1,count:100764263,average:50,stdev:0	GSM1847354_r1						1.0	3.8	0.03	9389044176	9350721926	8517771451	8530161918	99.59	100.15	94942925	80214892	202.134	1452.172	136	870587	82.54	90.94	108914280	78366654	108914280	78366654	87.76	87.96	108914280	83324381	108914280	75792214	727106205	7.74	1.52	0	8.71	0	0.28	0	0.16	0	0.00	0	5.34	0	94942925	0	100	0	98.99	0	1.36	0	0.00	0	1.14	0	0.00	0	472.95	0	0.25	0	1531819	0	100764263	0	8773438	0	283098	0	159348	0	0	0	5378892	0	12537	0	0	0	109421	0	14266486	0	29101	0	14417545	0	85.52	0	86169487	0	232175	14634761	63.033319694196	100764263.0	94942925.0	1531819.0	8773438.0	283098.0	159348.0	0.0	5378892.0	86169487.0	94.2	1.5	8.7	0.3	0.2	0.0	5.3	85.5	50	50	50.00	38	5038213150	24.6	25.1	25.5	24.8	0.0	35.9	21.6	bulk
1478703	SRR2153902	SRP062242	SRS1028433	SRX1140953	SRA288475	GEO		Gene expression profiling of neurons with Rbfox1 and Rbfox3 knockdown and rescue with cytoplasmic or nuclear Rbfox1 isoform [RNA-seq]	Human genetic studies have identified the neuronal RNA binding protein, Rbfox1, as a candidate gene for autism spectrum disorders. While Rbfox1 functions as a splicing regulator in the nucleus, it is also alternatively spliced to produce cytoplasmic isoforms. To investigate cytoplasmic Rbfox1, we knocked down Rbfox proteins in mouse neurons and rescued with cytoplasmic or nuclear Rbfox1. Transcriptome profiling showed that nuclear Rbfox1 rescued splicing changes induced by knockdown, whereas cytoplasmic Rbfox1 rescued changes in mRNA levels. iCLIP-seq of subcellular fractions revealed that in nascent RNA Rbfox1 bound predominantly to introns, while cytoplasmic Rbox1 bound to 3'' UTRs. Cytoplasmic Rbfox1 binding increased target mRNA stability and translation, and overlapped significantly with miRNA binding sites. Cytoplasmic Rbfox1 target mRNAs were enriched in genes involved in cortical development and autism. Our results uncover a new Rbfox1 regulatory network and highlight the importance of cytoplasmic RNA metabolism to cortical development and disease. In this data set, we included the data from RNA-seq experiments. Overall design: We performed RNA-seq to profile gene expression and splicing changes. The expression levels of Rbfox1 and Rbfox3 in cultured mouse hippocampal neurons were reduced by siRNAs. The reduction of Rbfox1 and 3 was rescued by expression of cytoplasmic or nuclear Rbfox1 splice isoform. The gene expression and splicing profiles were compared between different treatments. Eight samples were analyzed.		GSM1847355: siNT_EGFP_Rep2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted by RNeasy Mini kit (Qiagen) according to manufacturer's instruction. Ribosomal RNA was removed using Ribo-Zero™ rRNA Removal Kits (Epicentre), and the cDNA libraries were prepared using TruSeq RNA Sample Preparation Kit (Illumina). RNA-Seq HiSeq2000 (Illumina) paired-end 50 nt, non-strand specific.	Illumina HiSeq 2000	age;;14 DIV|cell_type;;hippocampal neurons|sirna;;Non-targeting|source_name;;Hippocampal culture_Control siRNAs_EGFP|treated with;;AAV2/9-SynI-EGFP and Non-targeting siRNAs	GEO Accession;;GSM1847355		GSM1847355	siNT_EGFP_Rep2	9273132100	92731321	2015-12-10 18:37:12	8213307065	9273132100	92731321	2	92731321	index:0,count:92731321,average:50,stdev:0|index:1,count:92731321,average:50,stdev:0	GSM1847355_r1						1.24	3.87	0.03	8695159710	8665514169	7908043776	7927595158	99.66	100.25	87908020	73911324	202.124	1472.719	135	796303	84.45	92.81	100724416	74236709	100724416	74236709	89.44	89.8	100724416	78620549	100724416	71825470	525858957	6.05	1.42	0	8.54	0	0.28	0	0.14	0	0.00	0	4.79	0	87908020	0	100	0	99.03	0	1.44	0	0.00	0	1.16	0	0.00	0	431.87	0	0.24	0	1317831	0	92731321	0	7923079	0	258601	0	126914	0	0	0	4437786	0	12128	0	0	0	104854	0	13626271	0	25611	0	13768864	0	86.25	0	79984941	0	227233	13986241	61.550219378347	92731321.0	87908020.0	1317831.0	7923079.0	258601.0	126914.0	0.0	4437786.0	79984941.0	94.8	1.4	8.5	0.3	0.1	0.0	4.8	86.3	50	50	50.00	38	4636566050	24.8	24.9	25.3	25.0	0.0	36.0	21.9	bulk
1478719	SRR2153903	SRP062242	SRS1028432	SRX1140954	SRA288475	GEO		Gene expression profiling of neurons with Rbfox1 and Rbfox3 knockdown and rescue with cytoplasmic or nuclear Rbfox1 isoform [RNA-seq]	Human genetic studies have identified the neuronal RNA binding protein, Rbfox1, as a candidate gene for autism spectrum disorders. While Rbfox1 functions as a splicing regulator in the nucleus, it is also alternatively spliced to produce cytoplasmic isoforms. To investigate cytoplasmic Rbfox1, we knocked down Rbfox proteins in mouse neurons and rescued with cytoplasmic or nuclear Rbfox1. Transcriptome profiling showed that nuclear Rbfox1 rescued splicing changes induced by knockdown, whereas cytoplasmic Rbfox1 rescued changes in mRNA levels. iCLIP-seq of subcellular fractions revealed that in nascent RNA Rbfox1 bound predominantly to introns, while cytoplasmic Rbox1 bound to 3'' UTRs. Cytoplasmic Rbfox1 binding increased target mRNA stability and translation, and overlapped significantly with miRNA binding sites. Cytoplasmic Rbfox1 target mRNAs were enriched in genes involved in cortical development and autism. Our results uncover a new Rbfox1 regulatory network and highlight the importance of cytoplasmic RNA metabolism to cortical development and disease. In this data set, we included the data from RNA-seq experiments. Overall design: We performed RNA-seq to profile gene expression and splicing changes. The expression levels of Rbfox1 and Rbfox3 in cultured mouse hippocampal neurons were reduced by siRNAs. The reduction of Rbfox1 and 3 was rescued by expression of cytoplasmic or nuclear Rbfox1 splice isoform. The gene expression and splicing profiles were compared between different treatments. Eight samples were analyzed.		GSM1847356: siRbfox1&3_EGFP_Rep1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted by RNeasy Mini kit (Qiagen) according to manufacturer's instruction. Ribosomal RNA was removed using Ribo-Zero™ rRNA Removal Kits (Epicentre), and the cDNA libraries were prepared using TruSeq RNA Sample Preparation Kit (Illumina). RNA-Seq HiSeq2000 (Illumina) paired-end 50 nt, non-strand specific.	Illumina HiSeq 2000	age;;14 DIV|cell_type;;hippocampal neurons|sirna;;Rbfox1 and Rbfox3|source_name;;Hippocampal culture_Rbfox1 and Rbfox3 siRNAs_EGFP|treated with;;AAV2/9-SynI-EGFP and Rbfox1 and Rbfox3 siRNAs	GEO Accession;;GSM1847356		GSM1847356	siRbfox1&3_EGFP_Rep1	10884832600	108848326	2015-12-10 18:37:12	9662418821	10884832600	108848326	2	108848326	index:0,count:108848326,average:50,stdev:0|index:1,count:108848326,average:50,stdev:0	GSM1847356_r1						1.38	3.88	0.03	10218936059	10188563007	9292127127	9316595298	99.7	100.26	103301556	87155702	201.412	1424.388	136	960679	83.92	92.25	118611270	86688673	118611270	86688673	89.0	89.28	118611270	91941206	118611270	83902932	681272644	6.67	1.31	0	8.57	0	0.28	0	0.15	0	0.00	0	4.66	0	103301556	0	100	0	99.04	0	1.35	0	0.00	0	1.14	0	0.00	0	441.28	0	0.25	0	1429901	0	108848326	0	9327947	0	308582	0	160964	0	0	0	5077224	0	14203	0	0	0	121572	0	15913848	0	30593	0	16080216	0	86.33	0	93973609	0	235329	16344308	69.453012590883	108848326.0	103301556.0	1429901.0	9327947.0	308582.0	160964.0	0.0	5077224.0	93973609.0	94.9	1.3	8.6	0.3	0.1	0.0	4.7	86.3	50	50	50.00	38	5442416300	24.8	24.9	25.2	25.1	0.0	35.9	21.8	bulk
1478735	SRR2153904	SRP062242	SRS1028431	SRX1140955	SRA288475	GEO		Gene expression profiling of neurons with Rbfox1 and Rbfox3 knockdown and rescue with cytoplasmic or nuclear Rbfox1 isoform [RNA-seq]	Human genetic studies have identified the neuronal RNA binding protein, Rbfox1, as a candidate gene for autism spectrum disorders. While Rbfox1 functions as a splicing regulator in the nucleus, it is also alternatively spliced to produce cytoplasmic isoforms. To investigate cytoplasmic Rbfox1, we knocked down Rbfox proteins in mouse neurons and rescued with cytoplasmic or nuclear Rbfox1. Transcriptome profiling showed that nuclear Rbfox1 rescued splicing changes induced by knockdown, whereas cytoplasmic Rbfox1 rescued changes in mRNA levels. iCLIP-seq of subcellular fractions revealed that in nascent RNA Rbfox1 bound predominantly to introns, while cytoplasmic Rbox1 bound to 3'' UTRs. Cytoplasmic Rbfox1 binding increased target mRNA stability and translation, and overlapped significantly with miRNA binding sites. Cytoplasmic Rbfox1 target mRNAs were enriched in genes involved in cortical development and autism. Our results uncover a new Rbfox1 regulatory network and highlight the importance of cytoplasmic RNA metabolism to cortical development and disease. In this data set, we included the data from RNA-seq experiments. Overall design: We performed RNA-seq to profile gene expression and splicing changes. The expression levels of Rbfox1 and Rbfox3 in cultured mouse hippocampal neurons were reduced by siRNAs. The reduction of Rbfox1 and 3 was rescued by expression of cytoplasmic or nuclear Rbfox1 splice isoform. The gene expression and splicing profiles were compared between different treatments. Eight samples were analyzed.		GSM1847357: siRbfox1&3_EGFP_Rep2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted by RNeasy Mini kit (Qiagen) according to manufacturer's instruction. Ribosomal RNA was removed using Ribo-Zero™ rRNA Removal Kits (Epicentre), and the cDNA libraries were prepared using TruSeq RNA Sample Preparation Kit (Illumina). RNA-Seq HiSeq2000 (Illumina) paired-end 50 nt, non-strand specific.	Illumina HiSeq 2000	age;;14 DIV|cell_type;;hippocampal neurons|sirna;;Rbfox1 and Rbfox3|source_name;;Hippocampal culture_Rbfox1 and Rbfox3 siRNAs_EGFP|treated with;;AAV2/9-SynI-EGFP and Rbfox1 and Rbfox3 siRNAs	GEO Accession;;GSM1847357		GSM1847357	siRbfox1&3_EGFP_Rep2	10230244900	102302449	2015-12-10 18:37:12	9068525859	10230244900	102302449	2	102302449	index:0,count:102302449,average:50,stdev:0|index:1,count:102302449,average:50,stdev:0	GSM1847357_r1						1.2	3.81	0.03	9557881888	9534451777	8651687829	8683473996	99.75	100.37	96614946	81164891	203.884	1461.126	136	863403	83.73	92.45	111573366	80892591	111573366	80892591	88.81	89.18	111573366	85807557	111573366	78029573	605376581	6.33	1.48	0	8.91	0	0.28	0	0.14	0	0.00	0	5.14	0	96614946	0	100	0	99.03	0	1.61	0	0.00	0	1.18	0	0.00	0	499.71	0	0.25	0	1512962	0	102302449	0	9118611	0	286231	0	143406	0	0	0	5257866	0	13429	0	0	0	113740	0	14886302	0	28628	0	15042099	0	85.53	0	87496335	0	229044	15298518	66.792921884005	102302449.0	96614946.0	1512962.0	9118611.0	286231.0	143406.0	0.0	5257866.0	87496335.0	94.4	1.5	8.9	0.3	0.1	0.0	5.1	85.5	50	50	50.00	38	5115122450	24.6	25.0	25.4	24.9	0.0	35.9	21.7	bulk
1478750	SRR2153905	SRP062242	SRS1028430	SRX1140956	SRA288475	GEO		Gene expression profiling of neurons with Rbfox1 and Rbfox3 knockdown and rescue with cytoplasmic or nuclear Rbfox1 isoform [RNA-seq]	Human genetic studies have identified the neuronal RNA binding protein, Rbfox1, as a candidate gene for autism spectrum disorders. While Rbfox1 functions as a splicing regulator in the nucleus, it is also alternatively spliced to produce cytoplasmic isoforms. To investigate cytoplasmic Rbfox1, we knocked down Rbfox proteins in mouse neurons and rescued with cytoplasmic or nuclear Rbfox1. Transcriptome profiling showed that nuclear Rbfox1 rescued splicing changes induced by knockdown, whereas cytoplasmic Rbfox1 rescued changes in mRNA levels. iCLIP-seq of subcellular fractions revealed that in nascent RNA Rbfox1 bound predominantly to introns, while cytoplasmic Rbox1 bound to 3'' UTRs. Cytoplasmic Rbfox1 binding increased target mRNA stability and translation, and overlapped significantly with miRNA binding sites. Cytoplasmic Rbfox1 target mRNAs were enriched in genes involved in cortical development and autism. Our results uncover a new Rbfox1 regulatory network and highlight the importance of cytoplasmic RNA metabolism to cortical development and disease. In this data set, we included the data from RNA-seq experiments. Overall design: We performed RNA-seq to profile gene expression and splicing changes. The expression levels of Rbfox1 and Rbfox3 in cultured mouse hippocampal neurons were reduced by siRNAs. The reduction of Rbfox1 and 3 was rescued by expression of cytoplasmic or nuclear Rbfox1 splice isoform. The gene expression and splicing profiles were compared between different treatments. Eight samples were analyzed.		GSM1847358: siRbfox1&3_Flag-Rbfox1_C_Rep1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted by RNeasy Mini kit (Qiagen) according to manufacturer's instruction. Ribosomal RNA was removed using Ribo-Zero™ rRNA Removal Kits (Epicentre), and the cDNA libraries were prepared using TruSeq RNA Sample Preparation Kit (Illumina). RNA-Seq HiSeq2000 (Illumina) paired-end 50 nt, non-strand specific.	Illumina HiSeq 2000	age;;14 DIV|cell_type;;hippocampal neurons|sirna;;Rbfox1 and Rbfox3|source_name;;Hippocampal culture_Rbfox1 and Rbfox3 siRNAs_Flag_Rbfox1_C|treated with;;AAV2/9-SynI-Flag-Rbfox1_C_siMt and Rbfox1 and Rbfox3 siRNAs	GEO Accession;;GSM1847358		GSM1847358	siRbfox1&3_Flag-Rbfox1_C_Rep1	10842318300	108423183	2015-12-10 18:37:12	9584759115	10842318300	108423183	2	108423183	index:0,count:108423183,average:50,stdev:0|index:1,count:108423183,average:50,stdev:0	GSM1847358_r1						1.25	3.69	0.04	10172786970	10124427063	9204890917	9213323076	99.52	100.09	102783480	87092511	201.580	1412.786	136	929580	80.13	88.52	118553359	82362272	118553359	82362272	85.46	85.43	118553359	87836022	118553359	79486351	1000265820	9.83	1.45	0	8.98	0	0.28	0	0.20	0	0.00	0	4.72	0	102783480	0	100	0	99.07	0	1.59	0	0.00	0	1.18	0	0.00	0	451.76	0	0.25	0	1567631	0	108423183	0	9736491	0	307169	0	216912	0	0	0	5115622	0	13616	0	0	0	117853	0	15126260	0	33123	0	15290852	0	85.82	0	93046989	0	229781	15527131	67.573607043228	108423183.0	102783480.0	1567631.0	9736491.0	307169.0	216912.0	0.0	5115622.0	93046989.0	94.8	1.4	9.0	0.3	0.2	0.0	4.7	85.8	50	50	50.00	38	5421159150	24.8	24.9	25.3	25.1	0.0	36.0	22.0	bulk
1478767	SRR2153906	SRP062242	SRS1028429	SRX1140957	SRA288475	GEO		Gene expression profiling of neurons with Rbfox1 and Rbfox3 knockdown and rescue with cytoplasmic or nuclear Rbfox1 isoform [RNA-seq]	Human genetic studies have identified the neuronal RNA binding protein, Rbfox1, as a candidate gene for autism spectrum disorders. While Rbfox1 functions as a splicing regulator in the nucleus, it is also alternatively spliced to produce cytoplasmic isoforms. To investigate cytoplasmic Rbfox1, we knocked down Rbfox proteins in mouse neurons and rescued with cytoplasmic or nuclear Rbfox1. Transcriptome profiling showed that nuclear Rbfox1 rescued splicing changes induced by knockdown, whereas cytoplasmic Rbfox1 rescued changes in mRNA levels. iCLIP-seq of subcellular fractions revealed that in nascent RNA Rbfox1 bound predominantly to introns, while cytoplasmic Rbox1 bound to 3'' UTRs. Cytoplasmic Rbfox1 binding increased target mRNA stability and translation, and overlapped significantly with miRNA binding sites. Cytoplasmic Rbfox1 target mRNAs were enriched in genes involved in cortical development and autism. Our results uncover a new Rbfox1 regulatory network and highlight the importance of cytoplasmic RNA metabolism to cortical development and disease. In this data set, we included the data from RNA-seq experiments. Overall design: We performed RNA-seq to profile gene expression and splicing changes. The expression levels of Rbfox1 and Rbfox3 in cultured mouse hippocampal neurons were reduced by siRNAs. The reduction of Rbfox1 and 3 was rescued by expression of cytoplasmic or nuclear Rbfox1 splice isoform. The gene expression and splicing profiles were compared between different treatments. Eight samples were analyzed.		GSM1847359: siRbfox1&3_Flag-Rbfox1_C_Rep2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted by RNeasy Mini kit (Qiagen) according to manufacturer's instruction. Ribosomal RNA was removed using Ribo-Zero™ rRNA Removal Kits (Epicentre), and the cDNA libraries were prepared using TruSeq RNA Sample Preparation Kit (Illumina). RNA-Seq HiSeq2000 (Illumina) paired-end 50 nt, non-strand specific.	Illumina HiSeq 2000	age;;14 DIV|cell_type;;hippocampal neurons|sirna;;Rbfox1 and Rbfox3|source_name;;Hippocampal culture_Rbfox1 and Rbfox3 siRNAs_Flag_Rbfox1_C|treated with;;AAV2/9-SynI-Flag-Rbfox1_C_siMt and Rbfox1 and Rbfox3 siRNAs	GEO Accession;;GSM1847359		GSM1847359	siRbfox1&3_Flag-Rbfox1_C_Rep2	11283711900	112837119	2015-12-10 18:37:12	10009806274	11283711900	112837119	2	112837119	index:0,count:112837119,average:50,stdev:0|index:1,count:112837119,average:50,stdev:0	GSM1847359_r1						1.13	3.77	0.04	10541975145	10507092632	9474816237	9497761657	99.67	100.24	106585972	90030137	202.918	1425.232	136	958067	81.79	90.95	123776948	87171739	123776948	87171739	87.72	87.86	123776948	93499657	123776948	84204979	816483828	7.75	1.50	0	9.52	0	0.29	0	0.16	0	0.00	0	5.09	0	106585972	0	100	0	99.01	0	1.41	0	0.00	0	1.15	0	0.00	0	541.62	0	0.26	0	1691522	0	112837119	0	10742604	0	329096	0	182290	0	0	0	5739761	0	14227	0	0	0	123317	0	15993755	0	33226	0	16164525	0	84.94	0	95843368	0	235169	16425362	69.844928540752	112837119.0	106585972.0	1691522.0	10742604.0	329096.0	182290.0	0.0	5739761.0	95843368.0	94.5	1.5	9.5	0.3	0.2	0.0	5.1	84.9	50	50	50.00	38	5641855950	24.6	25.1	25.4	24.9	0.0	35.9	21.7	bulk
1478783	SRR2153907	SRP062242	SRS1028428	SRX1140958	SRA288475	GEO		Gene expression profiling of neurons with Rbfox1 and Rbfox3 knockdown and rescue with cytoplasmic or nuclear Rbfox1 isoform [RNA-seq]	Human genetic studies have identified the neuronal RNA binding protein, Rbfox1, as a candidate gene for autism spectrum disorders. While Rbfox1 functions as a splicing regulator in the nucleus, it is also alternatively spliced to produce cytoplasmic isoforms. To investigate cytoplasmic Rbfox1, we knocked down Rbfox proteins in mouse neurons and rescued with cytoplasmic or nuclear Rbfox1. Transcriptome profiling showed that nuclear Rbfox1 rescued splicing changes induced by knockdown, whereas cytoplasmic Rbfox1 rescued changes in mRNA levels. iCLIP-seq of subcellular fractions revealed that in nascent RNA Rbfox1 bound predominantly to introns, while cytoplasmic Rbox1 bound to 3'' UTRs. Cytoplasmic Rbfox1 binding increased target mRNA stability and translation, and overlapped significantly with miRNA binding sites. Cytoplasmic Rbfox1 target mRNAs were enriched in genes involved in cortical development and autism. Our results uncover a new Rbfox1 regulatory network and highlight the importance of cytoplasmic RNA metabolism to cortical development and disease. In this data set, we included the data from RNA-seq experiments. Overall design: We performed RNA-seq to profile gene expression and splicing changes. The expression levels of Rbfox1 and Rbfox3 in cultured mouse hippocampal neurons were reduced by siRNAs. The reduction of Rbfox1 and 3 was rescued by expression of cytoplasmic or nuclear Rbfox1 splice isoform. The gene expression and splicing profiles were compared between different treatments. Eight samples were analyzed.		GSM1847360: siRbfox1&3_Flag-Rbfox1_N_Rep1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted by RNeasy Mini kit (Qiagen) according to manufacturer's instruction. Ribosomal RNA was removed using Ribo-Zero™ rRNA Removal Kits (Epicentre), and the cDNA libraries were prepared using TruSeq RNA Sample Preparation Kit (Illumina). RNA-Seq HiSeq2000 (Illumina) paired-end 50 nt, non-strand specific.	Illumina HiSeq 2000	age;;14 DIV|cell_type;;hippocampal neurons|sirna;;Rbfox1 and Rbfox3|source_name;;Hippocampal culture_Rbfox1 and Rbfox3 siRNAs_Flag_Rbfox1_N|treated with;;AAV2/9-SynI-Flag-Rbfox1_N_siMt and Rbfox1 and Rbfox3 siRNAs	GEO Accession;;GSM1847360		GSM1847360	siRbfox1&3_Flag-Rbfox1_N_Rep1	11409464700	114094647	2015-12-10 18:37:12	10135210147	11409464700	114094647	2	114094647	index:0,count:114094647,average:50,stdev:0|index:1,count:114094647,average:50,stdev:0	GSM1847360_r1						1.08	3.45	0.03	10204534749	10203292169	9113530455	9208454653	99.99	101.04	103269352	88073736	200.889	1356.112	136	941570	80.94	90.58	121117995	83586879	121117995	83586879	84.54	85.36	121117995	87306044	121117995	78764583	727240064	7.13	2.62	0	9.63	0	0.27	0	0.12	0	0.00	0	9.10	0	103269352	0	100	0	98.90	0	2.84	0	0.01	0	1.25	0	0.01	0	517.31	0	0.31	0	2986019	0	114094647	0	10991674	0	305968	0	142030	0	0	0	10377297	0	13550	0	0	0	112801	0	14726777	0	32257	0	14885385	0	80.88	0	92277678	0	230699	15130027	65.583409550973	114094647.0	103269352.0	2986019.0	10991674.0	305968.0	142030.0	0.0	10377297.0	92277678.0	90.5	2.6	9.6	0.3	0.1	0.0	9.1	80.9	50	50	50.00	38	5704732350	24.0	25.7	26.1	24.2	0.0	35.7	21.2	bulk
1478799	SRR2153908	SRP062242	SRS1028427	SRX1140959	SRA288475	GEO		Gene expression profiling of neurons with Rbfox1 and Rbfox3 knockdown and rescue with cytoplasmic or nuclear Rbfox1 isoform [RNA-seq]	Human genetic studies have identified the neuronal RNA binding protein, Rbfox1, as a candidate gene for autism spectrum disorders. While Rbfox1 functions as a splicing regulator in the nucleus, it is also alternatively spliced to produce cytoplasmic isoforms. To investigate cytoplasmic Rbfox1, we knocked down Rbfox proteins in mouse neurons and rescued with cytoplasmic or nuclear Rbfox1. Transcriptome profiling showed that nuclear Rbfox1 rescued splicing changes induced by knockdown, whereas cytoplasmic Rbfox1 rescued changes in mRNA levels. iCLIP-seq of subcellular fractions revealed that in nascent RNA Rbfox1 bound predominantly to introns, while cytoplasmic Rbox1 bound to 3'' UTRs. Cytoplasmic Rbfox1 binding increased target mRNA stability and translation, and overlapped significantly with miRNA binding sites. Cytoplasmic Rbfox1 target mRNAs were enriched in genes involved in cortical development and autism. Our results uncover a new Rbfox1 regulatory network and highlight the importance of cytoplasmic RNA metabolism to cortical development and disease. In this data set, we included the data from RNA-seq experiments. Overall design: We performed RNA-seq to profile gene expression and splicing changes. The expression levels of Rbfox1 and Rbfox3 in cultured mouse hippocampal neurons were reduced by siRNAs. The reduction of Rbfox1 and 3 was rescued by expression of cytoplasmic or nuclear Rbfox1 splice isoform. The gene expression and splicing profiles were compared between different treatments. Eight samples were analyzed.		GSM1847361: siRbfox1&3_Flag-Rbfox1_N_Rep2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted by RNeasy Mini kit (Qiagen) according to manufacturer's instruction. Ribosomal RNA was removed using Ribo-Zero™ rRNA Removal Kits (Epicentre), and the cDNA libraries were prepared using TruSeq RNA Sample Preparation Kit (Illumina). RNA-Seq HiSeq2000 (Illumina) paired-end 50 nt, non-strand specific.	Illumina HiSeq 2000	age;;14 DIV|cell_type;;hippocampal neurons|sirna;;Rbfox1 and Rbfox3|source_name;;Hippocampal culture_Rbfox1 and Rbfox3 siRNAs_Flag_Rbfox1_N|treated with;;AAV2/9-SynI-Flag-Rbfox1_N_siMt and Rbfox1 and Rbfox3 siRNAs	GEO Accession;;GSM1847361		GSM1847361	siRbfox1&3_Flag-Rbfox1_N_Rep2	10854008400	108540084	2015-12-10 18:37:12	9616248337	10854008400	108540084	2	108540084	index:0,count:108540084,average:50,stdev:0|index:1,count:108540084,average:50,stdev:0	GSM1847361_r1						1.37	3.66	0.03	10142445358	10107805684	9097620446	9119449830	99.66	100.24	102489273	86533801	202.096	1433.442	136	923300	81.97	91.33	119251857	84009551	119251857	84009551	87.94	88.1	119251857	90127062	119251857	81034545	739323709	7.29	1.46	0	9.68	0	0.28	0	0.15	0	0.00	0	5.15	0	102489273	0	100	0	99.06	0	1.56	0	0.00	0	1.18	0	0.00	0	516.17	0	0.25	0	1580107	0	108540084	0	10507544	0	302438	0	157998	0	0	0	5590375	0	14046	0	0	0	119122	0	15430258	0	28962	0	15592388	0	84.74	0	91981729	0	230962	15849753	68.624938301539	108540084.0	102489273.0	1580107.0	10507544.0	302438.0	157998.0	0.0	5590375.0	91981729.0	94.4	1.5	9.7	0.3	0.1	0.0	5.2	84.7	50	50	50.00	38	5427004200	24.6	25.1	25.5	24.9	0.0	35.9	21.8	bulk
1904728	SRR2443105	SRP063829	SRS1073638	SRX1258024	SRA299328	GEO		RNA sequencing of primary thymic, bone and skin mesenchymal cells	Purpose : Elucidate post-natal role of SCA1+ thymic mesenchymal cells (tMCs) and evaluate the functional overlap between thymic, bone and skin MCs. Method : By high speed cell sorting, we isolated primary MCs (Lin- SCA1+ cells) from mouse thymus, bone and skin. We extracted their respective total RNA and compared their transcriptome by high-throughput RNA-sequencing. Results : We found a total of 2036 differentially expressed genes (FC>5, p-adj<0.1 and RPKM>1) between the 3 MC populations. IPA analyses revealed that each MC population was enriched for genes associated to phagocyte chemotaxis. We also denoted 2850 genes with shared expression across MC populations. IPA analysis of those shared genes also revealed an enrichment for genes influencing phagocyte migration, chemotaxis and function. Finally, MC transcriptomes showed that all 3 MC populations were expressing genes associated with hematopoietic stem and progenitor cell (HSPC) support, strongly suggesting that MCs from thymic, bone and skin all possess the ability to support HSPCs. Conclusion : Overall, our study highlighted 3 potential novel roles for tMCs : 1) Promoting macrophage/monocyte chemotaxis, 2) Enhacing the apoptotic cell clearance process and 3) setting an inviting niche for hematopoietic progenitors. These novel biological roles for tMCs could have substantial effets on thymic biology. Finally, our RNA-seq data offer a valuable resource to the community that can be mined to explore multiple questions related mesenchymal cell biology. Overall design: Transcriptome comparison between MC populations		GSM1888151: Bone_SCA1p_1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			(thymus MCs): Thymi were extracted, mechanically disrupted and enzymatically digested at 37oC for 3x15 minutes using 0.01% (w/v) Liberase TM (Roche) and 0.1% (w/v) DNase I (Sigma-Aldrich). Final digests were harvested, pooled and maintained at 4oC in FACS buffer (PBS, 0.1% (w/v) BSA, 0.02% (w/v) NaN3). Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). (Bone MCs) Femurs, tibias and pelvis were collected, cleaned and washed 3 times in cold PBS. Using sharp surgical scissors, each bone was first cut longitudinally and then transversely to generate tiny fragments of ~1 mm2.  Bone fragments were then washed 3 times in cold PBS and incubated with agitation (80 RPM) for 3x20 minutes at 37oC in the same enzymatic cocktail as above. Following each incubation, supernatants were added to HBSS medium (Invitrogen) supplemented with 2% (v/v) FBS, 10mM HEPES and 1% (v/v) penicillin-streptomycin. To further retrieve endosteal stromal cells, remaining bone fragments were gently crushed in supplemented HBSS medium using a pestle and mortar (5 x 50 gentle taps) and supernatants were pooled to previous ones. Red blood cell lysis was then performed on the resulting cell suspension prior to its filtration and resuspension in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). (Skin MCs) Mouse trunk and dorsal skin (~12 cm2 / mouse) was aseptically dissected and incubated for 45 minutes in 0.01% (w/v) liberase. Dermis was then mechanically isolated and incubated with agitation (80 RPM) at 37oC for 2x30 minutes in the same enzymatic cocktail as above. Post-incubation, supernatants were filtered and pooled to 25 mL of PBS supplemented with 1% FBS and 5mM EDTA. Final cell suspension was then centrifuged and resuspended in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). Transcriptome librairies were generated from total RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina) following the manufacturer’s protocol. Enrichment of RNA-seq stranded libraries with adapter molecules on both ends was done using 15 cycles of PCR amplification using the Illumina PCR mix and primers cocktail. Paired-end (2 x 100 bp) sequencing was peformed using the Illumina HiSeq 2000 running TruSeq v3 chemistry. Three RNA-seq librairies were sequenced per lane (8 lanes per flow cell).	Illumina HiSeq 2000	age;;3 to 4 wks-old|cell type;;Mesenchymal cells (Lin- SCA1+ cells)|source_name;;Bone|strain;;C57BL/6|tissue;;Femur, tibia and pelvis	GEO Accession;;GSM1888151		GSM1888151	Bone_SCA1p_1	5185978200	25929891	2016-02-26 22:54:03	3578698938	5185978200	25929891	2	25929891	index:0,count:25929891,average:100,stdev:0|index:1,count:25929891,average:100,stdev:0	GSM1888151_r1				in_mesa	27183606	3.4	2.7	0.07	2879160524	2877405951	2711915155	2723300878	99.94	100.42	21506802	19780387	169.497	656.262	107	179843	86.68	92.25	23704051	18642912	23704051	18642912	88.85	89.17	23704051	19108533	23704051	18020000	208456700	7.24	1.12	0	5.01	0	0.28	0	0.08	0	0.00	0	16.70	0	21506802	0	200	0	190.51	0	1.50	0	0.01	0	1.22	0	0.00	0	243.09	0	0.22	0	289377	0	25929891	0	1298613	0	71808	0	21289	0	0	0	4329992	0	4142	0	0	0	52005	0	10141380	0	13187	0	10210714	0	77.93	0	20208189	0	101381	7952771	78.444392933587	25929891.0	21506802.0	289377.0	1298613.0	71808.0	21289.0	0.0	4329992.0	20208189.0	82.9	1.1	5.0	0.3	0.1	0.0	16.7	77.9	100	100	100.00	38	2592989100	21.5	21.4	22.7	24.1	10.3	35.0	18.2	bulk
1904744	SRR2443106	SRP063829	SRS1073638	SRX1258024	SRA299328	GEO		RNA sequencing of primary thymic, bone and skin mesenchymal cells	Purpose : Elucidate post-natal role of SCA1+ thymic mesenchymal cells (tMCs) and evaluate the functional overlap between thymic, bone and skin MCs. Method : By high speed cell sorting, we isolated primary MCs (Lin- SCA1+ cells) from mouse thymus, bone and skin. We extracted their respective total RNA and compared their transcriptome by high-throughput RNA-sequencing. Results : We found a total of 2036 differentially expressed genes (FC>5, p-adj<0.1 and RPKM>1) between the 3 MC populations. IPA analyses revealed that each MC population was enriched for genes associated to phagocyte chemotaxis. We also denoted 2850 genes with shared expression across MC populations. IPA analysis of those shared genes also revealed an enrichment for genes influencing phagocyte migration, chemotaxis and function. Finally, MC transcriptomes showed that all 3 MC populations were expressing genes associated with hematopoietic stem and progenitor cell (HSPC) support, strongly suggesting that MCs from thymic, bone and skin all possess the ability to support HSPCs. Conclusion : Overall, our study highlighted 3 potential novel roles for tMCs : 1) Promoting macrophage/monocyte chemotaxis, 2) Enhacing the apoptotic cell clearance process and 3) setting an inviting niche for hematopoietic progenitors. These novel biological roles for tMCs could have substantial effets on thymic biology. Finally, our RNA-seq data offer a valuable resource to the community that can be mined to explore multiple questions related mesenchymal cell biology. Overall design: Transcriptome comparison between MC populations		GSM1888151: Bone_SCA1p_1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			(thymus MCs): Thymi were extracted, mechanically disrupted and enzymatically digested at 37oC for 3x15 minutes using 0.01% (w/v) Liberase TM (Roche) and 0.1% (w/v) DNase I (Sigma-Aldrich). Final digests were harvested, pooled and maintained at 4oC in FACS buffer (PBS, 0.1% (w/v) BSA, 0.02% (w/v) NaN3). Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). (Bone MCs) Femurs, tibias and pelvis were collected, cleaned and washed 3 times in cold PBS. Using sharp surgical scissors, each bone was first cut longitudinally and then transversely to generate tiny fragments of ~1 mm2.  Bone fragments were then washed 3 times in cold PBS and incubated with agitation (80 RPM) for 3x20 minutes at 37oC in the same enzymatic cocktail as above. Following each incubation, supernatants were added to HBSS medium (Invitrogen) supplemented with 2% (v/v) FBS, 10mM HEPES and 1% (v/v) penicillin-streptomycin. To further retrieve endosteal stromal cells, remaining bone fragments were gently crushed in supplemented HBSS medium using a pestle and mortar (5 x 50 gentle taps) and supernatants were pooled to previous ones. Red blood cell lysis was then performed on the resulting cell suspension prior to its filtration and resuspension in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). (Skin MCs) Mouse trunk and dorsal skin (~12 cm2 / mouse) was aseptically dissected and incubated for 45 minutes in 0.01% (w/v) liberase. Dermis was then mechanically isolated and incubated with agitation (80 RPM) at 37oC for 2x30 minutes in the same enzymatic cocktail as above. Post-incubation, supernatants were filtered and pooled to 25 mL of PBS supplemented with 1% FBS and 5mM EDTA. Final cell suspension was then centrifuged and resuspended in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). Transcriptome librairies were generated from total RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina) following the manufacturer’s protocol. Enrichment of RNA-seq stranded libraries with adapter molecules on both ends was done using 15 cycles of PCR amplification using the Illumina PCR mix and primers cocktail. Paired-end (2 x 100 bp) sequencing was peformed using the Illumina HiSeq 2000 running TruSeq v3 chemistry. Three RNA-seq librairies were sequenced per lane (8 lanes per flow cell).	Illumina HiSeq 2000	age;;3 to 4 wks-old|cell type;;Mesenchymal cells (Lin- SCA1+ cells)|source_name;;Bone|strain;;C57BL/6|tissue;;Femur, tibia and pelvis	GEO Accession;;GSM1888151		GSM1888151	Bone_SCA1p_1	5227755800	26138779	2016-02-26 22:54:03	3602834427	5227755800	26138779	2	26138779	index:0,count:26138779,average:100,stdev:0|index:1,count:26138779,average:100,stdev:0	GSM1888151_r2				in_mesa	27183606	3.4	2.71	0.07	2892876536	2891353917	2724767193	2736377690	99.95	100.43	21632761	19896018	169.403	655.876	107	181062	86.68	92.26	23846915	18751928	23846915	18751928	88.85	89.17	23846915	19219837	23846915	18125244	209431943	7.24	1.12	0	5.00	0	0.28	0	0.08	0	0.00	0	16.88	0	21632761	0	200	0	190.50	0	1.49	0	0.01	0	1.22	0	0.00	0	321.16	0	0.21	0	293025	0	26138779	0	1306619	0	72539	0	22002	0	0	0	4411477	0	4290	0	0	0	52783	0	10217475	0	13208	0	10287756	0	77.76	0	20326142	0	101195	8001448	79.069598300311	26138779.0	21632761.0	293025.0	1306619.0	72539.0	22002.0	0.0	4411477.0	20326142.0	82.8	1.1	5.0	0.3	0.1	0.0	16.9	77.8	100	100	100.00	38	2613877900	21.5	21.3	22.7	24.0	10.4	35.0	18.3	bulk
1904921	SRR2443111	SRP063829	SRS1073635	SRX1258026	SRA299328	GEO		RNA sequencing of primary thymic, bone and skin mesenchymal cells	Purpose : Elucidate post-natal role of SCA1+ thymic mesenchymal cells (tMCs) and evaluate the functional overlap between thymic, bone and skin MCs. Method : By high speed cell sorting, we isolated primary MCs (Lin- SCA1+ cells) from mouse thymus, bone and skin. We extracted their respective total RNA and compared their transcriptome by high-throughput RNA-sequencing. Results : We found a total of 2036 differentially expressed genes (FC>5, p-adj<0.1 and RPKM>1) between the 3 MC populations. IPA analyses revealed that each MC population was enriched for genes associated to phagocyte chemotaxis. We also denoted 2850 genes with shared expression across MC populations. IPA analysis of those shared genes also revealed an enrichment for genes influencing phagocyte migration, chemotaxis and function. Finally, MC transcriptomes showed that all 3 MC populations were expressing genes associated with hematopoietic stem and progenitor cell (HSPC) support, strongly suggesting that MCs from thymic, bone and skin all possess the ability to support HSPCs. Conclusion : Overall, our study highlighted 3 potential novel roles for tMCs : 1) Promoting macrophage/monocyte chemotaxis, 2) Enhacing the apoptotic cell clearance process and 3) setting an inviting niche for hematopoietic progenitors. These novel biological roles for tMCs could have substantial effets on thymic biology. Finally, our RNA-seq data offer a valuable resource to the community that can be mined to explore multiple questions related mesenchymal cell biology. Overall design: Transcriptome comparison between MC populations		GSM1888153: Bone_SCA1p_3; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			(thymus MCs): Thymi were extracted, mechanically disrupted and enzymatically digested at 37oC for 3x15 minutes using 0.01% (w/v) Liberase TM (Roche) and 0.1% (w/v) DNase I (Sigma-Aldrich). Final digests were harvested, pooled and maintained at 4oC in FACS buffer (PBS, 0.1% (w/v) BSA, 0.02% (w/v) NaN3). Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). (Bone MCs) Femurs, tibias and pelvis were collected, cleaned and washed 3 times in cold PBS. Using sharp surgical scissors, each bone was first cut longitudinally and then transversely to generate tiny fragments of ~1 mm2.  Bone fragments were then washed 3 times in cold PBS and incubated with agitation (80 RPM) for 3x20 minutes at 37oC in the same enzymatic cocktail as above. Following each incubation, supernatants were added to HBSS medium (Invitrogen) supplemented with 2% (v/v) FBS, 10mM HEPES and 1% (v/v) penicillin-streptomycin. To further retrieve endosteal stromal cells, remaining bone fragments were gently crushed in supplemented HBSS medium using a pestle and mortar (5 x 50 gentle taps) and supernatants were pooled to previous ones. Red blood cell lysis was then performed on the resulting cell suspension prior to its filtration and resuspension in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). (Skin MCs) Mouse trunk and dorsal skin (~12 cm2 / mouse) was aseptically dissected and incubated for 45 minutes in 0.01% (w/v) liberase. Dermis was then mechanically isolated and incubated with agitation (80 RPM) at 37oC for 2x30 minutes in the same enzymatic cocktail as above. Post-incubation, supernatants were filtered and pooled to 25 mL of PBS supplemented with 1% FBS and 5mM EDTA. Final cell suspension was then centrifuged and resuspended in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). Transcriptome librairies were generated from total RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina) following the manufacturer’s protocol. Enrichment of RNA-seq stranded libraries with adapter molecules on both ends was done using 15 cycles of PCR amplification using the Illumina PCR mix and primers cocktail. Paired-end (2 x 100 bp) sequencing was peformed using the Illumina HiSeq 2000 running TruSeq v3 chemistry. Three RNA-seq librairies were sequenced per lane (8 lanes per flow cell).	Illumina HiSeq 2000	age;;3 to 4 wks-old|cell type;;Mesenchymal cells (Lin- SCA1+ cells)|source_name;;Bone|strain;;C57BL/6|tissue;;Femur, tibia and pelvis	GEO Accession;;GSM1888153		GSM1888153	Bone_SCA1p_3	4496567200	22482836	2016-02-26 22:54:03	3076397147	4496567200	22482836	2	22482836	index:0,count:22482836,average:100,stdev:0|index:1,count:22482836,average:100,stdev:0	GSM1888153_r1				in_mesa	27183606	3.7	2.74	0.09	2552493673	2549097033	2396540952	2405522574	99.87	100.37	19024686	17459328	170.359	657.124	107	158197	86.91	92.79	21053891	16534270	21053891	16534270	89.53	89.87	21053891	17033467	21053891	16014017	172374398	6.75	1.17	0	5.36	0	0.29	0	0.08	0	0.00	0	15.01	0	19024686	0	200	0	190.99	0	1.48	0	0.01	0	1.18	0	0.00	0	304.28	0	0.20	0	262160	0	22482836	0	1205034	0	64523	0	18549	0	0	0	3375078	0	3926	0	0	0	48893	0	9210958	0	11792	0	9275569	0	79.26	0	17819652	0	143738	7196732	50.068402231838	22482836.0	19024686.0	262160.0	1205034.0	64523.0	18549.0	0.0	3375078.0	17819652.0	84.6	1.2	5.4	0.3	0.1	0.0	15.0	79.3	100	100	100.00	38	2248283600	21.8	21.5	23.2	24.4	9.1	35.3	18.8	bulk
1904936	SRR2443112	SRP063829	SRS1073635	SRX1258026	SRA299328	GEO		RNA sequencing of primary thymic, bone and skin mesenchymal cells	Purpose : Elucidate post-natal role of SCA1+ thymic mesenchymal cells (tMCs) and evaluate the functional overlap between thymic, bone and skin MCs. Method : By high speed cell sorting, we isolated primary MCs (Lin- SCA1+ cells) from mouse thymus, bone and skin. We extracted their respective total RNA and compared their transcriptome by high-throughput RNA-sequencing. Results : We found a total of 2036 differentially expressed genes (FC>5, p-adj<0.1 and RPKM>1) between the 3 MC populations. IPA analyses revealed that each MC population was enriched for genes associated to phagocyte chemotaxis. We also denoted 2850 genes with shared expression across MC populations. IPA analysis of those shared genes also revealed an enrichment for genes influencing phagocyte migration, chemotaxis and function. Finally, MC transcriptomes showed that all 3 MC populations were expressing genes associated with hematopoietic stem and progenitor cell (HSPC) support, strongly suggesting that MCs from thymic, bone and skin all possess the ability to support HSPCs. Conclusion : Overall, our study highlighted 3 potential novel roles for tMCs : 1) Promoting macrophage/monocyte chemotaxis, 2) Enhacing the apoptotic cell clearance process and 3) setting an inviting niche for hematopoietic progenitors. These novel biological roles for tMCs could have substantial effets on thymic biology. Finally, our RNA-seq data offer a valuable resource to the community that can be mined to explore multiple questions related mesenchymal cell biology. Overall design: Transcriptome comparison between MC populations		GSM1888153: Bone_SCA1p_3; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			(thymus MCs): Thymi were extracted, mechanically disrupted and enzymatically digested at 37oC for 3x15 minutes using 0.01% (w/v) Liberase TM (Roche) and 0.1% (w/v) DNase I (Sigma-Aldrich). Final digests were harvested, pooled and maintained at 4oC in FACS buffer (PBS, 0.1% (w/v) BSA, 0.02% (w/v) NaN3). Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). (Bone MCs) Femurs, tibias and pelvis were collected, cleaned and washed 3 times in cold PBS. Using sharp surgical scissors, each bone was first cut longitudinally and then transversely to generate tiny fragments of ~1 mm2.  Bone fragments were then washed 3 times in cold PBS and incubated with agitation (80 RPM) for 3x20 minutes at 37oC in the same enzymatic cocktail as above. Following each incubation, supernatants were added to HBSS medium (Invitrogen) supplemented with 2% (v/v) FBS, 10mM HEPES and 1% (v/v) penicillin-streptomycin. To further retrieve endosteal stromal cells, remaining bone fragments were gently crushed in supplemented HBSS medium using a pestle and mortar (5 x 50 gentle taps) and supernatants were pooled to previous ones. Red blood cell lysis was then performed on the resulting cell suspension prior to its filtration and resuspension in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). (Skin MCs) Mouse trunk and dorsal skin (~12 cm2 / mouse) was aseptically dissected and incubated for 45 minutes in 0.01% (w/v) liberase. Dermis was then mechanically isolated and incubated with agitation (80 RPM) at 37oC for 2x30 minutes in the same enzymatic cocktail as above. Post-incubation, supernatants were filtered and pooled to 25 mL of PBS supplemented with 1% FBS and 5mM EDTA. Final cell suspension was then centrifuged and resuspended in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). Transcriptome librairies were generated from total RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina) following the manufacturer’s protocol. Enrichment of RNA-seq stranded libraries with adapter molecules on both ends was done using 15 cycles of PCR amplification using the Illumina PCR mix and primers cocktail. Paired-end (2 x 100 bp) sequencing was peformed using the Illumina HiSeq 2000 running TruSeq v3 chemistry. Three RNA-seq librairies were sequenced per lane (8 lanes per flow cell).	Illumina HiSeq 2000	age;;3 to 4 wks-old|cell type;;Mesenchymal cells (Lin- SCA1+ cells)|source_name;;Bone|strain;;C57BL/6|tissue;;Femur, tibia and pelvis	GEO Accession;;GSM1888153		GSM1888153	Bone_SCA1p_3	4482913200	22414566	2016-02-26 22:54:03	3062984841	4482913200	22414566	2	22414566	index:0,count:22414566,average:100,stdev:0|index:1,count:22414566,average:100,stdev:0	GSM1888153_r2				in_mesa	27183606	3.71	2.75	0.09	2539415038	2535804566	2384017908	2392756956	99.86	100.37	18944330	17384827	170.221	656.947	106	157998	86.9	92.79	20969677	16463240	20969677	16463240	89.54	89.88	20969677	16963583	20969677	15946564	171257085	6.74	1.17	0	5.36	0	0.29	0	0.08	0	0.00	0	15.11	0	18944330	0	200	0	190.98	0	1.49	0	0.01	0	1.18	0	0.00	0	274.46	0	0.19	0	261819	0	22414566	0	1202045	0	64662	0	18721	0	0	0	3386853	0	3996	0	0	0	48871	0	9177930	0	11502	0	9242299	0	79.16	0	17742285	0	143776	7167368	49.850934787447	22414566.0	18944330.0	261819.0	1202045.0	64662.0	18721.0	0.0	3386853.0	17742285.0	84.5	1.2	5.4	0.3	0.1	0.0	15.1	79.2	100	100	100.00	38	2241456600	21.7	21.5	23.2	24.4	9.2	35.3	18.9	bulk
1904953	SRR2443113	SRP063829	SRS1073635	SRX1258026	SRA299328	GEO		RNA sequencing of primary thymic, bone and skin mesenchymal cells	Purpose : Elucidate post-natal role of SCA1+ thymic mesenchymal cells (tMCs) and evaluate the functional overlap between thymic, bone and skin MCs. Method : By high speed cell sorting, we isolated primary MCs (Lin- SCA1+ cells) from mouse thymus, bone and skin. We extracted their respective total RNA and compared their transcriptome by high-throughput RNA-sequencing. Results : We found a total of 2036 differentially expressed genes (FC>5, p-adj<0.1 and RPKM>1) between the 3 MC populations. IPA analyses revealed that each MC population was enriched for genes associated to phagocyte chemotaxis. We also denoted 2850 genes with shared expression across MC populations. IPA analysis of those shared genes also revealed an enrichment for genes influencing phagocyte migration, chemotaxis and function. Finally, MC transcriptomes showed that all 3 MC populations were expressing genes associated with hematopoietic stem and progenitor cell (HSPC) support, strongly suggesting that MCs from thymic, bone and skin all possess the ability to support HSPCs. Conclusion : Overall, our study highlighted 3 potential novel roles for tMCs : 1) Promoting macrophage/monocyte chemotaxis, 2) Enhacing the apoptotic cell clearance process and 3) setting an inviting niche for hematopoietic progenitors. These novel biological roles for tMCs could have substantial effets on thymic biology. Finally, our RNA-seq data offer a valuable resource to the community that can be mined to explore multiple questions related mesenchymal cell biology. Overall design: Transcriptome comparison between MC populations		GSM1888153: Bone_SCA1p_3; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			(thymus MCs): Thymi were extracted, mechanically disrupted and enzymatically digested at 37oC for 3x15 minutes using 0.01% (w/v) Liberase TM (Roche) and 0.1% (w/v) DNase I (Sigma-Aldrich). Final digests were harvested, pooled and maintained at 4oC in FACS buffer (PBS, 0.1% (w/v) BSA, 0.02% (w/v) NaN3). Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). (Bone MCs) Femurs, tibias and pelvis were collected, cleaned and washed 3 times in cold PBS. Using sharp surgical scissors, each bone was first cut longitudinally and then transversely to generate tiny fragments of ~1 mm2.  Bone fragments were then washed 3 times in cold PBS and incubated with agitation (80 RPM) for 3x20 minutes at 37oC in the same enzymatic cocktail as above. Following each incubation, supernatants were added to HBSS medium (Invitrogen) supplemented with 2% (v/v) FBS, 10mM HEPES and 1% (v/v) penicillin-streptomycin. To further retrieve endosteal stromal cells, remaining bone fragments were gently crushed in supplemented HBSS medium using a pestle and mortar (5 x 50 gentle taps) and supernatants were pooled to previous ones. Red blood cell lysis was then performed on the resulting cell suspension prior to its filtration and resuspension in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). (Skin MCs) Mouse trunk and dorsal skin (~12 cm2 / mouse) was aseptically dissected and incubated for 45 minutes in 0.01% (w/v) liberase. Dermis was then mechanically isolated and incubated with agitation (80 RPM) at 37oC for 2x30 minutes in the same enzymatic cocktail as above. Post-incubation, supernatants were filtered and pooled to 25 mL of PBS supplemented with 1% FBS and 5mM EDTA. Final cell suspension was then centrifuged and resuspended in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). Transcriptome librairies were generated from total RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina) following the manufacturer’s protocol. Enrichment of RNA-seq stranded libraries with adapter molecules on both ends was done using 15 cycles of PCR amplification using the Illumina PCR mix and primers cocktail. Paired-end (2 x 100 bp) sequencing was peformed using the Illumina HiSeq 2000 running TruSeq v3 chemistry. Three RNA-seq librairies were sequenced per lane (8 lanes per flow cell).	Illumina HiSeq 2000	age;;3 to 4 wks-old|cell type;;Mesenchymal cells (Lin- SCA1+ cells)|source_name;;Bone|strain;;C57BL/6|tissue;;Femur, tibia and pelvis	GEO Accession;;GSM1888153		GSM1888153	Bone_SCA1p_3	4471209200	22356046	2016-02-26 22:54:03	3038882713	4471209200	22356046	2	22356046	index:0,count:22356046,average:100,stdev:0|index:1,count:22356046,average:100,stdev:0	GSM1888153_r3				in_mesa	27183606	3.7	2.74	0.09	2540953812	2537506841	2385651745	2394425820	99.86	100.37	18930432	17371261	170.479	656.243	106	156570	86.91	92.79	20952698	16451564	20952698	16451564	89.54	89.87	20952698	16950865	20952698	15935256	171459143	6.75	1.16	0	5.37	0	0.29	0	0.08	0	0.00	0	14.95	0	18930432	0	200	0	191.02	0	1.49	0	0.01	0	1.19	0	0.00	0	256.31	0	0.19	0	259783	0	22356046	0	1199878	0	64226	0	18727	0	0	0	3342661	0	3913	0	0	0	48690	0	9177385	0	11703	0	9241691	0	79.31	0	17730554	0	143872	7173270	49.858693838968	22356046.0	18930432.0	259783.0	1199878.0	64226.0	18727.0	0.0	3342661.0	17730554.0	84.7	1.2	5.4	0.3	0.1	0.0	15.0	79.3	100	100	100.00	38	2235604600	21.7	21.5	23.2	24.4	9.2	35.4	19.1	bulk
1904970	SRR2443114	SRP063829	SRS1073640	SRX1258027	SRA299328	GEO		RNA sequencing of primary thymic, bone and skin mesenchymal cells	Purpose : Elucidate post-natal role of SCA1+ thymic mesenchymal cells (tMCs) and evaluate the functional overlap between thymic, bone and skin MCs. Method : By high speed cell sorting, we isolated primary MCs (Lin- SCA1+ cells) from mouse thymus, bone and skin. We extracted their respective total RNA and compared their transcriptome by high-throughput RNA-sequencing. Results : We found a total of 2036 differentially expressed genes (FC>5, p-adj<0.1 and RPKM>1) between the 3 MC populations. IPA analyses revealed that each MC population was enriched for genes associated to phagocyte chemotaxis. We also denoted 2850 genes with shared expression across MC populations. IPA analysis of those shared genes also revealed an enrichment for genes influencing phagocyte migration, chemotaxis and function. Finally, MC transcriptomes showed that all 3 MC populations were expressing genes associated with hematopoietic stem and progenitor cell (HSPC) support, strongly suggesting that MCs from thymic, bone and skin all possess the ability to support HSPCs. Conclusion : Overall, our study highlighted 3 potential novel roles for tMCs : 1) Promoting macrophage/monocyte chemotaxis, 2) Enhacing the apoptotic cell clearance process and 3) setting an inviting niche for hematopoietic progenitors. These novel biological roles for tMCs could have substantial effets on thymic biology. Finally, our RNA-seq data offer a valuable resource to the community that can be mined to explore multiple questions related mesenchymal cell biology. Overall design: Transcriptome comparison between MC populations		GSM1888154: Skin_SCA1p_1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			(thymus MCs): Thymi were extracted, mechanically disrupted and enzymatically digested at 37oC for 3x15 minutes using 0.01% (w/v) Liberase TM (Roche) and 0.1% (w/v) DNase I (Sigma-Aldrich). Final digests were harvested, pooled and maintained at 4oC in FACS buffer (PBS, 0.1% (w/v) BSA, 0.02% (w/v) NaN3). Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). (Bone MCs) Femurs, tibias and pelvis were collected, cleaned and washed 3 times in cold PBS. Using sharp surgical scissors, each bone was first cut longitudinally and then transversely to generate tiny fragments of ~1 mm2.  Bone fragments were then washed 3 times in cold PBS and incubated with agitation (80 RPM) for 3x20 minutes at 37oC in the same enzymatic cocktail as above. Following each incubation, supernatants were added to HBSS medium (Invitrogen) supplemented with 2% (v/v) FBS, 10mM HEPES and 1% (v/v) penicillin-streptomycin. To further retrieve endosteal stromal cells, remaining bone fragments were gently crushed in supplemented HBSS medium using a pestle and mortar (5 x 50 gentle taps) and supernatants were pooled to previous ones. Red blood cell lysis was then performed on the resulting cell suspension prior to its filtration and resuspension in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). (Skin MCs) Mouse trunk and dorsal skin (~12 cm2 / mouse) was aseptically dissected and incubated for 45 minutes in 0.01% (w/v) liberase. Dermis was then mechanically isolated and incubated with agitation (80 RPM) at 37oC for 2x30 minutes in the same enzymatic cocktail as above. Post-incubation, supernatants were filtered and pooled to 25 mL of PBS supplemented with 1% FBS and 5mM EDTA. Final cell suspension was then centrifuged and resuspended in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). Transcriptome librairies were generated from total RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina) following the manufacturer’s protocol. Enrichment of RNA-seq stranded libraries with adapter molecules on both ends was done using 15 cycles of PCR amplification using the Illumina PCR mix and primers cocktail. Paired-end (2 x 100 bp) sequencing was peformed using the Illumina HiSeq 2000 running TruSeq v3 chemistry. Three RNA-seq librairies were sequenced per lane (8 lanes per flow cell).	Illumina HiSeq 2000	age;;3 to 4 wks-old|cell type;;Mesenchymal cells (Lin- SCA1+ cells)|source_name;;Skin|strain;;C57BL/6|tissue;;abdominal and back dermis (truncal skin)	GEO Accession;;GSM1888154		GSM1888154	Skin_SCA1p_1	493262000	2466310	2016-02-26 22:54:03	339092247	493262000	2466310	2	2466310	index:0,count:2466310,average:100,stdev:0|index:1,count:2466310,average:100,stdev:0	GSM1888154_r1				in_mesa	27183606	2.37	2.08	0.04	318441364	319785685	304232264	306544592	100.42	100.76	2248534	2053848	186.291	622.147	118	20487	93.1	97.61	2426672	2093371	2426672	2093371	94.33	94.83	2426672	2120973	2426672	2033640	6642828	2.09	0.85	0	4.22	0	0.24	0	0.03	0	0.00	0	8.56	0	2248534	0	200	0	194.31	0	1.54	0	0.00	0	1.29	0	0.00	0	79.27	0	0.21	0	21057	0	2466310	0	103965	0	5942	0	796	0	0	0	211038	0	375	0	0	0	4856	0	1482976	0	1227	0	1489434	0	86.95	0	2144569	0	82581	1183395	14.330112253424	2466310.0	2248534.0	21057.0	103965.0	5942.0	796.0	0.0	211038.0	2144569.0	91.2	0.9	4.2	0.2	0.0	0.0	8.6	87.0	100	100	100.00	38	246631000	21.3	23.6	25.0	24.0	6.2	34.9	18.0	bulk
1904985	SRR2443115	SRP063829	SRS1073640	SRX1258027	SRA299328	GEO		RNA sequencing of primary thymic, bone and skin mesenchymal cells	Purpose : Elucidate post-natal role of SCA1+ thymic mesenchymal cells (tMCs) and evaluate the functional overlap between thymic, bone and skin MCs. Method : By high speed cell sorting, we isolated primary MCs (Lin- SCA1+ cells) from mouse thymus, bone and skin. We extracted their respective total RNA and compared their transcriptome by high-throughput RNA-sequencing. Results : We found a total of 2036 differentially expressed genes (FC>5, p-adj<0.1 and RPKM>1) between the 3 MC populations. IPA analyses revealed that each MC population was enriched for genes associated to phagocyte chemotaxis. We also denoted 2850 genes with shared expression across MC populations. IPA analysis of those shared genes also revealed an enrichment for genes influencing phagocyte migration, chemotaxis and function. Finally, MC transcriptomes showed that all 3 MC populations were expressing genes associated with hematopoietic stem and progenitor cell (HSPC) support, strongly suggesting that MCs from thymic, bone and skin all possess the ability to support HSPCs. Conclusion : Overall, our study highlighted 3 potential novel roles for tMCs : 1) Promoting macrophage/monocyte chemotaxis, 2) Enhacing the apoptotic cell clearance process and 3) setting an inviting niche for hematopoietic progenitors. These novel biological roles for tMCs could have substantial effets on thymic biology. Finally, our RNA-seq data offer a valuable resource to the community that can be mined to explore multiple questions related mesenchymal cell biology. Overall design: Transcriptome comparison between MC populations		GSM1888154: Skin_SCA1p_1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			(thymus MCs): Thymi were extracted, mechanically disrupted and enzymatically digested at 37oC for 3x15 minutes using 0.01% (w/v) Liberase TM (Roche) and 0.1% (w/v) DNase I (Sigma-Aldrich). Final digests were harvested, pooled and maintained at 4oC in FACS buffer (PBS, 0.1% (w/v) BSA, 0.02% (w/v) NaN3). Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). (Bone MCs) Femurs, tibias and pelvis were collected, cleaned and washed 3 times in cold PBS. Using sharp surgical scissors, each bone was first cut longitudinally and then transversely to generate tiny fragments of ~1 mm2.  Bone fragments were then washed 3 times in cold PBS and incubated with agitation (80 RPM) for 3x20 minutes at 37oC in the same enzymatic cocktail as above. Following each incubation, supernatants were added to HBSS medium (Invitrogen) supplemented with 2% (v/v) FBS, 10mM HEPES and 1% (v/v) penicillin-streptomycin. To further retrieve endosteal stromal cells, remaining bone fragments were gently crushed in supplemented HBSS medium using a pestle and mortar (5 x 50 gentle taps) and supernatants were pooled to previous ones. Red blood cell lysis was then performed on the resulting cell suspension prior to its filtration and resuspension in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). (Skin MCs) Mouse trunk and dorsal skin (~12 cm2 / mouse) was aseptically dissected and incubated for 45 minutes in 0.01% (w/v) liberase. Dermis was then mechanically isolated and incubated with agitation (80 RPM) at 37oC for 2x30 minutes in the same enzymatic cocktail as above. Post-incubation, supernatants were filtered and pooled to 25 mL of PBS supplemented with 1% FBS and 5mM EDTA. Final cell suspension was then centrifuged and resuspended in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). Transcriptome librairies were generated from total RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina) following the manufacturer’s protocol. Enrichment of RNA-seq stranded libraries with adapter molecules on both ends was done using 15 cycles of PCR amplification using the Illumina PCR mix and primers cocktail. Paired-end (2 x 100 bp) sequencing was peformed using the Illumina HiSeq 2000 running TruSeq v3 chemistry. Three RNA-seq librairies were sequenced per lane (8 lanes per flow cell).	Illumina HiSeq 2000	age;;3 to 4 wks-old|cell type;;Mesenchymal cells (Lin- SCA1+ cells)|source_name;;Skin|strain;;C57BL/6|tissue;;abdominal and back dermis (truncal skin)	GEO Accession;;GSM1888154		GSM1888154	Skin_SCA1p_1	491868200	2459341	2016-02-26 22:54:03	337672120	491868200	2459341	2	2459341	index:0,count:2459341,average:100,stdev:0|index:1,count:2459341,average:100,stdev:0	GSM1888154_r2				in_mesa	27183606	2.4	2.06	0.04	316994642	318330484	302777486	305070066	100.42	100.76	2240136	2046260	186.048	616.513	118	20353	93.07	97.6	2419110	2084968	2419110	2084968	94.3	94.79	2419110	2112472	2419110	2025042	6593776	2.08	0.86	0	4.22	0	0.24	0	0.03	0	0.00	0	8.64	0	2240136	0	200	0	194.32	0	1.51	0	0.00	0	1.27	0	0.00	0	196.75	0	0.20	0	21190	0	2459341	0	103895	0	5974	0	784	0	0	0	212447	0	386	0	0	0	4825	0	1477546	0	1150	0	1483907	0	86.86	0	2136241	0	82464	1178308	14.288756305782	2459341.0	2240136.0	21190.0	103895.0	5974.0	784.0	0.0	212447.0	2136241.0	91.1	0.9	4.2	0.2	0.0	0.0	8.6	86.9	100	100	100.00	38	245934100	21.3	23.5	24.9	24.0	6.3	34.9	18.1	bulk
1905002	SRR2443116	SRP063829	SRS1073640	SRX1258027	SRA299328	GEO		RNA sequencing of primary thymic, bone and skin mesenchymal cells	Purpose : Elucidate post-natal role of SCA1+ thymic mesenchymal cells (tMCs) and evaluate the functional overlap between thymic, bone and skin MCs. Method : By high speed cell sorting, we isolated primary MCs (Lin- SCA1+ cells) from mouse thymus, bone and skin. We extracted their respective total RNA and compared their transcriptome by high-throughput RNA-sequencing. Results : We found a total of 2036 differentially expressed genes (FC>5, p-adj<0.1 and RPKM>1) between the 3 MC populations. IPA analyses revealed that each MC population was enriched for genes associated to phagocyte chemotaxis. We also denoted 2850 genes with shared expression across MC populations. IPA analysis of those shared genes also revealed an enrichment for genes influencing phagocyte migration, chemotaxis and function. Finally, MC transcriptomes showed that all 3 MC populations were expressing genes associated with hematopoietic stem and progenitor cell (HSPC) support, strongly suggesting that MCs from thymic, bone and skin all possess the ability to support HSPCs. Conclusion : Overall, our study highlighted 3 potential novel roles for tMCs : 1) Promoting macrophage/monocyte chemotaxis, 2) Enhacing the apoptotic cell clearance process and 3) setting an inviting niche for hematopoietic progenitors. These novel biological roles for tMCs could have substantial effets on thymic biology. Finally, our RNA-seq data offer a valuable resource to the community that can be mined to explore multiple questions related mesenchymal cell biology. Overall design: Transcriptome comparison between MC populations		GSM1888154: Skin_SCA1p_1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			(thymus MCs): Thymi were extracted, mechanically disrupted and enzymatically digested at 37oC for 3x15 minutes using 0.01% (w/v) Liberase TM (Roche) and 0.1% (w/v) DNase I (Sigma-Aldrich). Final digests were harvested, pooled and maintained at 4oC in FACS buffer (PBS, 0.1% (w/v) BSA, 0.02% (w/v) NaN3). Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). (Bone MCs) Femurs, tibias and pelvis were collected, cleaned and washed 3 times in cold PBS. Using sharp surgical scissors, each bone was first cut longitudinally and then transversely to generate tiny fragments of ~1 mm2.  Bone fragments were then washed 3 times in cold PBS and incubated with agitation (80 RPM) for 3x20 minutes at 37oC in the same enzymatic cocktail as above. Following each incubation, supernatants were added to HBSS medium (Invitrogen) supplemented with 2% (v/v) FBS, 10mM HEPES and 1% (v/v) penicillin-streptomycin. To further retrieve endosteal stromal cells, remaining bone fragments were gently crushed in supplemented HBSS medium using a pestle and mortar (5 x 50 gentle taps) and supernatants were pooled to previous ones. Red blood cell lysis was then performed on the resulting cell suspension prior to its filtration and resuspension in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). (Skin MCs) Mouse trunk and dorsal skin (~12 cm2 / mouse) was aseptically dissected and incubated for 45 minutes in 0.01% (w/v) liberase. Dermis was then mechanically isolated and incubated with agitation (80 RPM) at 37oC for 2x30 minutes in the same enzymatic cocktail as above. Post-incubation, supernatants were filtered and pooled to 25 mL of PBS supplemented with 1% FBS and 5mM EDTA. Final cell suspension was then centrifuged and resuspended in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). Transcriptome librairies were generated from total RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina) following the manufacturer’s protocol. Enrichment of RNA-seq stranded libraries with adapter molecules on both ends was done using 15 cycles of PCR amplification using the Illumina PCR mix and primers cocktail. Paired-end (2 x 100 bp) sequencing was peformed using the Illumina HiSeq 2000 running TruSeq v3 chemistry. Three RNA-seq librairies were sequenced per lane (8 lanes per flow cell).	Illumina HiSeq 2000	age;;3 to 4 wks-old|cell type;;Mesenchymal cells (Lin- SCA1+ cells)|source_name;;Skin|strain;;C57BL/6|tissue;;abdominal and back dermis (truncal skin)	GEO Accession;;GSM1888154		GSM1888154	Skin_SCA1p_1	496703400	2483517	2016-02-26 22:54:03	339382936	496703400	2483517	2	2483517	index:0,count:2483517,average:100,stdev:0|index:1,count:2483517,average:100,stdev:0	GSM1888154_r3				in_mesa	27183606	2.38	2.07	0.04	320431477	321819268	306059723	308414379	100.43	100.77	2263962	2066808	186.089	628.195	118	20212	93.08	97.61	2444129	2107290	2444129	2107290	94.3	94.8	2444129	2134902	2444129	2046482	6635802	2.07	0.85	0	4.23	0	0.24	0	0.03	0	0.00	0	8.57	0	2263962	0	200	0	194.33	0	1.54	0	0.00	0	1.28	0	0.00	0	80.55	0	0.20	0	21197	0	2483517	0	105166	0	5963	0	803	0	0	0	212789	0	428	0	0	0	4703	0	1494619	0	1119	0	1500869	0	86.92	0	2158796	0	82928	1191844	14.372033571291	2483517.0	2263962.0	21197.0	105166.0	5963.0	803.0	0.0	212789.0	2158796.0	91.2	0.9	4.2	0.2	0.0	0.0	8.6	86.9	100	100	100.00	38	248351700	21.2	23.5	24.9	24.0	6.3	35.0	18.3	bulk
1905018	SRR2443117	SRP063829	SRS1073640	SRX1258027	SRA299328	GEO		RNA sequencing of primary thymic, bone and skin mesenchymal cells	Purpose : Elucidate post-natal role of SCA1+ thymic mesenchymal cells (tMCs) and evaluate the functional overlap between thymic, bone and skin MCs. Method : By high speed cell sorting, we isolated primary MCs (Lin- SCA1+ cells) from mouse thymus, bone and skin. We extracted their respective total RNA and compared their transcriptome by high-throughput RNA-sequencing. Results : We found a total of 2036 differentially expressed genes (FC>5, p-adj<0.1 and RPKM>1) between the 3 MC populations. IPA analyses revealed that each MC population was enriched for genes associated to phagocyte chemotaxis. We also denoted 2850 genes with shared expression across MC populations. IPA analysis of those shared genes also revealed an enrichment for genes influencing phagocyte migration, chemotaxis and function. Finally, MC transcriptomes showed that all 3 MC populations were expressing genes associated with hematopoietic stem and progenitor cell (HSPC) support, strongly suggesting that MCs from thymic, bone and skin all possess the ability to support HSPCs. Conclusion : Overall, our study highlighted 3 potential novel roles for tMCs : 1) Promoting macrophage/monocyte chemotaxis, 2) Enhacing the apoptotic cell clearance process and 3) setting an inviting niche for hematopoietic progenitors. These novel biological roles for tMCs could have substantial effets on thymic biology. Finally, our RNA-seq data offer a valuable resource to the community that can be mined to explore multiple questions related mesenchymal cell biology. Overall design: Transcriptome comparison between MC populations		GSM1888154: Skin_SCA1p_1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			(thymus MCs): Thymi were extracted, mechanically disrupted and enzymatically digested at 37oC for 3x15 minutes using 0.01% (w/v) Liberase TM (Roche) and 0.1% (w/v) DNase I (Sigma-Aldrich). Final digests were harvested, pooled and maintained at 4oC in FACS buffer (PBS, 0.1% (w/v) BSA, 0.02% (w/v) NaN3). Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). (Bone MCs) Femurs, tibias and pelvis were collected, cleaned and washed 3 times in cold PBS. Using sharp surgical scissors, each bone was first cut longitudinally and then transversely to generate tiny fragments of ~1 mm2.  Bone fragments were then washed 3 times in cold PBS and incubated with agitation (80 RPM) for 3x20 minutes at 37oC in the same enzymatic cocktail as above. Following each incubation, supernatants were added to HBSS medium (Invitrogen) supplemented with 2% (v/v) FBS, 10mM HEPES and 1% (v/v) penicillin-streptomycin. To further retrieve endosteal stromal cells, remaining bone fragments were gently crushed in supplemented HBSS medium using a pestle and mortar (5 x 50 gentle taps) and supernatants were pooled to previous ones. Red blood cell lysis was then performed on the resulting cell suspension prior to its filtration and resuspension in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). (Skin MCs) Mouse trunk and dorsal skin (~12 cm2 / mouse) was aseptically dissected and incubated for 45 minutes in 0.01% (w/v) liberase. Dermis was then mechanically isolated and incubated with agitation (80 RPM) at 37oC for 2x30 minutes in the same enzymatic cocktail as above. Post-incubation, supernatants were filtered and pooled to 25 mL of PBS supplemented with 1% FBS and 5mM EDTA. Final cell suspension was then centrifuged and resuspended in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). Transcriptome librairies were generated from total RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina) following the manufacturer’s protocol. Enrichment of RNA-seq stranded libraries with adapter molecules on both ends was done using 15 cycles of PCR amplification using the Illumina PCR mix and primers cocktail. Paired-end (2 x 100 bp) sequencing was peformed using the Illumina HiSeq 2000 running TruSeq v3 chemistry. Three RNA-seq librairies were sequenced per lane (8 lanes per flow cell).	Illumina HiSeq 2000	age;;3 to 4 wks-old|cell type;;Mesenchymal cells (Lin- SCA1+ cells)|source_name;;Skin|strain;;C57BL/6|tissue;;abdominal and back dermis (truncal skin)	GEO Accession;;GSM1888154		GSM1888154	Skin_SCA1p_1	5894803200	29474016	2016-02-26 22:54:03	3796651644	5894803200	29474016	2	29474016	index:0,count:29474016,average:100,stdev:0|index:1,count:29474016,average:100,stdev:0	GSM1888154_r4				in_mesa	27183606	2.32	2.04	0.04	3793262113	3810085014	3626290422	3654224827	100.44	100.77	26712630	24340525	187.637	634.475	118	234940	93.22	97.68	28812792	24902160	28812792	24902160	94.4	94.89	28812792	25216236	28812792	24191442	76311996	2.01	0.87	0	4.14	0	0.24	0	0.08	0	0.00	0	9.05	0	26712630	0	200	0	194.34	0	1.55	0	0.00	0	1.28	0	0.00	0	237.37	0	0.14	0	255271	0	29474016	0	1219268	0	69624	0	24955	0	0	0	2666807	0	4920	0	0	0	57254	0	17906288	0	14302	0	17982764	0	86.49	0	25493362	0	137463	14301199	104.036715334308	29474016.0	26712630.0	255271.0	1219268.0	69624.0	24955.0	0.0	2666807.0	25493362.0	90.6	0.9	4.1	0.2	0.1	0.0	9.0	86.5	100	100	100.00	38	2947401600	21.0	23.4	24.8	23.8	7.0	35.8	19.1	bulk
1905036	SRR2443118	SRP063829	SRS1073640	SRX1258027	SRA299328	GEO		RNA sequencing of primary thymic, bone and skin mesenchymal cells	Purpose : Elucidate post-natal role of SCA1+ thymic mesenchymal cells (tMCs) and evaluate the functional overlap between thymic, bone and skin MCs. Method : By high speed cell sorting, we isolated primary MCs (Lin- SCA1+ cells) from mouse thymus, bone and skin. We extracted their respective total RNA and compared their transcriptome by high-throughput RNA-sequencing. Results : We found a total of 2036 differentially expressed genes (FC>5, p-adj<0.1 and RPKM>1) between the 3 MC populations. IPA analyses revealed that each MC population was enriched for genes associated to phagocyte chemotaxis. We also denoted 2850 genes with shared expression across MC populations. IPA analysis of those shared genes also revealed an enrichment for genes influencing phagocyte migration, chemotaxis and function. Finally, MC transcriptomes showed that all 3 MC populations were expressing genes associated with hematopoietic stem and progenitor cell (HSPC) support, strongly suggesting that MCs from thymic, bone and skin all possess the ability to support HSPCs. Conclusion : Overall, our study highlighted 3 potential novel roles for tMCs : 1) Promoting macrophage/monocyte chemotaxis, 2) Enhacing the apoptotic cell clearance process and 3) setting an inviting niche for hematopoietic progenitors. These novel biological roles for tMCs could have substantial effets on thymic biology. Finally, our RNA-seq data offer a valuable resource to the community that can be mined to explore multiple questions related mesenchymal cell biology. Overall design: Transcriptome comparison between MC populations		GSM1888154: Skin_SCA1p_1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			(thymus MCs): Thymi were extracted, mechanically disrupted and enzymatically digested at 37oC for 3x15 minutes using 0.01% (w/v) Liberase TM (Roche) and 0.1% (w/v) DNase I (Sigma-Aldrich). Final digests were harvested, pooled and maintained at 4oC in FACS buffer (PBS, 0.1% (w/v) BSA, 0.02% (w/v) NaN3). Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). (Bone MCs) Femurs, tibias and pelvis were collected, cleaned and washed 3 times in cold PBS. Using sharp surgical scissors, each bone was first cut longitudinally and then transversely to generate tiny fragments of ~1 mm2.  Bone fragments were then washed 3 times in cold PBS and incubated with agitation (80 RPM) for 3x20 minutes at 37oC in the same enzymatic cocktail as above. Following each incubation, supernatants were added to HBSS medium (Invitrogen) supplemented with 2% (v/v) FBS, 10mM HEPES and 1% (v/v) penicillin-streptomycin. To further retrieve endosteal stromal cells, remaining bone fragments were gently crushed in supplemented HBSS medium using a pestle and mortar (5 x 50 gentle taps) and supernatants were pooled to previous ones. Red blood cell lysis was then performed on the resulting cell suspension prior to its filtration and resuspension in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). (Skin MCs) Mouse trunk and dorsal skin (~12 cm2 / mouse) was aseptically dissected and incubated for 45 minutes in 0.01% (w/v) liberase. Dermis was then mechanically isolated and incubated with agitation (80 RPM) at 37oC for 2x30 minutes in the same enzymatic cocktail as above. Post-incubation, supernatants were filtered and pooled to 25 mL of PBS supplemented with 1% FBS and 5mM EDTA. Final cell suspension was then centrifuged and resuspended in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). Transcriptome librairies were generated from total RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina) following the manufacturer’s protocol. Enrichment of RNA-seq stranded libraries with adapter molecules on both ends was done using 15 cycles of PCR amplification using the Illumina PCR mix and primers cocktail. Paired-end (2 x 100 bp) sequencing was peformed using the Illumina HiSeq 2000 running TruSeq v3 chemistry. Three RNA-seq librairies were sequenced per lane (8 lanes per flow cell).	Illumina HiSeq 2000	age;;3 to 4 wks-old|cell type;;Mesenchymal cells (Lin- SCA1+ cells)|source_name;;Skin|strain;;C57BL/6|tissue;;abdominal and back dermis (truncal skin)	GEO Accession;;GSM1888154		GSM1888154	Skin_SCA1p_1	8131548800	40657744	2016-02-26 22:54:03	5171948516	8131548800	40657744	2	40657744	index:0,count:40657744,average:100,stdev:0|index:1,count:40657744,average:100,stdev:0	GSM1888154_r5				in_mesa	27183606	2.32	2.04	0.04	5225239710	5248757472	4994971758	5033633244	100.45	100.77	36814101	33540507	187.668	635.229	118	323095	93.22	97.68	39709243	34317092	39709243	34317092	94.39	94.89	39709243	34750165	39709243	33337184	105623239	2.02	0.87	0	4.14	0	0.24	0	0.03	0	0.00	0	9.19	0	36814101	0	200	0	194.32	0	1.54	0	0.00	0	1.28	0	0.00	0	146.81	0	0.13	0	352693	0	40657744	0	1681696	0	96850	0	12289	0	0	0	3734504	0	6726	0	0	0	78739	0	24735363	0	19393	0	24840221	0	86.41	0	35132405	0	140520	19733934	140.435055508113	40657744.0	36814101.0	352693.0	1681696.0	96850.0	12289.0	0.0	3734504.0	35132405.0	90.5	0.9	4.1	0.2	0.0	0.0	9.2	86.4	100	100	100.00	38	4065774400	21.0	23.4	24.7	23.8	7.1	35.9	19.3	bulk
1905051	SRR2443119	SRP063829	SRS1073634	SRX1258028	SRA299328	GEO		RNA sequencing of primary thymic, bone and skin mesenchymal cells	Purpose : Elucidate post-natal role of SCA1+ thymic mesenchymal cells (tMCs) and evaluate the functional overlap between thymic, bone and skin MCs. Method : By high speed cell sorting, we isolated primary MCs (Lin- SCA1+ cells) from mouse thymus, bone and skin. We extracted their respective total RNA and compared their transcriptome by high-throughput RNA-sequencing. Results : We found a total of 2036 differentially expressed genes (FC>5, p-adj<0.1 and RPKM>1) between the 3 MC populations. IPA analyses revealed that each MC population was enriched for genes associated to phagocyte chemotaxis. We also denoted 2850 genes with shared expression across MC populations. IPA analysis of those shared genes also revealed an enrichment for genes influencing phagocyte migration, chemotaxis and function. Finally, MC transcriptomes showed that all 3 MC populations were expressing genes associated with hematopoietic stem and progenitor cell (HSPC) support, strongly suggesting that MCs from thymic, bone and skin all possess the ability to support HSPCs. Conclusion : Overall, our study highlighted 3 potential novel roles for tMCs : 1) Promoting macrophage/monocyte chemotaxis, 2) Enhacing the apoptotic cell clearance process and 3) setting an inviting niche for hematopoietic progenitors. These novel biological roles for tMCs could have substantial effets on thymic biology. Finally, our RNA-seq data offer a valuable resource to the community that can be mined to explore multiple questions related mesenchymal cell biology. Overall design: Transcriptome comparison between MC populations		GSM1888155: Skin_SCA1p_2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			(thymus MCs): Thymi were extracted, mechanically disrupted and enzymatically digested at 37oC for 3x15 minutes using 0.01% (w/v) Liberase TM (Roche) and 0.1% (w/v) DNase I (Sigma-Aldrich). Final digests were harvested, pooled and maintained at 4oC in FACS buffer (PBS, 0.1% (w/v) BSA, 0.02% (w/v) NaN3). Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). (Bone MCs) Femurs, tibias and pelvis were collected, cleaned and washed 3 times in cold PBS. Using sharp surgical scissors, each bone was first cut longitudinally and then transversely to generate tiny fragments of ~1 mm2.  Bone fragments were then washed 3 times in cold PBS and incubated with agitation (80 RPM) for 3x20 minutes at 37oC in the same enzymatic cocktail as above. Following each incubation, supernatants were added to HBSS medium (Invitrogen) supplemented with 2% (v/v) FBS, 10mM HEPES and 1% (v/v) penicillin-streptomycin. To further retrieve endosteal stromal cells, remaining bone fragments were gently crushed in supplemented HBSS medium using a pestle and mortar (5 x 50 gentle taps) and supernatants were pooled to previous ones. Red blood cell lysis was then performed on the resulting cell suspension prior to its filtration and resuspension in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). (Skin MCs) Mouse trunk and dorsal skin (~12 cm2 / mouse) was aseptically dissected and incubated for 45 minutes in 0.01% (w/v) liberase. Dermis was then mechanically isolated and incubated with agitation (80 RPM) at 37oC for 2x30 minutes in the same enzymatic cocktail as above. Post-incubation, supernatants were filtered and pooled to 25 mL of PBS supplemented with 1% FBS and 5mM EDTA. Final cell suspension was then centrifuged and resuspended in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). Transcriptome librairies were generated from total RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina) following the manufacturer’s protocol. Enrichment of RNA-seq stranded libraries with adapter molecules on both ends was done using 15 cycles of PCR amplification using the Illumina PCR mix and primers cocktail. Paired-end (2 x 100 bp) sequencing was peformed using the Illumina HiSeq 2000 running TruSeq v3 chemistry. Three RNA-seq librairies were sequenced per lane (8 lanes per flow cell).	Illumina HiSeq 2000	age;;3 to 4 wks-old|cell type;;Mesenchymal cells (Lin- SCA1+ cells)|source_name;;Skin|strain;;C57BL/6|tissue;;abdominal and back dermis (truncal skin)	GEO Accession;;GSM1888155		GSM1888155	Skin_SCA1p_2	1795183600	8975918	2016-02-26 22:54:03	1138557433	1795183600	8975918	2	8975918	index:0,count:8975918,average:100,stdev:0|index:1,count:8975918,average:100,stdev:0	GSM1888155_r1				in_mesa	27183606	2.03	1.94	0.03	1236134922	1243554976	1182549181	1193062694	100.6	100.89	8482021	7721359	192.534	634.611	128	69814	93.76	98.18	9142788	7952522	9142788	7952522	94.92	95.4	9142788	8051034	9142788	7726925	19660342	1.59	0.80	0	4.26	0	0.24	0	0.02	0	0.00	0	5.24	0	8482021	0	200	0	194.82	0	1.50	0	0.00	0	1.30	0	0.00	0	260.59	0	0.15	0	72066	0	8975918	0	382131	0	21950	0	2031	0	0	0	469916	0	1601	0	0	0	18158	0	5779436	0	4265	0	5803460	0	90.24	0	8099890	0	119103	4721785	39.644551354710	8975918.0	8482021.0	72066.0	382131.0	21950.0	2031.0	0.0	469916.0	8099890.0	94.5	0.8	4.3	0.2	0.0	0.0	5.2	90.2	100	100	100.00	38	897591800	21.7	24.5	26.5	24.4	3.0	36.4	22.1	bulk
1905163	SRR2443120	SRP063829	SRS1073634	SRX1258028	SRA299328	GEO		RNA sequencing of primary thymic, bone and skin mesenchymal cells	Purpose : Elucidate post-natal role of SCA1+ thymic mesenchymal cells (tMCs) and evaluate the functional overlap between thymic, bone and skin MCs. Method : By high speed cell sorting, we isolated primary MCs (Lin- SCA1+ cells) from mouse thymus, bone and skin. We extracted their respective total RNA and compared their transcriptome by high-throughput RNA-sequencing. Results : We found a total of 2036 differentially expressed genes (FC>5, p-adj<0.1 and RPKM>1) between the 3 MC populations. IPA analyses revealed that each MC population was enriched for genes associated to phagocyte chemotaxis. We also denoted 2850 genes with shared expression across MC populations. IPA analysis of those shared genes also revealed an enrichment for genes influencing phagocyte migration, chemotaxis and function. Finally, MC transcriptomes showed that all 3 MC populations were expressing genes associated with hematopoietic stem and progenitor cell (HSPC) support, strongly suggesting that MCs from thymic, bone and skin all possess the ability to support HSPCs. Conclusion : Overall, our study highlighted 3 potential novel roles for tMCs : 1) Promoting macrophage/monocyte chemotaxis, 2) Enhacing the apoptotic cell clearance process and 3) setting an inviting niche for hematopoietic progenitors. These novel biological roles for tMCs could have substantial effets on thymic biology. Finally, our RNA-seq data offer a valuable resource to the community that can be mined to explore multiple questions related mesenchymal cell biology. Overall design: Transcriptome comparison between MC populations		GSM1888155: Skin_SCA1p_2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			(thymus MCs): Thymi were extracted, mechanically disrupted and enzymatically digested at 37oC for 3x15 minutes using 0.01% (w/v) Liberase TM (Roche) and 0.1% (w/v) DNase I (Sigma-Aldrich). Final digests were harvested, pooled and maintained at 4oC in FACS buffer (PBS, 0.1% (w/v) BSA, 0.02% (w/v) NaN3). Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). (Bone MCs) Femurs, tibias and pelvis were collected, cleaned and washed 3 times in cold PBS. Using sharp surgical scissors, each bone was first cut longitudinally and then transversely to generate tiny fragments of ~1 mm2.  Bone fragments were then washed 3 times in cold PBS and incubated with agitation (80 RPM) for 3x20 minutes at 37oC in the same enzymatic cocktail as above. Following each incubation, supernatants were added to HBSS medium (Invitrogen) supplemented with 2% (v/v) FBS, 10mM HEPES and 1% (v/v) penicillin-streptomycin. To further retrieve endosteal stromal cells, remaining bone fragments were gently crushed in supplemented HBSS medium using a pestle and mortar (5 x 50 gentle taps) and supernatants were pooled to previous ones. Red blood cell lysis was then performed on the resulting cell suspension prior to its filtration and resuspension in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). (Skin MCs) Mouse trunk and dorsal skin (~12 cm2 / mouse) was aseptically dissected and incubated for 45 minutes in 0.01% (w/v) liberase. Dermis was then mechanically isolated and incubated with agitation (80 RPM) at 37oC for 2x30 minutes in the same enzymatic cocktail as above. Post-incubation, supernatants were filtered and pooled to 25 mL of PBS supplemented with 1% FBS and 5mM EDTA. Final cell suspension was then centrifuged and resuspended in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). Transcriptome librairies were generated from total RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina) following the manufacturer’s protocol. Enrichment of RNA-seq stranded libraries with adapter molecules on both ends was done using 15 cycles of PCR amplification using the Illumina PCR mix and primers cocktail. Paired-end (2 x 100 bp) sequencing was peformed using the Illumina HiSeq 2000 running TruSeq v3 chemistry. Three RNA-seq librairies were sequenced per lane (8 lanes per flow cell).	Illumina HiSeq 2000	age;;3 to 4 wks-old|cell type;;Mesenchymal cells (Lin- SCA1+ cells)|source_name;;Skin|strain;;C57BL/6|tissue;;abdominal and back dermis (truncal skin)	GEO Accession;;GSM1888155		GSM1888155	Skin_SCA1p_2	4413817200	22069086	2016-02-26 22:54:03	2866436689	4413817200	22069086	2	22069086	index:0,count:22069086,average:100,stdev:0|index:1,count:22069086,average:100,stdev:0	GSM1888155_r2				in_mesa	27183606	2.06	1.96	0.04	3035430953	3053638999	2902129742	2928054761	100.6	100.89	20846920	18971927	192.515	637.929	128	171941	93.69	98.17	22488590	19531840	22488590	19531840	94.89	95.37	22488590	19781462	22488590	18975233	48833735	1.61	0.81	0	4.31	0	0.24	0	0.03	0	0.00	0	5.26	0	20846920	0	200	0	194.74	0	1.52	0	0.00	0	1.29	0	0.00	0	383.81	0	0.14	0	179553	0	22069086	0	950705	0	53928	0	6619	0	0	0	1161619	0	3977	0	0	0	45122	0	14221786	0	10660	0	14281545	0	90.15	0	19896215	0	141060	11608060	82.291648943712	22069086.0	20846920.0	179553.0	950705.0	53928.0	6619.0	0.0	1161619.0	19896215.0	94.5	0.8	4.3	0.2	0.0	0.0	5.3	90.2	100	100	100.00	38	2206908600	21.8	24.5	26.3	24.5	3.0	36.1	21.8	bulk
1905179	SRR2443121	SRP063829	SRS1073634	SRX1258028	SRA299328	GEO		RNA sequencing of primary thymic, bone and skin mesenchymal cells	Purpose : Elucidate post-natal role of SCA1+ thymic mesenchymal cells (tMCs) and evaluate the functional overlap between thymic, bone and skin MCs. Method : By high speed cell sorting, we isolated primary MCs (Lin- SCA1+ cells) from mouse thymus, bone and skin. We extracted their respective total RNA and compared their transcriptome by high-throughput RNA-sequencing. Results : We found a total of 2036 differentially expressed genes (FC>5, p-adj<0.1 and RPKM>1) between the 3 MC populations. IPA analyses revealed that each MC population was enriched for genes associated to phagocyte chemotaxis. We also denoted 2850 genes with shared expression across MC populations. IPA analysis of those shared genes also revealed an enrichment for genes influencing phagocyte migration, chemotaxis and function. Finally, MC transcriptomes showed that all 3 MC populations were expressing genes associated with hematopoietic stem and progenitor cell (HSPC) support, strongly suggesting that MCs from thymic, bone and skin all possess the ability to support HSPCs. Conclusion : Overall, our study highlighted 3 potential novel roles for tMCs : 1) Promoting macrophage/monocyte chemotaxis, 2) Enhacing the apoptotic cell clearance process and 3) setting an inviting niche for hematopoietic progenitors. These novel biological roles for tMCs could have substantial effets on thymic biology. Finally, our RNA-seq data offer a valuable resource to the community that can be mined to explore multiple questions related mesenchymal cell biology. Overall design: Transcriptome comparison between MC populations		GSM1888155: Skin_SCA1p_2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			(thymus MCs): Thymi were extracted, mechanically disrupted and enzymatically digested at 37oC for 3x15 minutes using 0.01% (w/v) Liberase TM (Roche) and 0.1% (w/v) DNase I (Sigma-Aldrich). Final digests were harvested, pooled and maintained at 4oC in FACS buffer (PBS, 0.1% (w/v) BSA, 0.02% (w/v) NaN3). Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). (Bone MCs) Femurs, tibias and pelvis were collected, cleaned and washed 3 times in cold PBS. Using sharp surgical scissors, each bone was first cut longitudinally and then transversely to generate tiny fragments of ~1 mm2.  Bone fragments were then washed 3 times in cold PBS and incubated with agitation (80 RPM) for 3x20 minutes at 37oC in the same enzymatic cocktail as above. Following each incubation, supernatants were added to HBSS medium (Invitrogen) supplemented with 2% (v/v) FBS, 10mM HEPES and 1% (v/v) penicillin-streptomycin. To further retrieve endosteal stromal cells, remaining bone fragments were gently crushed in supplemented HBSS medium using a pestle and mortar (5 x 50 gentle taps) and supernatants were pooled to previous ones. Red blood cell lysis was then performed on the resulting cell suspension prior to its filtration and resuspension in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). (Skin MCs) Mouse trunk and dorsal skin (~12 cm2 / mouse) was aseptically dissected and incubated for 45 minutes in 0.01% (w/v) liberase. Dermis was then mechanically isolated and incubated with agitation (80 RPM) at 37oC for 2x30 minutes in the same enzymatic cocktail as above. Post-incubation, supernatants were filtered and pooled to 25 mL of PBS supplemented with 1% FBS and 5mM EDTA. Final cell suspension was then centrifuged and resuspended in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). Transcriptome librairies were generated from total RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina) following the manufacturer’s protocol. Enrichment of RNA-seq stranded libraries with adapter molecules on both ends was done using 15 cycles of PCR amplification using the Illumina PCR mix and primers cocktail. Paired-end (2 x 100 bp) sequencing was peformed using the Illumina HiSeq 2000 running TruSeq v3 chemistry. Three RNA-seq librairies were sequenced per lane (8 lanes per flow cell).	Illumina HiSeq 2000	age;;3 to 4 wks-old|cell type;;Mesenchymal cells (Lin- SCA1+ cells)|source_name;;Skin|strain;;C57BL/6|tissue;;abdominal and back dermis (truncal skin)	GEO Accession;;GSM1888155		GSM1888155	Skin_SCA1p_2	6096519600	30482598	2016-02-26 22:54:03	3907489125	6096519600	30482598	2	30482598	index:0,count:30482598,average:100,stdev:0|index:1,count:30482598,average:100,stdev:0	GSM1888155_r3				in_mesa	27183606	2.06	1.96	0.04	4191293976	4216156193	4007501470	4043113941	100.59	100.89	28797519	26201884	192.520	638.947	128	237062	93.7	98.17	31059762	26982507	31059762	26982507	94.89	95.38	31059762	27327103	31059762	26215498	67436256	1.61	0.81	0	4.30	0	0.25	0	0.02	0	0.00	0	5.26	0	28797519	0	200	0	194.72	0	1.51	0	0.00	0	1.29	0	0.00	0	292.63	0	0.13	0	247958	0	30482598	0	1310771	0	75007	0	6931	0	0	0	1603141	0	5578	0	0	0	62603	0	19682941	0	14763	0	19765885	0	90.17	0	27486748	0	148073	16059072	108.453749164264	30482598.0	28797519.0	247958.0	1310771.0	75007.0	6931.0	0.0	1603141.0	27486748.0	94.5	0.8	4.3	0.2	0.0	0.0	5.3	90.2	100	100	100.00	38	3048259800	21.8	24.5	26.2	24.5	3.0	36.3	22.3	bulk
1905194	SRR2443122	SRP063829	SRS1073637	SRX1258029	SRA299328	GEO		RNA sequencing of primary thymic, bone and skin mesenchymal cells	Purpose : Elucidate post-natal role of SCA1+ thymic mesenchymal cells (tMCs) and evaluate the functional overlap between thymic, bone and skin MCs. Method : By high speed cell sorting, we isolated primary MCs (Lin- SCA1+ cells) from mouse thymus, bone and skin. We extracted their respective total RNA and compared their transcriptome by high-throughput RNA-sequencing. Results : We found a total of 2036 differentially expressed genes (FC>5, p-adj<0.1 and RPKM>1) between the 3 MC populations. IPA analyses revealed that each MC population was enriched for genes associated to phagocyte chemotaxis. We also denoted 2850 genes with shared expression across MC populations. IPA analysis of those shared genes also revealed an enrichment for genes influencing phagocyte migration, chemotaxis and function. Finally, MC transcriptomes showed that all 3 MC populations were expressing genes associated with hematopoietic stem and progenitor cell (HSPC) support, strongly suggesting that MCs from thymic, bone and skin all possess the ability to support HSPCs. Conclusion : Overall, our study highlighted 3 potential novel roles for tMCs : 1) Promoting macrophage/monocyte chemotaxis, 2) Enhacing the apoptotic cell clearance process and 3) setting an inviting niche for hematopoietic progenitors. These novel biological roles for tMCs could have substantial effets on thymic biology. Finally, our RNA-seq data offer a valuable resource to the community that can be mined to explore multiple questions related mesenchymal cell biology. Overall design: Transcriptome comparison between MC populations		GSM1888156: Skin_SCA1p_3; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			(thymus MCs): Thymi were extracted, mechanically disrupted and enzymatically digested at 37oC for 3x15 minutes using 0.01% (w/v) Liberase TM (Roche) and 0.1% (w/v) DNase I (Sigma-Aldrich). Final digests were harvested, pooled and maintained at 4oC in FACS buffer (PBS, 0.1% (w/v) BSA, 0.02% (w/v) NaN3). Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). (Bone MCs) Femurs, tibias and pelvis were collected, cleaned and washed 3 times in cold PBS. Using sharp surgical scissors, each bone was first cut longitudinally and then transversely to generate tiny fragments of ~1 mm2.  Bone fragments were then washed 3 times in cold PBS and incubated with agitation (80 RPM) for 3x20 minutes at 37oC in the same enzymatic cocktail as above. Following each incubation, supernatants were added to HBSS medium (Invitrogen) supplemented with 2% (v/v) FBS, 10mM HEPES and 1% (v/v) penicillin-streptomycin. To further retrieve endosteal stromal cells, remaining bone fragments were gently crushed in supplemented HBSS medium using a pestle and mortar (5 x 50 gentle taps) and supernatants were pooled to previous ones. Red blood cell lysis was then performed on the resulting cell suspension prior to its filtration and resuspension in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). (Skin MCs) Mouse trunk and dorsal skin (~12 cm2 / mouse) was aseptically dissected and incubated for 45 minutes in 0.01% (w/v) liberase. Dermis was then mechanically isolated and incubated with agitation (80 RPM) at 37oC for 2x30 minutes in the same enzymatic cocktail as above. Post-incubation, supernatants were filtered and pooled to 25 mL of PBS supplemented with 1% FBS and 5mM EDTA. Final cell suspension was then centrifuged and resuspended in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). Transcriptome librairies were generated from total RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina) following the manufacturer’s protocol. Enrichment of RNA-seq stranded libraries with adapter molecules on both ends was done using 15 cycles of PCR amplification using the Illumina PCR mix and primers cocktail. Paired-end (2 x 100 bp) sequencing was peformed using the Illumina HiSeq 2000 running TruSeq v3 chemistry. Three RNA-seq librairies were sequenced per lane (8 lanes per flow cell).	Illumina HiSeq 2000	age;;3 to 4 wks-old|cell type;;Mesenchymal cells (Lin- SCA1+ cells)|source_name;;Skin|strain;;C57BL/6|tissue;;abdominal and back dermis (truncal skin)	GEO Accession;;GSM1888156		GSM1888156	Skin_SCA1p_3	972818000	4864090	2016-02-26 22:54:03	668891608	972818000	4864090	2	4864090	index:0,count:4864090,average:100,stdev:0|index:1,count:4864090,average:100,stdev:0	GSM1888156_r1				in_mesa	27183606	2.33	2.06	0.04	655088883	657575539	622144625	626738746	100.38	100.74	4471652	4108142	189.018	598.810	128	38564	93.08	98.2	4868893	4162196	4868893	4162196	94.96	95.51	4868893	4246396	4868893	4048059	9832072	1.50	0.89	0	4.79	0	0.24	0	0.02	0	0.00	0	7.81	0	4471652	0	200	0	195.04	0	1.51	0	0.00	0	1.22	0	0.00	0	233.48	0	0.23	0	43089	0	4864090	0	233135	0	11464	0	1153	0	0	0	379821	0	900	0	0	0	8858	0	2741022	0	2304	0	2753084	0	87.14	0	4238517	0	100090	2268806	22.667659106804	4864090.0	4471652.0	43089.0	233135.0	11464.0	1153.0	0.0	379821.0	4238517.0	91.9	0.9	4.8	0.2	0.0	0.0	7.8	87.1	100	100	100.00	38	486409000	22.4	24.0	26.2	25.0	2.4	35.3	19.9	bulk
1905210	SRR2443123	SRP063829	SRS1073637	SRX1258029	SRA299328	GEO		RNA sequencing of primary thymic, bone and skin mesenchymal cells	Purpose : Elucidate post-natal role of SCA1+ thymic mesenchymal cells (tMCs) and evaluate the functional overlap between thymic, bone and skin MCs. Method : By high speed cell sorting, we isolated primary MCs (Lin- SCA1+ cells) from mouse thymus, bone and skin. We extracted their respective total RNA and compared their transcriptome by high-throughput RNA-sequencing. Results : We found a total of 2036 differentially expressed genes (FC>5, p-adj<0.1 and RPKM>1) between the 3 MC populations. IPA analyses revealed that each MC population was enriched for genes associated to phagocyte chemotaxis. We also denoted 2850 genes with shared expression across MC populations. IPA analysis of those shared genes also revealed an enrichment for genes influencing phagocyte migration, chemotaxis and function. Finally, MC transcriptomes showed that all 3 MC populations were expressing genes associated with hematopoietic stem and progenitor cell (HSPC) support, strongly suggesting that MCs from thymic, bone and skin all possess the ability to support HSPCs. Conclusion : Overall, our study highlighted 3 potential novel roles for tMCs : 1) Promoting macrophage/monocyte chemotaxis, 2) Enhacing the apoptotic cell clearance process and 3) setting an inviting niche for hematopoietic progenitors. These novel biological roles for tMCs could have substantial effets on thymic biology. Finally, our RNA-seq data offer a valuable resource to the community that can be mined to explore multiple questions related mesenchymal cell biology. Overall design: Transcriptome comparison between MC populations		GSM1888156: Skin_SCA1p_3; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			(thymus MCs): Thymi were extracted, mechanically disrupted and enzymatically digested at 37oC for 3x15 minutes using 0.01% (w/v) Liberase TM (Roche) and 0.1% (w/v) DNase I (Sigma-Aldrich). Final digests were harvested, pooled and maintained at 4oC in FACS buffer (PBS, 0.1% (w/v) BSA, 0.02% (w/v) NaN3). Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). (Bone MCs) Femurs, tibias and pelvis were collected, cleaned and washed 3 times in cold PBS. Using sharp surgical scissors, each bone was first cut longitudinally and then transversely to generate tiny fragments of ~1 mm2.  Bone fragments were then washed 3 times in cold PBS and incubated with agitation (80 RPM) for 3x20 minutes at 37oC in the same enzymatic cocktail as above. Following each incubation, supernatants were added to HBSS medium (Invitrogen) supplemented with 2% (v/v) FBS, 10mM HEPES and 1% (v/v) penicillin-streptomycin. To further retrieve endosteal stromal cells, remaining bone fragments were gently crushed in supplemented HBSS medium using a pestle and mortar (5 x 50 gentle taps) and supernatants were pooled to previous ones. Red blood cell lysis was then performed on the resulting cell suspension prior to its filtration and resuspension in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). (Skin MCs) Mouse trunk and dorsal skin (~12 cm2 / mouse) was aseptically dissected and incubated for 45 minutes in 0.01% (w/v) liberase. Dermis was then mechanically isolated and incubated with agitation (80 RPM) at 37oC for 2x30 minutes in the same enzymatic cocktail as above. Post-incubation, supernatants were filtered and pooled to 25 mL of PBS supplemented with 1% FBS and 5mM EDTA. Final cell suspension was then centrifuged and resuspended in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). Transcriptome librairies were generated from total RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina) following the manufacturer’s protocol. Enrichment of RNA-seq stranded libraries with adapter molecules on both ends was done using 15 cycles of PCR amplification using the Illumina PCR mix and primers cocktail. Paired-end (2 x 100 bp) sequencing was peformed using the Illumina HiSeq 2000 running TruSeq v3 chemistry. Three RNA-seq librairies were sequenced per lane (8 lanes per flow cell).	Illumina HiSeq 2000	age;;3 to 4 wks-old|cell type;;Mesenchymal cells (Lin- SCA1+ cells)|source_name;;Skin|strain;;C57BL/6|tissue;;abdominal and back dermis (truncal skin)	GEO Accession;;GSM1888156		GSM1888156	Skin_SCA1p_3	970703400	4853517	2016-02-26 22:54:03	666803586	970703400	4853517	2	4853517	index:0,count:4853517,average:100,stdev:0|index:1,count:4853517,average:100,stdev:0	GSM1888156_r2				in_mesa	27183606	2.34	2.08	0.04	654215033	656662515	621217935	625770197	100.37	100.73	4467939	4103986	188.725	597.373	128	38616	93.06	98.19	4867912	4157825	4867912	4157825	94.95	95.5	4867912	4242245	4867912	4044008	9922284	1.52	0.89	0	4.81	0	0.24	0	0.02	0	0.00	0	7.68	0	4467939	0	200	0	195.06	0	1.52	0	0.00	0	1.22	0	0.00	0	232.97	0	0.22	0	43174	0	4853517	0	233366	0	11674	0	1210	0	0	0	372694	0	849	0	0	0	8807	0	2738975	0	2398	0	2751029	0	87.25	0	4234573	0	100074	2264241	22.625667006415	4853517.0	4467939.0	43174.0	233366.0	11674.0	1210.0	0.0	372694.0	4234573.0	92.1	0.9	4.8	0.2	0.0	0.0	7.7	87.2	100	100	100.00	38	485351700	22.4	24.0	26.2	25.0	2.4	35.3	20.1	bulk
1905225	SRR2443124	SRP063829	SRS1073637	SRX1258029	SRA299328	GEO		RNA sequencing of primary thymic, bone and skin mesenchymal cells	Purpose : Elucidate post-natal role of SCA1+ thymic mesenchymal cells (tMCs) and evaluate the functional overlap between thymic, bone and skin MCs. Method : By high speed cell sorting, we isolated primary MCs (Lin- SCA1+ cells) from mouse thymus, bone and skin. We extracted their respective total RNA and compared their transcriptome by high-throughput RNA-sequencing. Results : We found a total of 2036 differentially expressed genes (FC>5, p-adj<0.1 and RPKM>1) between the 3 MC populations. IPA analyses revealed that each MC population was enriched for genes associated to phagocyte chemotaxis. We also denoted 2850 genes with shared expression across MC populations. IPA analysis of those shared genes also revealed an enrichment for genes influencing phagocyte migration, chemotaxis and function. Finally, MC transcriptomes showed that all 3 MC populations were expressing genes associated with hematopoietic stem and progenitor cell (HSPC) support, strongly suggesting that MCs from thymic, bone and skin all possess the ability to support HSPCs. Conclusion : Overall, our study highlighted 3 potential novel roles for tMCs : 1) Promoting macrophage/monocyte chemotaxis, 2) Enhacing the apoptotic cell clearance process and 3) setting an inviting niche for hematopoietic progenitors. These novel biological roles for tMCs could have substantial effets on thymic biology. Finally, our RNA-seq data offer a valuable resource to the community that can be mined to explore multiple questions related mesenchymal cell biology. Overall design: Transcriptome comparison between MC populations		GSM1888156: Skin_SCA1p_3; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			(thymus MCs): Thymi were extracted, mechanically disrupted and enzymatically digested at 37oC for 3x15 minutes using 0.01% (w/v) Liberase TM (Roche) and 0.1% (w/v) DNase I (Sigma-Aldrich). Final digests were harvested, pooled and maintained at 4oC in FACS buffer (PBS, 0.1% (w/v) BSA, 0.02% (w/v) NaN3). Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). (Bone MCs) Femurs, tibias and pelvis were collected, cleaned and washed 3 times in cold PBS. Using sharp surgical scissors, each bone was first cut longitudinally and then transversely to generate tiny fragments of ~1 mm2.  Bone fragments were then washed 3 times in cold PBS and incubated with agitation (80 RPM) for 3x20 minutes at 37oC in the same enzymatic cocktail as above. Following each incubation, supernatants were added to HBSS medium (Invitrogen) supplemented with 2% (v/v) FBS, 10mM HEPES and 1% (v/v) penicillin-streptomycin. To further retrieve endosteal stromal cells, remaining bone fragments were gently crushed in supplemented HBSS medium using a pestle and mortar (5 x 50 gentle taps) and supernatants were pooled to previous ones. Red blood cell lysis was then performed on the resulting cell suspension prior to its filtration and resuspension in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). (Skin MCs) Mouse trunk and dorsal skin (~12 cm2 / mouse) was aseptically dissected and incubated for 45 minutes in 0.01% (w/v) liberase. Dermis was then mechanically isolated and incubated with agitation (80 RPM) at 37oC for 2x30 minutes in the same enzymatic cocktail as above. Post-incubation, supernatants were filtered and pooled to 25 mL of PBS supplemented with 1% FBS and 5mM EDTA. Final cell suspension was then centrifuged and resuspended in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). Transcriptome librairies were generated from total RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina) following the manufacturer’s protocol. Enrichment of RNA-seq stranded libraries with adapter molecules on both ends was done using 15 cycles of PCR amplification using the Illumina PCR mix and primers cocktail. Paired-end (2 x 100 bp) sequencing was peformed using the Illumina HiSeq 2000 running TruSeq v3 chemistry. Three RNA-seq librairies were sequenced per lane (8 lanes per flow cell).	Illumina HiSeq 2000	age;;3 to 4 wks-old|cell type;;Mesenchymal cells (Lin- SCA1+ cells)|source_name;;Skin|strain;;C57BL/6|tissue;;abdominal and back dermis (truncal skin)	GEO Accession;;GSM1888156		GSM1888156	Skin_SCA1p_3	986865800	4934329	2016-02-26 22:54:03	675162550	986865800	4934329	2	4934329	index:0,count:4934329,average:100,stdev:0|index:1,count:4934329,average:100,stdev:0	GSM1888156_r3				in_mesa	27183606	2.33	2.07	0.04	668683158	671184676	634973709	639632065	100.37	100.73	4562788	4191096	189.068	599.206	128	39110	93.07	98.2	4968883	4246630	4968883	4246630	94.97	95.51	4968883	4333145	4968883	4130428	10057463	1.50	0.89	0	4.83	0	0.24	0	0.03	0	0.00	0	7.27	0	4562788	0	200	0	195.07	0	1.51	0	0.00	0	1.21	0	0.00	0	208.98	0	0.22	0	43834	0	4934329	0	238384	0	11752	0	1272	0	0	0	358517	0	869	0	0	0	9381	0	2804282	0	2273	0	2816805	0	87.64	0	4324404	0	100643	2321462	23.066303667418	4934329.0	4562788.0	43834.0	238384.0	11752.0	1272.0	0.0	358517.0	4324404.0	92.5	0.9	4.8	0.2	0.0	0.0	7.3	87.6	100	100	100.00	38	493432900	22.4	24.0	26.2	25.0	2.4	35.4	20.3	bulk
1905464	SRR2443133	SRP063829	SRS1073631	SRX1258032	SRA299328	GEO		RNA sequencing of primary thymic, bone and skin mesenchymal cells	Purpose : Elucidate post-natal role of SCA1+ thymic mesenchymal cells (tMCs) and evaluate the functional overlap between thymic, bone and skin MCs. Method : By high speed cell sorting, we isolated primary MCs (Lin- SCA1+ cells) from mouse thymus, bone and skin. We extracted their respective total RNA and compared their transcriptome by high-throughput RNA-sequencing. Results : We found a total of 2036 differentially expressed genes (FC>5, p-adj<0.1 and RPKM>1) between the 3 MC populations. IPA analyses revealed that each MC population was enriched for genes associated to phagocyte chemotaxis. We also denoted 2850 genes with shared expression across MC populations. IPA analysis of those shared genes also revealed an enrichment for genes influencing phagocyte migration, chemotaxis and function. Finally, MC transcriptomes showed that all 3 MC populations were expressing genes associated with hematopoietic stem and progenitor cell (HSPC) support, strongly suggesting that MCs from thymic, bone and skin all possess the ability to support HSPCs. Conclusion : Overall, our study highlighted 3 potential novel roles for tMCs : 1) Promoting macrophage/monocyte chemotaxis, 2) Enhacing the apoptotic cell clearance process and 3) setting an inviting niche for hematopoietic progenitors. These novel biological roles for tMCs could have substantial effets on thymic biology. Finally, our RNA-seq data offer a valuable resource to the community that can be mined to explore multiple questions related mesenchymal cell biology. Overall design: Transcriptome comparison between MC populations		GSM1888159: Thymus_SCA1p_1-3; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			(thymus MCs): Thymi were extracted, mechanically disrupted and enzymatically digested at 37oC for 3x15 minutes using 0.01% (w/v) Liberase TM (Roche) and 0.1% (w/v) DNase I (Sigma-Aldrich). Final digests were harvested, pooled and maintained at 4oC in FACS buffer (PBS, 0.1% (w/v) BSA, 0.02% (w/v) NaN3). Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). (Bone MCs) Femurs, tibias and pelvis were collected, cleaned and washed 3 times in cold PBS. Using sharp surgical scissors, each bone was first cut longitudinally and then transversely to generate tiny fragments of ~1 mm2.  Bone fragments were then washed 3 times in cold PBS and incubated with agitation (80 RPM) for 3x20 minutes at 37oC in the same enzymatic cocktail as above. Following each incubation, supernatants were added to HBSS medium (Invitrogen) supplemented with 2% (v/v) FBS, 10mM HEPES and 1% (v/v) penicillin-streptomycin. To further retrieve endosteal stromal cells, remaining bone fragments were gently crushed in supplemented HBSS medium using a pestle and mortar (5 x 50 gentle taps) and supernatants were pooled to previous ones. Red blood cell lysis was then performed on the resulting cell suspension prior to its filtration and resuspension in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). (Skin MCs) Mouse trunk and dorsal skin (~12 cm2 / mouse) was aseptically dissected and incubated for 45 minutes in 0.01% (w/v) liberase. Dermis was then mechanically isolated and incubated with agitation (80 RPM) at 37oC for 2x30 minutes in the same enzymatic cocktail as above. Post-incubation, supernatants were filtered and pooled to 25 mL of PBS supplemented with 1% FBS and 5mM EDTA. Final cell suspension was then centrifuged and resuspended in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). Transcriptome librairies were generated from total RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina) following the manufacturer’s protocol. Enrichment of RNA-seq stranded libraries with adapter molecules on both ends was done using 15 cycles of PCR amplification using the Illumina PCR mix and primers cocktail. Paired-end (2 x 100 bp) sequencing was peformed using the Illumina HiSeq 2000 running TruSeq v3 chemistry. Three RNA-seq librairies were sequenced per lane (8 lanes per flow cell).	Illumina HiSeq 2000	age;;3 to 4 wks-old|cell type;;Mesenchymal cells (Lin- SCA1+ cells)|source_name;;Thymus|strain;;C57BL/6|tissue;;Thymus	GEO Accession;;GSM1888159		GSM1888159	Thymus_SCA1p_1-3	4301652400	21508262	2016-02-26 22:54:03	2784693875	4301652400	21508262	2	21508262	index:0,count:21508262,average:100,stdev:0|index:1,count:21508262,average:100,stdev:0	GSM1888159_r1				in_mesa	27183606	3.85	3.26	0.07	2604592041	2599918819	2462497160	2471108127	99.82	100.35	19697979	18043326	163.657	693.918	104	211723	89.54	94.93	21570346	17637779	21570346	17637779	91.23	91.75	21570346	17970486	21570346	17047003	115956859	4.45	1.31	0	5.20	0	0.24	0	0.05	0	0.00	0	8.12	0	19697979	0	200	0	192.44	0	1.52	0	0.00	0	1.20	0	0.00	0	227.07	0	0.13	0	282607	0	21508262	0	1117439	0	52561	0	10363	0	0	0	1747359	0	3697	0	0	0	61002	0	9452198	0	9966	0	9526863	0	86.39	0	18580540	0	148423	7152808	48.192045707202	21508262.0	19697979.0	282607.0	1117439.0	52561.0	10363.0	0.0	1747359.0	18580540.0	91.6	1.3	5.2	0.2	0.0	0.0	8.1	86.4	100	100	100.00	38	2150826200	22.7	22.3	25.5	25.2	4.3	36.3	22.4	bulk
1905481	SRR2443134	SRP063829	SRS1073631	SRX1258032	SRA299328	GEO		RNA sequencing of primary thymic, bone and skin mesenchymal cells	Purpose : Elucidate post-natal role of SCA1+ thymic mesenchymal cells (tMCs) and evaluate the functional overlap between thymic, bone and skin MCs. Method : By high speed cell sorting, we isolated primary MCs (Lin- SCA1+ cells) from mouse thymus, bone and skin. We extracted their respective total RNA and compared their transcriptome by high-throughput RNA-sequencing. Results : We found a total of 2036 differentially expressed genes (FC>5, p-adj<0.1 and RPKM>1) between the 3 MC populations. IPA analyses revealed that each MC population was enriched for genes associated to phagocyte chemotaxis. We also denoted 2850 genes with shared expression across MC populations. IPA analysis of those shared genes also revealed an enrichment for genes influencing phagocyte migration, chemotaxis and function. Finally, MC transcriptomes showed that all 3 MC populations were expressing genes associated with hematopoietic stem and progenitor cell (HSPC) support, strongly suggesting that MCs from thymic, bone and skin all possess the ability to support HSPCs. Conclusion : Overall, our study highlighted 3 potential novel roles for tMCs : 1) Promoting macrophage/monocyte chemotaxis, 2) Enhacing the apoptotic cell clearance process and 3) setting an inviting niche for hematopoietic progenitors. These novel biological roles for tMCs could have substantial effets on thymic biology. Finally, our RNA-seq data offer a valuable resource to the community that can be mined to explore multiple questions related mesenchymal cell biology. Overall design: Transcriptome comparison between MC populations		GSM1888159: Thymus_SCA1p_1-3; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			(thymus MCs): Thymi were extracted, mechanically disrupted and enzymatically digested at 37oC for 3x15 minutes using 0.01% (w/v) Liberase TM (Roche) and 0.1% (w/v) DNase I (Sigma-Aldrich). Final digests were harvested, pooled and maintained at 4oC in FACS buffer (PBS, 0.1% (w/v) BSA, 0.02% (w/v) NaN3). Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). (Bone MCs) Femurs, tibias and pelvis were collected, cleaned and washed 3 times in cold PBS. Using sharp surgical scissors, each bone was first cut longitudinally and then transversely to generate tiny fragments of ~1 mm2.  Bone fragments were then washed 3 times in cold PBS and incubated with agitation (80 RPM) for 3x20 minutes at 37oC in the same enzymatic cocktail as above. Following each incubation, supernatants were added to HBSS medium (Invitrogen) supplemented with 2% (v/v) FBS, 10mM HEPES and 1% (v/v) penicillin-streptomycin. To further retrieve endosteal stromal cells, remaining bone fragments were gently crushed in supplemented HBSS medium using a pestle and mortar (5 x 50 gentle taps) and supernatants were pooled to previous ones. Red blood cell lysis was then performed on the resulting cell suspension prior to its filtration and resuspension in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). (Skin MCs) Mouse trunk and dorsal skin (~12 cm2 / mouse) was aseptically dissected and incubated for 45 minutes in 0.01% (w/v) liberase. Dermis was then mechanically isolated and incubated with agitation (80 RPM) at 37oC for 2x30 minutes in the same enzymatic cocktail as above. Post-incubation, supernatants were filtered and pooled to 25 mL of PBS supplemented with 1% FBS and 5mM EDTA. Final cell suspension was then centrifuged and resuspended in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). Transcriptome librairies were generated from total RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina) following the manufacturer’s protocol. Enrichment of RNA-seq stranded libraries with adapter molecules on both ends was done using 15 cycles of PCR amplification using the Illumina PCR mix and primers cocktail. Paired-end (2 x 100 bp) sequencing was peformed using the Illumina HiSeq 2000 running TruSeq v3 chemistry. Three RNA-seq librairies were sequenced per lane (8 lanes per flow cell).	Illumina HiSeq 2000	age;;3 to 4 wks-old|cell type;;Mesenchymal cells (Lin- SCA1+ cells)|source_name;;Thymus|strain;;C57BL/6|tissue;;Thymus	GEO Accession;;GSM1888159		GSM1888159	Thymus_SCA1p_1-3	9417297600	47086488	2016-02-26 22:54:03	6003279833	9417297600	47086488	2	47086488	index:0,count:47086488,average:100,stdev:0|index:1,count:47086488,average:100,stdev:0	GSM1888159_r2				in_mesa	27183606	3.84	3.26	0.07	5697439916	5686911947	5385909014	5404770933	99.82	100.35	43118644	39492511	163.589	691.879	104	464226	89.52	94.92	47227154	38599416	47227154	38599416	91.22	91.73	47227154	39330767	47227154	37304999	254348757	4.46	1.32	0	5.21	0	0.24	0	0.05	0	0.00	0	8.14	0	43118644	0	200	0	192.41	0	1.52	0	0.00	0	1.21	0	0.00	0	140.91	0	0.12	0	619848	0	47086488	0	2452362	0	114944	0	21211	0	0	0	3831689	0	8476	0	0	0	134761	0	20712947	0	21530	0	20877714	0	86.37	0	40666282	0	165967	15659529	94.353269023360	47086488.0	43118644.0	619848.0	2452362.0	114944.0	21211.0	0.0	3831689.0	40666282.0	91.6	1.3	5.2	0.2	0.0	0.0	8.1	86.4	100	100	100.00	38	4708648800	22.7	22.3	25.4	25.3	4.4	36.4	23.0	bulk
952383	SRR2443107	SRP063829	SRS1073638	SRX1258024	SRA299328	GEO		RNA sequencing of primary thymic, bone and skin mesenchymal cells	Purpose : Elucidate post-natal role of SCA1+ thymic mesenchymal cells (tMCs) and evaluate the functional overlap between thymic, bone and skin MCs. Method : By high speed cell sorting, we isolated primary MCs (Lin- SCA1+ cells) from mouse thymus, bone and skin. We extracted their respective total RNA and compared their transcriptome by high-throughput RNA-sequencing. Results : We found a total of 2036 differentially expressed genes (FC>5, p-adj<0.1 and RPKM>1) between the 3 MC populations. IPA analyses revealed that each MC population was enriched for genes associated to phagocyte chemotaxis. We also denoted 2850 genes with shared expression across MC populations. IPA analysis of those shared genes also revealed an enrichment for genes influencing phagocyte migration, chemotaxis and function. Finally, MC transcriptomes showed that all 3 MC populations were expressing genes associated with hematopoietic stem and progenitor cell (HSPC) support, strongly suggesting that MCs from thymic, bone and skin all possess the ability to support HSPCs. Conclusion : Overall, our study highlighted 3 potential novel roles for tMCs : 1) Promoting macrophage/monocyte chemotaxis, 2) Enhacing the apoptotic cell clearance process and 3) setting an inviting niche for hematopoietic progenitors. These novel biological roles for tMCs could have substantial effets on thymic biology. Finally, our RNA-seq data offer a valuable resource to the community that can be mined to explore multiple questions related mesenchymal cell biology. Overall design: Transcriptome comparison between MC populations		GSM1888151: Bone_SCA1p_1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			(thymus MCs): Thymi were extracted, mechanically disrupted and enzymatically digested at 37oC for 3x15 minutes using 0.01% (w/v) Liberase TM (Roche) and 0.1% (w/v) DNase I (Sigma-Aldrich). Final digests were harvested, pooled and maintained at 4oC in FACS buffer (PBS, 0.1% (w/v) BSA, 0.02% (w/v) NaN3). Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). (Bone MCs) Femurs, tibias and pelvis were collected, cleaned and washed 3 times in cold PBS. Using sharp surgical scissors, each bone was first cut longitudinally and then transversely to generate tiny fragments of ~1 mm2.  Bone fragments were then washed 3 times in cold PBS and incubated with agitation (80 RPM) for 3x20 minutes at 37oC in the same enzymatic cocktail as above. Following each incubation, supernatants were added to HBSS medium (Invitrogen) supplemented with 2% (v/v) FBS, 10mM HEPES and 1% (v/v) penicillin-streptomycin. To further retrieve endosteal stromal cells, remaining bone fragments were gently crushed in supplemented HBSS medium using a pestle and mortar (5 x 50 gentle taps) and supernatants were pooled to previous ones. Red blood cell lysis was then performed on the resulting cell suspension prior to its filtration and resuspension in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). (Skin MCs) Mouse trunk and dorsal skin (~12 cm2 / mouse) was aseptically dissected and incubated for 45 minutes in 0.01% (w/v) liberase. Dermis was then mechanically isolated and incubated with agitation (80 RPM) at 37oC for 2x30 minutes in the same enzymatic cocktail as above. Post-incubation, supernatants were filtered and pooled to 25 mL of PBS supplemented with 1% FBS and 5mM EDTA. Final cell suspension was then centrifuged and resuspended in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). Transcriptome librairies were generated from total RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina) following the manufacturer’s protocol. Enrichment of RNA-seq stranded libraries with adapter molecules on both ends was done using 15 cycles of PCR amplification using the Illumina PCR mix and primers cocktail. Paired-end (2 x 100 bp) sequencing was peformed using the Illumina HiSeq 2000 running TruSeq v3 chemistry. Three RNA-seq librairies were sequenced per lane (8 lanes per flow cell).	Illumina HiSeq 2000	age;;3 to 4 wks-old|cell type;;Mesenchymal cells (Lin- SCA1+ cells)|source_name;;Bone|strain;;C57BL/6|tissue;;Femur, tibia and pelvis	GEO Accession;;GSM1888151		GSM1888151	Bone_SCA1p_1	5258056400	26290282	2016-02-26 22:54:03	3606115477	5258056400	26290282	2	26290282	index:0,count:26290282,average:100,stdev:0|index:1,count:26290282,average:100,stdev:0	GSM1888151_r3				in_mesa	27183606	3.39	2.71	0.07	2916318271	2914769138	2746856789	2758549473	99.95	100.43	21790493	20038207	169.489	656.273	107	182037	86.7	92.28	24021997	18892931	24021997	18892931	88.87	89.2	24021997	19365130	24021997	18262566	210600383	7.22	1.12	0	5.01	0	0.28	0	0.08	0	0.00	0	16.75	0	21790493	0	200	0	190.51	0	1.50	0	0.01	0	1.22	0	0.00	0	144.28	0	0.21	0	294009	0	26290282	0	1316088	0	72739	0	22311	0	0	0	4404739	0	4345	0	0	0	53113	0	10293148	0	13529	0	10364135	0	77.88	0	20474405	0	101368	8068718	79.598275589930	26290282.0	21790493.0	294009.0	1316088.0	72739.0	22311.0	0.0	4404739.0	20474405.0	82.9	1.1	5.0	0.3	0.1	0.0	16.8	77.9	100	100	100.00	38	2629028200	21.5	21.3	22.7	24.0	10.4	35.1	18.4	bulk
952391	SRR2443108	SRP063829	SRS1073636	SRX1258025	SRA299328	GEO		RNA sequencing of primary thymic, bone and skin mesenchymal cells	Purpose : Elucidate post-natal role of SCA1+ thymic mesenchymal cells (tMCs) and evaluate the functional overlap between thymic, bone and skin MCs. Method : By high speed cell sorting, we isolated primary MCs (Lin- SCA1+ cells) from mouse thymus, bone and skin. We extracted their respective total RNA and compared their transcriptome by high-throughput RNA-sequencing. Results : We found a total of 2036 differentially expressed genes (FC>5, p-adj<0.1 and RPKM>1) between the 3 MC populations. IPA analyses revealed that each MC population was enriched for genes associated to phagocyte chemotaxis. We also denoted 2850 genes with shared expression across MC populations. IPA analysis of those shared genes also revealed an enrichment for genes influencing phagocyte migration, chemotaxis and function. Finally, MC transcriptomes showed that all 3 MC populations were expressing genes associated with hematopoietic stem and progenitor cell (HSPC) support, strongly suggesting that MCs from thymic, bone and skin all possess the ability to support HSPCs. Conclusion : Overall, our study highlighted 3 potential novel roles for tMCs : 1) Promoting macrophage/monocyte chemotaxis, 2) Enhacing the apoptotic cell clearance process and 3) setting an inviting niche for hematopoietic progenitors. These novel biological roles for tMCs could have substantial effets on thymic biology. Finally, our RNA-seq data offer a valuable resource to the community that can be mined to explore multiple questions related mesenchymal cell biology. Overall design: Transcriptome comparison between MC populations		GSM1888152: Bone_SCA1p_2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			(thymus MCs): Thymi were extracted, mechanically disrupted and enzymatically digested at 37oC for 3x15 minutes using 0.01% (w/v) Liberase TM (Roche) and 0.1% (w/v) DNase I (Sigma-Aldrich). Final digests were harvested, pooled and maintained at 4oC in FACS buffer (PBS, 0.1% (w/v) BSA, 0.02% (w/v) NaN3). Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). (Bone MCs) Femurs, tibias and pelvis were collected, cleaned and washed 3 times in cold PBS. Using sharp surgical scissors, each bone was first cut longitudinally and then transversely to generate tiny fragments of ~1 mm2.  Bone fragments were then washed 3 times in cold PBS and incubated with agitation (80 RPM) for 3x20 minutes at 37oC in the same enzymatic cocktail as above. Following each incubation, supernatants were added to HBSS medium (Invitrogen) supplemented with 2% (v/v) FBS, 10mM HEPES and 1% (v/v) penicillin-streptomycin. To further retrieve endosteal stromal cells, remaining bone fragments were gently crushed in supplemented HBSS medium using a pestle and mortar (5 x 50 gentle taps) and supernatants were pooled to previous ones. Red blood cell lysis was then performed on the resulting cell suspension prior to its filtration and resuspension in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). (Skin MCs) Mouse trunk and dorsal skin (~12 cm2 / mouse) was aseptically dissected and incubated for 45 minutes in 0.01% (w/v) liberase. Dermis was then mechanically isolated and incubated with agitation (80 RPM) at 37oC for 2x30 minutes in the same enzymatic cocktail as above. Post-incubation, supernatants were filtered and pooled to 25 mL of PBS supplemented with 1% FBS and 5mM EDTA. Final cell suspension was then centrifuged and resuspended in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). Transcriptome librairies were generated from total RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina) following the manufacturer’s protocol. Enrichment of RNA-seq stranded libraries with adapter molecules on both ends was done using 15 cycles of PCR amplification using the Illumina PCR mix and primers cocktail. Paired-end (2 x 100 bp) sequencing was peformed using the Illumina HiSeq 2000 running TruSeq v3 chemistry. Three RNA-seq librairies were sequenced per lane (8 lanes per flow cell).	Illumina HiSeq 2000	age;;3 to 4 wks-old|cell type;;Mesenchymal cells (Lin- SCA1+ cells)|source_name;;Bone|strain;;C57BL/6|tissue;;Femur, tibia and pelvis	GEO Accession;;GSM1888152		GSM1888152	Bone_SCA1p_2	5065071400	25325357	2016-02-26 22:54:03	3503560424	5065071400	25325357	2	25325357	index:0,count:25325357,average:100,stdev:0|index:1,count:25325357,average:100,stdev:0	GSM1888152_r1				in_mesa	27183606	3.2	2.83	0.07	3109603823	3105426139	2941207825	2950524893	99.87	100.32	22503374	20690800	173.529	649.833	116	177233	86.57	91.73	24634036	19481728	24634036	19481728	88.4	88.7	24634036	19893381	24634036	18837685	242080733	7.78	1.27	0	4.99	0	0.28	0	0.09	0	0.00	0	10.78	0	22503374	0	200	0	192.02	0	1.51	0	0.01	0	1.22	0	0.00	0	241.83	0	0.21	0	321088	0	25325357	0	1264664	0	70380	0	21530	0	0	0	2730073	0	4843	0	0	0	54027	0	10871366	0	13755	0	10943991	0	83.86	0	21238710	0	132955	8664596	65.169388138844	25325357.0	22503374.0	321088.0	1264664.0	70380.0	21530.0	0.0	2730073.0	21238710.0	88.9	1.3	5.0	0.3	0.1	0.0	10.8	83.9	100	100	100.00	38	2532535700	22.7	22.4	24.1	24.9	5.9	35.4	19.7	bulk
952399	SRR2443109	SRP063829	SRS1073636	SRX1258025	SRA299328	GEO		RNA sequencing of primary thymic, bone and skin mesenchymal cells	Purpose : Elucidate post-natal role of SCA1+ thymic mesenchymal cells (tMCs) and evaluate the functional overlap between thymic, bone and skin MCs. Method : By high speed cell sorting, we isolated primary MCs (Lin- SCA1+ cells) from mouse thymus, bone and skin. We extracted their respective total RNA and compared their transcriptome by high-throughput RNA-sequencing. Results : We found a total of 2036 differentially expressed genes (FC>5, p-adj<0.1 and RPKM>1) between the 3 MC populations. IPA analyses revealed that each MC population was enriched for genes associated to phagocyte chemotaxis. We also denoted 2850 genes with shared expression across MC populations. IPA analysis of those shared genes also revealed an enrichment for genes influencing phagocyte migration, chemotaxis and function. Finally, MC transcriptomes showed that all 3 MC populations were expressing genes associated with hematopoietic stem and progenitor cell (HSPC) support, strongly suggesting that MCs from thymic, bone and skin all possess the ability to support HSPCs. Conclusion : Overall, our study highlighted 3 potential novel roles for tMCs : 1) Promoting macrophage/monocyte chemotaxis, 2) Enhacing the apoptotic cell clearance process and 3) setting an inviting niche for hematopoietic progenitors. These novel biological roles for tMCs could have substantial effets on thymic biology. Finally, our RNA-seq data offer a valuable resource to the community that can be mined to explore multiple questions related mesenchymal cell biology. Overall design: Transcriptome comparison between MC populations		GSM1888152: Bone_SCA1p_2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			(thymus MCs): Thymi were extracted, mechanically disrupted and enzymatically digested at 37oC for 3x15 minutes using 0.01% (w/v) Liberase TM (Roche) and 0.1% (w/v) DNase I (Sigma-Aldrich). Final digests were harvested, pooled and maintained at 4oC in FACS buffer (PBS, 0.1% (w/v) BSA, 0.02% (w/v) NaN3). Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). (Bone MCs) Femurs, tibias and pelvis were collected, cleaned and washed 3 times in cold PBS. Using sharp surgical scissors, each bone was first cut longitudinally and then transversely to generate tiny fragments of ~1 mm2.  Bone fragments were then washed 3 times in cold PBS and incubated with agitation (80 RPM) for 3x20 minutes at 37oC in the same enzymatic cocktail as above. Following each incubation, supernatants were added to HBSS medium (Invitrogen) supplemented with 2% (v/v) FBS, 10mM HEPES and 1% (v/v) penicillin-streptomycin. To further retrieve endosteal stromal cells, remaining bone fragments were gently crushed in supplemented HBSS medium using a pestle and mortar (5 x 50 gentle taps) and supernatants were pooled to previous ones. Red blood cell lysis was then performed on the resulting cell suspension prior to its filtration and resuspension in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). (Skin MCs) Mouse trunk and dorsal skin (~12 cm2 / mouse) was aseptically dissected and incubated for 45 minutes in 0.01% (w/v) liberase. Dermis was then mechanically isolated and incubated with agitation (80 RPM) at 37oC for 2x30 minutes in the same enzymatic cocktail as above. Post-incubation, supernatants were filtered and pooled to 25 mL of PBS supplemented with 1% FBS and 5mM EDTA. Final cell suspension was then centrifuged and resuspended in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). Transcriptome librairies were generated from total RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina) following the manufacturer’s protocol. Enrichment of RNA-seq stranded libraries with adapter molecules on both ends was done using 15 cycles of PCR amplification using the Illumina PCR mix and primers cocktail. Paired-end (2 x 100 bp) sequencing was peformed using the Illumina HiSeq 2000 running TruSeq v3 chemistry. Three RNA-seq librairies were sequenced per lane (8 lanes per flow cell).	Illumina HiSeq 2000	age;;3 to 4 wks-old|cell type;;Mesenchymal cells (Lin- SCA1+ cells)|source_name;;Bone|strain;;C57BL/6|tissue;;Femur, tibia and pelvis	GEO Accession;;GSM1888152		GSM1888152	Bone_SCA1p_2	5094580000	25472900	2016-02-26 22:54:03	3519467448	5094580000	25472900	2	25472900	index:0,count:25472900,average:100,stdev:0|index:1,count:25472900,average:100,stdev:0	GSM1888152_r2				in_mesa	27183606	3.21	2.83	0.07	3123281472	3118772688	2953919963	2963015091	99.86	100.31	22623906	20800860	173.407	652.901	106	179008	86.55	91.71	24772897	19580872	24772897	19580872	88.39	88.68	24772897	19996343	24772897	18933124	243286728	7.79	1.27	0	5.00	0	0.28	0	0.09	0	0.00	0	10.82	0	22623906	0	200	0	192.01	0	1.52	0	0.01	0	1.22	0	0.00	0	115.64	0	0.20	0	323791	0	25472900	0	1273361	0	71198	0	21793	0	0	0	2756003	0	4602	0	0	0	54688	0	10939841	0	13713	0	11012844	0	83.82	0	21350545	0	132921	8707664	65.510069891138	25472900.0	22623906.0	323791.0	1273361.0	71198.0	21793.0	0.0	2756003.0	21350545.0	88.8	1.3	5.0	0.3	0.1	0.0	10.8	83.8	100	100	100.00	38	2547290000	22.6	22.4	24.1	24.9	5.9	35.4	19.9	bulk
952455	SRR2443110	SRP063829	SRS1073636	SRX1258025	SRA299328	GEO		RNA sequencing of primary thymic, bone and skin mesenchymal cells	Purpose : Elucidate post-natal role of SCA1+ thymic mesenchymal cells (tMCs) and evaluate the functional overlap between thymic, bone and skin MCs. Method : By high speed cell sorting, we isolated primary MCs (Lin- SCA1+ cells) from mouse thymus, bone and skin. We extracted their respective total RNA and compared their transcriptome by high-throughput RNA-sequencing. Results : We found a total of 2036 differentially expressed genes (FC>5, p-adj<0.1 and RPKM>1) between the 3 MC populations. IPA analyses revealed that each MC population was enriched for genes associated to phagocyte chemotaxis. We also denoted 2850 genes with shared expression across MC populations. IPA analysis of those shared genes also revealed an enrichment for genes influencing phagocyte migration, chemotaxis and function. Finally, MC transcriptomes showed that all 3 MC populations were expressing genes associated with hematopoietic stem and progenitor cell (HSPC) support, strongly suggesting that MCs from thymic, bone and skin all possess the ability to support HSPCs. Conclusion : Overall, our study highlighted 3 potential novel roles for tMCs : 1) Promoting macrophage/monocyte chemotaxis, 2) Enhacing the apoptotic cell clearance process and 3) setting an inviting niche for hematopoietic progenitors. These novel biological roles for tMCs could have substantial effets on thymic biology. Finally, our RNA-seq data offer a valuable resource to the community that can be mined to explore multiple questions related mesenchymal cell biology. Overall design: Transcriptome comparison between MC populations		GSM1888152: Bone_SCA1p_2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			(thymus MCs): Thymi were extracted, mechanically disrupted and enzymatically digested at 37oC for 3x15 minutes using 0.01% (w/v) Liberase TM (Roche) and 0.1% (w/v) DNase I (Sigma-Aldrich). Final digests were harvested, pooled and maintained at 4oC in FACS buffer (PBS, 0.1% (w/v) BSA, 0.02% (w/v) NaN3). Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). (Bone MCs) Femurs, tibias and pelvis were collected, cleaned and washed 3 times in cold PBS. Using sharp surgical scissors, each bone was first cut longitudinally and then transversely to generate tiny fragments of ~1 mm2.  Bone fragments were then washed 3 times in cold PBS and incubated with agitation (80 RPM) for 3x20 minutes at 37oC in the same enzymatic cocktail as above. Following each incubation, supernatants were added to HBSS medium (Invitrogen) supplemented with 2% (v/v) FBS, 10mM HEPES and 1% (v/v) penicillin-streptomycin. To further retrieve endosteal stromal cells, remaining bone fragments were gently crushed in supplemented HBSS medium using a pestle and mortar (5 x 50 gentle taps) and supernatants were pooled to previous ones. Red blood cell lysis was then performed on the resulting cell suspension prior to its filtration and resuspension in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). (Skin MCs) Mouse trunk and dorsal skin (~12 cm2 / mouse) was aseptically dissected and incubated for 45 minutes in 0.01% (w/v) liberase. Dermis was then mechanically isolated and incubated with agitation (80 RPM) at 37oC for 2x30 minutes in the same enzymatic cocktail as above. Post-incubation, supernatants were filtered and pooled to 25 mL of PBS supplemented with 1% FBS and 5mM EDTA. Final cell suspension was then centrifuged and resuspended in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). Transcriptome librairies were generated from total RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina) following the manufacturer’s protocol. Enrichment of RNA-seq stranded libraries with adapter molecules on both ends was done using 15 cycles of PCR amplification using the Illumina PCR mix and primers cocktail. Paired-end (2 x 100 bp) sequencing was peformed using the Illumina HiSeq 2000 running TruSeq v3 chemistry. Three RNA-seq librairies were sequenced per lane (8 lanes per flow cell).	Illumina HiSeq 2000	age;;3 to 4 wks-old|cell type;;Mesenchymal cells (Lin- SCA1+ cells)|source_name;;Bone|strain;;C57BL/6|tissue;;Femur, tibia and pelvis	GEO Accession;;GSM1888152		GSM1888152	Bone_SCA1p_2	5118917000	25594585	2016-02-26 22:54:03	3516895786	5118917000	25594585	2	25594585	index:0,count:25594585,average:100,stdev:0|index:1,count:25594585,average:100,stdev:0	GSM1888152_r3				in_mesa	27183606	3.2	2.83	0.07	3145113224	3140963281	2974890027	2984340450	99.87	100.32	22760185	20921410	173.609	652.276	116	179485	86.57	91.72	24914528	19703398	24914528	19703398	88.39	88.68	24914528	20118125	24914528	19049421	244698186	7.78	1.27	0	5.00	0	0.28	0	0.09	0	0.00	0	10.71	0	22760185	0	200	0	192.03	0	1.51	0	0.01	0	1.22	0	0.00	0	253.13	0	0.20	0	324478	0	25594585	0	1278720	0	71222	0	21917	0	0	0	2741261	0	4720	0	0	0	55318	0	11011113	0	13904	0	11085055	0	83.93	0	21481465	0	133048	8770057	65.916488786002	25594585.0	22760185.0	324478.0	1278720.0	71222.0	21917.0	0.0	2741261.0	21481465.0	88.9	1.3	5.0	0.3	0.1	0.0	10.7	83.9	100	100	100.00	38	2559458500	22.6	22.4	24.1	24.9	5.9	35.5	20.1	bulk
952623	SRR2443125	SRP063829	SRS1073637	SRX1258029	SRA299328	GEO		RNA sequencing of primary thymic, bone and skin mesenchymal cells	Purpose : Elucidate post-natal role of SCA1+ thymic mesenchymal cells (tMCs) and evaluate the functional overlap between thymic, bone and skin MCs. Method : By high speed cell sorting, we isolated primary MCs (Lin- SCA1+ cells) from mouse thymus, bone and skin. We extracted their respective total RNA and compared their transcriptome by high-throughput RNA-sequencing. Results : We found a total of 2036 differentially expressed genes (FC>5, p-adj<0.1 and RPKM>1) between the 3 MC populations. IPA analyses revealed that each MC population was enriched for genes associated to phagocyte chemotaxis. We also denoted 2850 genes with shared expression across MC populations. IPA analysis of those shared genes also revealed an enrichment for genes influencing phagocyte migration, chemotaxis and function. Finally, MC transcriptomes showed that all 3 MC populations were expressing genes associated with hematopoietic stem and progenitor cell (HSPC) support, strongly suggesting that MCs from thymic, bone and skin all possess the ability to support HSPCs. Conclusion : Overall, our study highlighted 3 potential novel roles for tMCs : 1) Promoting macrophage/monocyte chemotaxis, 2) Enhacing the apoptotic cell clearance process and 3) setting an inviting niche for hematopoietic progenitors. These novel biological roles for tMCs could have substantial effets on thymic biology. Finally, our RNA-seq data offer a valuable resource to the community that can be mined to explore multiple questions related mesenchymal cell biology. Overall design: Transcriptome comparison between MC populations		GSM1888156: Skin_SCA1p_3; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			(thymus MCs): Thymi were extracted, mechanically disrupted and enzymatically digested at 37oC for 3x15 minutes using 0.01% (w/v) Liberase TM (Roche) and 0.1% (w/v) DNase I (Sigma-Aldrich). Final digests were harvested, pooled and maintained at 4oC in FACS buffer (PBS, 0.1% (w/v) BSA, 0.02% (w/v) NaN3). Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). (Bone MCs) Femurs, tibias and pelvis were collected, cleaned and washed 3 times in cold PBS. Using sharp surgical scissors, each bone was first cut longitudinally and then transversely to generate tiny fragments of ~1 mm2.  Bone fragments were then washed 3 times in cold PBS and incubated with agitation (80 RPM) for 3x20 minutes at 37oC in the same enzymatic cocktail as above. Following each incubation, supernatants were added to HBSS medium (Invitrogen) supplemented with 2% (v/v) FBS, 10mM HEPES and 1% (v/v) penicillin-streptomycin. To further retrieve endosteal stromal cells, remaining bone fragments were gently crushed in supplemented HBSS medium using a pestle and mortar (5 x 50 gentle taps) and supernatants were pooled to previous ones. Red blood cell lysis was then performed on the resulting cell suspension prior to its filtration and resuspension in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). (Skin MCs) Mouse trunk and dorsal skin (~12 cm2 / mouse) was aseptically dissected and incubated for 45 minutes in 0.01% (w/v) liberase. Dermis was then mechanically isolated and incubated with agitation (80 RPM) at 37oC for 2x30 minutes in the same enzymatic cocktail as above. Post-incubation, supernatants were filtered and pooled to 25 mL of PBS supplemented with 1% FBS and 5mM EDTA. Final cell suspension was then centrifuged and resuspended in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). Transcriptome librairies were generated from total RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina) following the manufacturer’s protocol. Enrichment of RNA-seq stranded libraries with adapter molecules on both ends was done using 15 cycles of PCR amplification using the Illumina PCR mix and primers cocktail. Paired-end (2 x 100 bp) sequencing was peformed using the Illumina HiSeq 2000 running TruSeq v3 chemistry. Three RNA-seq librairies were sequenced per lane (8 lanes per flow cell).	Illumina HiSeq 2000	age;;3 to 4 wks-old|cell type;;Mesenchymal cells (Lin- SCA1+ cells)|source_name;;Skin|strain;;C57BL/6|tissue;;abdominal and back dermis (truncal skin)	GEO Accession;;GSM1888156		GSM1888156	Skin_SCA1p_3	5092070600	25460353	2016-02-26 22:54:03	3295331522	5092070600	25460353	2	25460353	index:0,count:25460353,average:100,stdev:0|index:1,count:25460353,average:100,stdev:0	GSM1888156_r4				in_mesa	27183606	2.28	2.06	0.04	3463916864	3477942914	3291387833	3316090625	100.4	100.75	23555678	21589816	190.518	610.164	127	198009	93.15	98.22	25636774	21941521	25636774	21941521	94.99	95.53	25636774	22375536	25636774	21340711	51829070	1.50	0.92	0	4.78	0	0.24	0	0.03	0	0.00	0	7.22	0	23555678	0	200	0	195.07	0	1.52	0	0.00	0	1.22	0	0.00	0	277.75	0	0.16	0	234504	0	25460353	0	1216238	0	60486	0	6836	0	0	0	1837353	0	4504	0	0	0	48682	0	14645132	0	12578	0	14710896	0	87.74	0	22339440	0	137186	12131803	88.433243917018	25460353.0	23555678.0	234504.0	1216238.0	60486.0	6836.0	0.0	1837353.0	22339440.0	92.5	0.9	4.8	0.2	0.0	0.0	7.2	87.7	100	100	100.00	38	2546035300	22.3	24.1	26.2	25.0	2.4	36.2	22.1	bulk
952631	SRR2443126	SRP063829	SRS1073637	SRX1258029	SRA299328	GEO		RNA sequencing of primary thymic, bone and skin mesenchymal cells	Purpose : Elucidate post-natal role of SCA1+ thymic mesenchymal cells (tMCs) and evaluate the functional overlap between thymic, bone and skin MCs. Method : By high speed cell sorting, we isolated primary MCs (Lin- SCA1+ cells) from mouse thymus, bone and skin. We extracted their respective total RNA and compared their transcriptome by high-throughput RNA-sequencing. Results : We found a total of 2036 differentially expressed genes (FC>5, p-adj<0.1 and RPKM>1) between the 3 MC populations. IPA analyses revealed that each MC population was enriched for genes associated to phagocyte chemotaxis. We also denoted 2850 genes with shared expression across MC populations. IPA analysis of those shared genes also revealed an enrichment for genes influencing phagocyte migration, chemotaxis and function. Finally, MC transcriptomes showed that all 3 MC populations were expressing genes associated with hematopoietic stem and progenitor cell (HSPC) support, strongly suggesting that MCs from thymic, bone and skin all possess the ability to support HSPCs. Conclusion : Overall, our study highlighted 3 potential novel roles for tMCs : 1) Promoting macrophage/monocyte chemotaxis, 2) Enhacing the apoptotic cell clearance process and 3) setting an inviting niche for hematopoietic progenitors. These novel biological roles for tMCs could have substantial effets on thymic biology. Finally, our RNA-seq data offer a valuable resource to the community that can be mined to explore multiple questions related mesenchymal cell biology. Overall design: Transcriptome comparison between MC populations		GSM1888156: Skin_SCA1p_3; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			(thymus MCs): Thymi were extracted, mechanically disrupted and enzymatically digested at 37oC for 3x15 minutes using 0.01% (w/v) Liberase TM (Roche) and 0.1% (w/v) DNase I (Sigma-Aldrich). Final digests were harvested, pooled and maintained at 4oC in FACS buffer (PBS, 0.1% (w/v) BSA, 0.02% (w/v) NaN3). Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). (Bone MCs) Femurs, tibias and pelvis were collected, cleaned and washed 3 times in cold PBS. Using sharp surgical scissors, each bone was first cut longitudinally and then transversely to generate tiny fragments of ~1 mm2.  Bone fragments were then washed 3 times in cold PBS and incubated with agitation (80 RPM) for 3x20 minutes at 37oC in the same enzymatic cocktail as above. Following each incubation, supernatants were added to HBSS medium (Invitrogen) supplemented with 2% (v/v) FBS, 10mM HEPES and 1% (v/v) penicillin-streptomycin. To further retrieve endosteal stromal cells, remaining bone fragments were gently crushed in supplemented HBSS medium using a pestle and mortar (5 x 50 gentle taps) and supernatants were pooled to previous ones. Red blood cell lysis was then performed on the resulting cell suspension prior to its filtration and resuspension in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). (Skin MCs) Mouse trunk and dorsal skin (~12 cm2 / mouse) was aseptically dissected and incubated for 45 minutes in 0.01% (w/v) liberase. Dermis was then mechanically isolated and incubated with agitation (80 RPM) at 37oC for 2x30 minutes in the same enzymatic cocktail as above. Post-incubation, supernatants were filtered and pooled to 25 mL of PBS supplemented with 1% FBS and 5mM EDTA. Final cell suspension was then centrifuged and resuspended in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). Transcriptome librairies were generated from total RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina) following the manufacturer’s protocol. Enrichment of RNA-seq stranded libraries with adapter molecules on both ends was done using 15 cycles of PCR amplification using the Illumina PCR mix and primers cocktail. Paired-end (2 x 100 bp) sequencing was peformed using the Illumina HiSeq 2000 running TruSeq v3 chemistry. Three RNA-seq librairies were sequenced per lane (8 lanes per flow cell).	Illumina HiSeq 2000	age;;3 to 4 wks-old|cell type;;Mesenchymal cells (Lin- SCA1+ cells)|source_name;;Skin|strain;;C57BL/6|tissue;;abdominal and back dermis (truncal skin)	GEO Accession;;GSM1888156		GSM1888156	Skin_SCA1p_3	6885948200	34429741	2016-02-26 22:54:03	4392327813	6885948200	34429741	2	34429741	index:0,count:34429741,average:100,stdev:0|index:1,count:34429741,average:100,stdev:0	GSM1888156_r5				in_mesa	27183606	2.28	2.06	0.04	4686525946	4705622277	4452877617	4486375521	100.41	100.75	31879304	29215856	190.550	610.858	127	267352	93.14	98.22	34698203	29693334	34698203	29693334	94.99	95.53	34698203	30283044	34698203	28881348	70209509	1.50	0.92	0	4.79	0	0.24	0	0.02	0	0.00	0	7.15	0	31879304	0	200	0	195.07	0	1.51	0	0.00	0	1.23	0	0.00	0	150.79	0	0.14	0	318383	0	34429741	0	1647597	0	81896	0	8128	0	0	0	2460413	0	5955	0	0	0	65879	0	19862222	0	17281	0	19951337	0	87.81	0	30231707	0	141393	16449958	116.342096143373	34429741.0	31879304.0	318383.0	1647597.0	81896.0	8128.0	0.0	2460413.0	30231707.0	92.6	0.9	4.8	0.2	0.0	0.0	7.1	87.8	100	100	100.00	38	3442974100	22.3	24.1	26.2	25.0	2.4	36.4	22.8	bulk
952639	SRR2443127	SRP063829	SRS1073633	SRX1258030	SRA299328	GEO		RNA sequencing of primary thymic, bone and skin mesenchymal cells	Purpose : Elucidate post-natal role of SCA1+ thymic mesenchymal cells (tMCs) and evaluate the functional overlap between thymic, bone and skin MCs. Method : By high speed cell sorting, we isolated primary MCs (Lin- SCA1+ cells) from mouse thymus, bone and skin. We extracted their respective total RNA and compared their transcriptome by high-throughput RNA-sequencing. Results : We found a total of 2036 differentially expressed genes (FC>5, p-adj<0.1 and RPKM>1) between the 3 MC populations. IPA analyses revealed that each MC population was enriched for genes associated to phagocyte chemotaxis. We also denoted 2850 genes with shared expression across MC populations. IPA analysis of those shared genes also revealed an enrichment for genes influencing phagocyte migration, chemotaxis and function. Finally, MC transcriptomes showed that all 3 MC populations were expressing genes associated with hematopoietic stem and progenitor cell (HSPC) support, strongly suggesting that MCs from thymic, bone and skin all possess the ability to support HSPCs. Conclusion : Overall, our study highlighted 3 potential novel roles for tMCs : 1) Promoting macrophage/monocyte chemotaxis, 2) Enhacing the apoptotic cell clearance process and 3) setting an inviting niche for hematopoietic progenitors. These novel biological roles for tMCs could have substantial effets on thymic biology. Finally, our RNA-seq data offer a valuable resource to the community that can be mined to explore multiple questions related mesenchymal cell biology. Overall design: Transcriptome comparison between MC populations		GSM1888157: Thymus_SCA1p_2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			(thymus MCs): Thymi were extracted, mechanically disrupted and enzymatically digested at 37oC for 3x15 minutes using 0.01% (w/v) Liberase TM (Roche) and 0.1% (w/v) DNase I (Sigma-Aldrich). Final digests were harvested, pooled and maintained at 4oC in FACS buffer (PBS, 0.1% (w/v) BSA, 0.02% (w/v) NaN3). Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). (Bone MCs) Femurs, tibias and pelvis were collected, cleaned and washed 3 times in cold PBS. Using sharp surgical scissors, each bone was first cut longitudinally and then transversely to generate tiny fragments of ~1 mm2.  Bone fragments were then washed 3 times in cold PBS and incubated with agitation (80 RPM) for 3x20 minutes at 37oC in the same enzymatic cocktail as above. Following each incubation, supernatants were added to HBSS medium (Invitrogen) supplemented with 2% (v/v) FBS, 10mM HEPES and 1% (v/v) penicillin-streptomycin. To further retrieve endosteal stromal cells, remaining bone fragments were gently crushed in supplemented HBSS medium using a pestle and mortar (5 x 50 gentle taps) and supernatants were pooled to previous ones. Red blood cell lysis was then performed on the resulting cell suspension prior to its filtration and resuspension in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). (Skin MCs) Mouse trunk and dorsal skin (~12 cm2 / mouse) was aseptically dissected and incubated for 45 minutes in 0.01% (w/v) liberase. Dermis was then mechanically isolated and incubated with agitation (80 RPM) at 37oC for 2x30 minutes in the same enzymatic cocktail as above. Post-incubation, supernatants were filtered and pooled to 25 mL of PBS supplemented with 1% FBS and 5mM EDTA. Final cell suspension was then centrifuged and resuspended in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). Transcriptome librairies were generated from total RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina) following the manufacturer’s protocol. Enrichment of RNA-seq stranded libraries with adapter molecules on both ends was done using 15 cycles of PCR amplification using the Illumina PCR mix and primers cocktail. Paired-end (2 x 100 bp) sequencing was peformed using the Illumina HiSeq 2000 running TruSeq v3 chemistry. Three RNA-seq librairies were sequenced per lane (8 lanes per flow cell).	Illumina HiSeq 2000	age;;3 to 4 wks-old|cell type;;Mesenchymal cells (Lin- SCA1+ cells)|source_name;;Thymus|strain;;C57BL/6|tissue;;Thymus	GEO Accession;;GSM1888157		GSM1888157	Thymus_SCA1p_2	5511880600	27559403	2016-02-26 22:54:03	3833609487	5511880600	27559403	2	27559403	index:0,count:27559403,average:100,stdev:0|index:1,count:27559403,average:100,stdev:0	GSM1888157_r1				in_mesa	27183606	2.09	3.17	0.06	3160674715	3162229446	3012217705	3026493483	100.05	100.47	23611366	21375847	171.214	775.791	105	191080	89.64	94.29	25657063	21165716	25657063	21165716	90.63	91.13	25657063	21398438	25657063	20456886	165765233	5.24	1.15	0	4.22	0	0.24	0	0.05	0	0.00	0	14.04	0	23611366	0	200	0	190.45	0	1.52	0	0.01	0	1.17	0	0.00	0	311.02	0	0.21	0	317068	0	27559403	0	1162878	0	65207	0	14703	0	0	0	3868127	0	5203	0	0	0	82283	0	12660039	0	13778	0	12761303	0	81.45	0	22448488	0	129343	9781337	75.623242077267	27559403.0	23611366.0	317068.0	1162878.0	65207.0	14703.0	0.0	3868127.0	22448488.0	85.7	1.2	4.2	0.2	0.1	0.0	14.0	81.5	100	100	100.00	38	2755940300	22.1	22.6	23.5	24.1	7.8	35.3	19.8	bulk
952646	SRR2443128	SRP063829	SRS1073633	SRX1258030	SRA299328	GEO		RNA sequencing of primary thymic, bone and skin mesenchymal cells	Purpose : Elucidate post-natal role of SCA1+ thymic mesenchymal cells (tMCs) and evaluate the functional overlap between thymic, bone and skin MCs. Method : By high speed cell sorting, we isolated primary MCs (Lin- SCA1+ cells) from mouse thymus, bone and skin. We extracted their respective total RNA and compared their transcriptome by high-throughput RNA-sequencing. Results : We found a total of 2036 differentially expressed genes (FC>5, p-adj<0.1 and RPKM>1) between the 3 MC populations. IPA analyses revealed that each MC population was enriched for genes associated to phagocyte chemotaxis. We also denoted 2850 genes with shared expression across MC populations. IPA analysis of those shared genes also revealed an enrichment for genes influencing phagocyte migration, chemotaxis and function. Finally, MC transcriptomes showed that all 3 MC populations were expressing genes associated with hematopoietic stem and progenitor cell (HSPC) support, strongly suggesting that MCs from thymic, bone and skin all possess the ability to support HSPCs. Conclusion : Overall, our study highlighted 3 potential novel roles for tMCs : 1) Promoting macrophage/monocyte chemotaxis, 2) Enhacing the apoptotic cell clearance process and 3) setting an inviting niche for hematopoietic progenitors. These novel biological roles for tMCs could have substantial effets on thymic biology. Finally, our RNA-seq data offer a valuable resource to the community that can be mined to explore multiple questions related mesenchymal cell biology. Overall design: Transcriptome comparison between MC populations		GSM1888157: Thymus_SCA1p_2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			(thymus MCs): Thymi were extracted, mechanically disrupted and enzymatically digested at 37oC for 3x15 minutes using 0.01% (w/v) Liberase TM (Roche) and 0.1% (w/v) DNase I (Sigma-Aldrich). Final digests were harvested, pooled and maintained at 4oC in FACS buffer (PBS, 0.1% (w/v) BSA, 0.02% (w/v) NaN3). Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). (Bone MCs) Femurs, tibias and pelvis were collected, cleaned and washed 3 times in cold PBS. Using sharp surgical scissors, each bone was first cut longitudinally and then transversely to generate tiny fragments of ~1 mm2.  Bone fragments were then washed 3 times in cold PBS and incubated with agitation (80 RPM) for 3x20 minutes at 37oC in the same enzymatic cocktail as above. Following each incubation, supernatants were added to HBSS medium (Invitrogen) supplemented with 2% (v/v) FBS, 10mM HEPES and 1% (v/v) penicillin-streptomycin. To further retrieve endosteal stromal cells, remaining bone fragments were gently crushed in supplemented HBSS medium using a pestle and mortar (5 x 50 gentle taps) and supernatants were pooled to previous ones. Red blood cell lysis was then performed on the resulting cell suspension prior to its filtration and resuspension in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). (Skin MCs) Mouse trunk and dorsal skin (~12 cm2 / mouse) was aseptically dissected and incubated for 45 minutes in 0.01% (w/v) liberase. Dermis was then mechanically isolated and incubated with agitation (80 RPM) at 37oC for 2x30 minutes in the same enzymatic cocktail as above. Post-incubation, supernatants were filtered and pooled to 25 mL of PBS supplemented with 1% FBS and 5mM EDTA. Final cell suspension was then centrifuged and resuspended in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). Transcriptome librairies were generated from total RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina) following the manufacturer’s protocol. Enrichment of RNA-seq stranded libraries with adapter molecules on both ends was done using 15 cycles of PCR amplification using the Illumina PCR mix and primers cocktail. Paired-end (2 x 100 bp) sequencing was peformed using the Illumina HiSeq 2000 running TruSeq v3 chemistry. Three RNA-seq librairies were sequenced per lane (8 lanes per flow cell).	Illumina HiSeq 2000	age;;3 to 4 wks-old|cell type;;Mesenchymal cells (Lin- SCA1+ cells)|source_name;;Thymus|strain;;C57BL/6|tissue;;Thymus	GEO Accession;;GSM1888157		GSM1888157	Thymus_SCA1p_2	5566826400	27834132	2016-02-26 22:54:03	3866518143	5566826400	27834132	2	27834132	index:0,count:27834132,average:100,stdev:0|index:1,count:27834132,average:100,stdev:0	GSM1888157_r2				in_mesa	27183606	2.09	3.17	0.06	3186679038	3188198053	3036750012	3051212668	100.05	100.48	23826522	21570708	171.008	776.199	105	193802	89.63	94.28	25895494	21356710	25895494	21356710	90.62	91.12	25895494	21590475	25895494	20639461	167285963	5.25	1.15	0	4.22	0	0.24	0	0.05	0	0.00	0	14.11	0	23826522	0	200	0	190.44	0	1.52	0	0.01	0	1.17	0	0.00	0	310.23	0	0.20	0	321012	0	27834132	0	1175175	0	66096	0	15116	0	0	0	3926398	0	5390	0	0	0	83098	0	12780168	0	13951	0	12882607	0	81.38	0	22651347	0	129303	9864557	76.290240752341	27834132.0	23826522.0	321012.0	1175175.0	66096.0	15116.0	0.0	3926398.0	22651347.0	85.6	1.2	4.2	0.2	0.1	0.0	14.1	81.4	100	100	100.00	38	2783413200	22.1	22.6	23.4	24.0	7.8	35.4	20.0	bulk
952654	SRR2443129	SRP063829	SRS1073633	SRX1258030	SRA299328	GEO		RNA sequencing of primary thymic, bone and skin mesenchymal cells	Purpose : Elucidate post-natal role of SCA1+ thymic mesenchymal cells (tMCs) and evaluate the functional overlap between thymic, bone and skin MCs. Method : By high speed cell sorting, we isolated primary MCs (Lin- SCA1+ cells) from mouse thymus, bone and skin. We extracted their respective total RNA and compared their transcriptome by high-throughput RNA-sequencing. Results : We found a total of 2036 differentially expressed genes (FC>5, p-adj<0.1 and RPKM>1) between the 3 MC populations. IPA analyses revealed that each MC population was enriched for genes associated to phagocyte chemotaxis. We also denoted 2850 genes with shared expression across MC populations. IPA analysis of those shared genes also revealed an enrichment for genes influencing phagocyte migration, chemotaxis and function. Finally, MC transcriptomes showed that all 3 MC populations were expressing genes associated with hematopoietic stem and progenitor cell (HSPC) support, strongly suggesting that MCs from thymic, bone and skin all possess the ability to support HSPCs. Conclusion : Overall, our study highlighted 3 potential novel roles for tMCs : 1) Promoting macrophage/monocyte chemotaxis, 2) Enhacing the apoptotic cell clearance process and 3) setting an inviting niche for hematopoietic progenitors. These novel biological roles for tMCs could have substantial effets on thymic biology. Finally, our RNA-seq data offer a valuable resource to the community that can be mined to explore multiple questions related mesenchymal cell biology. Overall design: Transcriptome comparison between MC populations		GSM1888157: Thymus_SCA1p_2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			(thymus MCs): Thymi were extracted, mechanically disrupted and enzymatically digested at 37oC for 3x15 minutes using 0.01% (w/v) Liberase TM (Roche) and 0.1% (w/v) DNase I (Sigma-Aldrich). Final digests were harvested, pooled and maintained at 4oC in FACS buffer (PBS, 0.1% (w/v) BSA, 0.02% (w/v) NaN3). Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). (Bone MCs) Femurs, tibias and pelvis were collected, cleaned and washed 3 times in cold PBS. Using sharp surgical scissors, each bone was first cut longitudinally and then transversely to generate tiny fragments of ~1 mm2.  Bone fragments were then washed 3 times in cold PBS and incubated with agitation (80 RPM) for 3x20 minutes at 37oC in the same enzymatic cocktail as above. Following each incubation, supernatants were added to HBSS medium (Invitrogen) supplemented with 2% (v/v) FBS, 10mM HEPES and 1% (v/v) penicillin-streptomycin. To further retrieve endosteal stromal cells, remaining bone fragments were gently crushed in supplemented HBSS medium using a pestle and mortar (5 x 50 gentle taps) and supernatants were pooled to previous ones. Red blood cell lysis was then performed on the resulting cell suspension prior to its filtration and resuspension in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). (Skin MCs) Mouse trunk and dorsal skin (~12 cm2 / mouse) was aseptically dissected and incubated for 45 minutes in 0.01% (w/v) liberase. Dermis was then mechanically isolated and incubated with agitation (80 RPM) at 37oC for 2x30 minutes in the same enzymatic cocktail as above. Post-incubation, supernatants were filtered and pooled to 25 mL of PBS supplemented with 1% FBS and 5mM EDTA. Final cell suspension was then centrifuged and resuspended in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). Transcriptome librairies were generated from total RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina) following the manufacturer’s protocol. Enrichment of RNA-seq stranded libraries with adapter molecules on both ends was done using 15 cycles of PCR amplification using the Illumina PCR mix and primers cocktail. Paired-end (2 x 100 bp) sequencing was peformed using the Illumina HiSeq 2000 running TruSeq v3 chemistry. Three RNA-seq librairies were sequenced per lane (8 lanes per flow cell).	Illumina HiSeq 2000	age;;3 to 4 wks-old|cell type;;Mesenchymal cells (Lin- SCA1+ cells)|source_name;;Thymus|strain;;C57BL/6|tissue;;Thymus	GEO Accession;;GSM1888157		GSM1888157	Thymus_SCA1p_2	5616852800	28084264	2016-02-26 22:54:03	3878967566	5616852800	28084264	2	28084264	index:0,count:28084264,average:100,stdev:0|index:1,count:28084264,average:100,stdev:0	GSM1888157_r3				in_mesa	27183606	2.08	3.17	0.06	3224045645	3225864767	3072681942	3087563738	100.06	100.48	24080789	21797655	171.244	774.686	105	195379	89.64	94.28	26168144	21585679	26168144	21585679	90.62	91.12	26168144	21820935	26168144	20861492	169380942	5.25	1.15	0	4.22	0	0.24	0	0.05	0	0.00	0	13.96	0	24080789	0	200	0	190.47	0	1.52	0	0.01	0	1.17	0	0.00	0	346.24	0	0.20	0	322119	0	28084264	0	1185515	0	66347	0	15416	0	0	0	3921712	0	5336	0	0	0	83945	0	12928994	0	14008	0	13032283	0	81.52	0	22895274	0	129505	9989680	77.137407822092	28084264.0	24080789.0	322119.0	1185515.0	66347.0	15416.0	0.0	3921712.0	22895274.0	85.7	1.1	4.2	0.2	0.1	0.0	14.0	81.5	100	100	100.00	38	2808426400	22.1	22.6	23.5	24.0	7.8	35.5	20.2	bulk
952710	SRR2443130	SRP063829	SRS1073632	SRX1258031	SRA299328	GEO		RNA sequencing of primary thymic, bone and skin mesenchymal cells	Purpose : Elucidate post-natal role of SCA1+ thymic mesenchymal cells (tMCs) and evaluate the functional overlap between thymic, bone and skin MCs. Method : By high speed cell sorting, we isolated primary MCs (Lin- SCA1+ cells) from mouse thymus, bone and skin. We extracted their respective total RNA and compared their transcriptome by high-throughput RNA-sequencing. Results : We found a total of 2036 differentially expressed genes (FC>5, p-adj<0.1 and RPKM>1) between the 3 MC populations. IPA analyses revealed that each MC population was enriched for genes associated to phagocyte chemotaxis. We also denoted 2850 genes with shared expression across MC populations. IPA analysis of those shared genes also revealed an enrichment for genes influencing phagocyte migration, chemotaxis and function. Finally, MC transcriptomes showed that all 3 MC populations were expressing genes associated with hematopoietic stem and progenitor cell (HSPC) support, strongly suggesting that MCs from thymic, bone and skin all possess the ability to support HSPCs. Conclusion : Overall, our study highlighted 3 potential novel roles for tMCs : 1) Promoting macrophage/monocyte chemotaxis, 2) Enhacing the apoptotic cell clearance process and 3) setting an inviting niche for hematopoietic progenitors. These novel biological roles for tMCs could have substantial effets on thymic biology. Finally, our RNA-seq data offer a valuable resource to the community that can be mined to explore multiple questions related mesenchymal cell biology. Overall design: Transcriptome comparison between MC populations		GSM1888158: Thymus_SCA1p_3; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			(thymus MCs): Thymi were extracted, mechanically disrupted and enzymatically digested at 37oC for 3x15 minutes using 0.01% (w/v) Liberase TM (Roche) and 0.1% (w/v) DNase I (Sigma-Aldrich). Final digests were harvested, pooled and maintained at 4oC in FACS buffer (PBS, 0.1% (w/v) BSA, 0.02% (w/v) NaN3). Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). (Bone MCs) Femurs, tibias and pelvis were collected, cleaned and washed 3 times in cold PBS. Using sharp surgical scissors, each bone was first cut longitudinally and then transversely to generate tiny fragments of ~1 mm2.  Bone fragments were then washed 3 times in cold PBS and incubated with agitation (80 RPM) for 3x20 minutes at 37oC in the same enzymatic cocktail as above. Following each incubation, supernatants were added to HBSS medium (Invitrogen) supplemented with 2% (v/v) FBS, 10mM HEPES and 1% (v/v) penicillin-streptomycin. To further retrieve endosteal stromal cells, remaining bone fragments were gently crushed in supplemented HBSS medium using a pestle and mortar (5 x 50 gentle taps) and supernatants were pooled to previous ones. Red blood cell lysis was then performed on the resulting cell suspension prior to its filtration and resuspension in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). (Skin MCs) Mouse trunk and dorsal skin (~12 cm2 / mouse) was aseptically dissected and incubated for 45 minutes in 0.01% (w/v) liberase. Dermis was then mechanically isolated and incubated with agitation (80 RPM) at 37oC for 2x30 minutes in the same enzymatic cocktail as above. Post-incubation, supernatants were filtered and pooled to 25 mL of PBS supplemented with 1% FBS and 5mM EDTA. Final cell suspension was then centrifuged and resuspended in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). Transcriptome librairies were generated from total RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina) following the manufacturer’s protocol. Enrichment of RNA-seq stranded libraries with adapter molecules on both ends was done using 15 cycles of PCR amplification using the Illumina PCR mix and primers cocktail. Paired-end (2 x 100 bp) sequencing was peformed using the Illumina HiSeq 2000 running TruSeq v3 chemistry. Three RNA-seq librairies were sequenced per lane (8 lanes per flow cell).	Illumina HiSeq 2000	age;;3 to 4 wks-old|cell type;;Mesenchymal cells (Lin- SCA1+ cells)|source_name;;Thymus|strain;;C57BL/6|tissue;;Thymus	GEO Accession;;GSM1888158		GSM1888158	Thymus_SCA1p_3	5249543200	26247716	2016-02-26 22:54:03	3624206425	5249543200	26247716	2	26247716	index:0,count:26247716,average:100,stdev:0|index:1,count:26247716,average:100,stdev:0	GSM1888158_r1				in_mesa	27183606	2.56	3.14	0.06	3138474454	3136294223	2975246413	2987617020	99.93	100.42	22975560	20827056	173.584	747.961	106	179209	89.76	94.92	25150840	20622020	25150840	20622020	91.22	91.77	25150840	20959177	25150840	19939046	141575339	4.51	1.25	0	4.76	0	0.26	0	0.06	0	0.00	0	12.15	0	22975560	0	200	0	191.28	0	1.52	0	0.01	0	1.20	0	0.00	0	306.79	0	0.20	0	327150	0	26247716	0	1249511	0	68159	0	15651	0	0	0	3188346	0	5222	0	0	0	78328	0	12286016	0	13277	0	12382843	0	82.77	0	21726049	0	147665	9665351	65.454583008838	26247716.0	22975560.0	327150.0	1249511.0	68159.0	15651.0	0.0	3188346.0	21726049.0	87.5	1.2	4.8	0.3	0.1	0.0	12.1	82.8	100	100	100.00	38	2624771600	22.3	22.8	23.5	24.6	6.8	35.5	20.1	bulk
952719	SRR2443131	SRP063829	SRS1073632	SRX1258031	SRA299328	GEO		RNA sequencing of primary thymic, bone and skin mesenchymal cells	Purpose : Elucidate post-natal role of SCA1+ thymic mesenchymal cells (tMCs) and evaluate the functional overlap between thymic, bone and skin MCs. Method : By high speed cell sorting, we isolated primary MCs (Lin- SCA1+ cells) from mouse thymus, bone and skin. We extracted their respective total RNA and compared their transcriptome by high-throughput RNA-sequencing. Results : We found a total of 2036 differentially expressed genes (FC>5, p-adj<0.1 and RPKM>1) between the 3 MC populations. IPA analyses revealed that each MC population was enriched for genes associated to phagocyte chemotaxis. We also denoted 2850 genes with shared expression across MC populations. IPA analysis of those shared genes also revealed an enrichment for genes influencing phagocyte migration, chemotaxis and function. Finally, MC transcriptomes showed that all 3 MC populations were expressing genes associated with hematopoietic stem and progenitor cell (HSPC) support, strongly suggesting that MCs from thymic, bone and skin all possess the ability to support HSPCs. Conclusion : Overall, our study highlighted 3 potential novel roles for tMCs : 1) Promoting macrophage/monocyte chemotaxis, 2) Enhacing the apoptotic cell clearance process and 3) setting an inviting niche for hematopoietic progenitors. These novel biological roles for tMCs could have substantial effets on thymic biology. Finally, our RNA-seq data offer a valuable resource to the community that can be mined to explore multiple questions related mesenchymal cell biology. Overall design: Transcriptome comparison between MC populations		GSM1888158: Thymus_SCA1p_3; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			(thymus MCs): Thymi were extracted, mechanically disrupted and enzymatically digested at 37oC for 3x15 minutes using 0.01% (w/v) Liberase TM (Roche) and 0.1% (w/v) DNase I (Sigma-Aldrich). Final digests were harvested, pooled and maintained at 4oC in FACS buffer (PBS, 0.1% (w/v) BSA, 0.02% (w/v) NaN3). Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). (Bone MCs) Femurs, tibias and pelvis were collected, cleaned and washed 3 times in cold PBS. Using sharp surgical scissors, each bone was first cut longitudinally and then transversely to generate tiny fragments of ~1 mm2.  Bone fragments were then washed 3 times in cold PBS and incubated with agitation (80 RPM) for 3x20 minutes at 37oC in the same enzymatic cocktail as above. Following each incubation, supernatants were added to HBSS medium (Invitrogen) supplemented with 2% (v/v) FBS, 10mM HEPES and 1% (v/v) penicillin-streptomycin. To further retrieve endosteal stromal cells, remaining bone fragments were gently crushed in supplemented HBSS medium using a pestle and mortar (5 x 50 gentle taps) and supernatants were pooled to previous ones. Red blood cell lysis was then performed on the resulting cell suspension prior to its filtration and resuspension in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). (Skin MCs) Mouse trunk and dorsal skin (~12 cm2 / mouse) was aseptically dissected and incubated for 45 minutes in 0.01% (w/v) liberase. Dermis was then mechanically isolated and incubated with agitation (80 RPM) at 37oC for 2x30 minutes in the same enzymatic cocktail as above. Post-incubation, supernatants were filtered and pooled to 25 mL of PBS supplemented with 1% FBS and 5mM EDTA. Final cell suspension was then centrifuged and resuspended in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). Transcriptome librairies were generated from total RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina) following the manufacturer’s protocol. Enrichment of RNA-seq stranded libraries with adapter molecules on both ends was done using 15 cycles of PCR amplification using the Illumina PCR mix and primers cocktail. Paired-end (2 x 100 bp) sequencing was peformed using the Illumina HiSeq 2000 running TruSeq v3 chemistry. Three RNA-seq librairies were sequenced per lane (8 lanes per flow cell).	Illumina HiSeq 2000	age;;3 to 4 wks-old|cell type;;Mesenchymal cells (Lin- SCA1+ cells)|source_name;;Thymus|strain;;C57BL/6|tissue;;Thymus	GEO Accession;;GSM1888158		GSM1888158	Thymus_SCA1p_3	5238871400	26194357	2016-02-26 22:54:03	3611870653	5238871400	26194357	2	26194357	index:0,count:26194357,average:100,stdev:0|index:1,count:26194357,average:100,stdev:0	GSM1888158_r2				in_mesa	27183606	2.56	3.14	0.06	3126229135	3124220113	2963857120	2976129149	99.94	100.41	22905947	20762686	173.438	749.465	106	178807	89.76	94.92	25074778	20559975	25074778	20559975	91.22	91.77	25074778	20895578	25074778	19878584	140954957	4.51	1.25	0	4.75	0	0.26	0	0.06	0	0.00	0	12.23	0	22905947	0	200	0	191.27	0	1.52	0	0.01	0	1.20	0	0.00	0	287.50	0	0.19	0	327397	0	26194357	0	1244640	0	68058	0	15898	0	0	0	3204454	0	5174	0	0	0	77020	0	12260998	0	13163	0	12356355	0	82.69	0	21661307	0	147567	9637794	65.311309439102	26194357.0	22905947.0	327397.0	1244640.0	68058.0	15898.0	0.0	3204454.0	21661307.0	87.4	1.2	4.8	0.3	0.1	0.0	12.2	82.7	100	100	100.00	38	2619435700	22.3	22.7	23.5	24.6	6.9	35.6	20.3	bulk
952727	SRR2443132	SRP063829	SRS1073632	SRX1258031	SRA299328	GEO		RNA sequencing of primary thymic, bone and skin mesenchymal cells	Purpose : Elucidate post-natal role of SCA1+ thymic mesenchymal cells (tMCs) and evaluate the functional overlap between thymic, bone and skin MCs. Method : By high speed cell sorting, we isolated primary MCs (Lin- SCA1+ cells) from mouse thymus, bone and skin. We extracted their respective total RNA and compared their transcriptome by high-throughput RNA-sequencing. Results : We found a total of 2036 differentially expressed genes (FC>5, p-adj<0.1 and RPKM>1) between the 3 MC populations. IPA analyses revealed that each MC population was enriched for genes associated to phagocyte chemotaxis. We also denoted 2850 genes with shared expression across MC populations. IPA analysis of those shared genes also revealed an enrichment for genes influencing phagocyte migration, chemotaxis and function. Finally, MC transcriptomes showed that all 3 MC populations were expressing genes associated with hematopoietic stem and progenitor cell (HSPC) support, strongly suggesting that MCs from thymic, bone and skin all possess the ability to support HSPCs. Conclusion : Overall, our study highlighted 3 potential novel roles for tMCs : 1) Promoting macrophage/monocyte chemotaxis, 2) Enhacing the apoptotic cell clearance process and 3) setting an inviting niche for hematopoietic progenitors. These novel biological roles for tMCs could have substantial effets on thymic biology. Finally, our RNA-seq data offer a valuable resource to the community that can be mined to explore multiple questions related mesenchymal cell biology. Overall design: Transcriptome comparison between MC populations		GSM1888158: Thymus_SCA1p_3; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			(thymus MCs): Thymi were extracted, mechanically disrupted and enzymatically digested at 37oC for 3x15 minutes using 0.01% (w/v) Liberase TM (Roche) and 0.1% (w/v) DNase I (Sigma-Aldrich). Final digests were harvested, pooled and maintained at 4oC in FACS buffer (PBS, 0.1% (w/v) BSA, 0.02% (w/v) NaN3). Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). (Bone MCs) Femurs, tibias and pelvis were collected, cleaned and washed 3 times in cold PBS. Using sharp surgical scissors, each bone was first cut longitudinally and then transversely to generate tiny fragments of ~1 mm2.  Bone fragments were then washed 3 times in cold PBS and incubated with agitation (80 RPM) for 3x20 minutes at 37oC in the same enzymatic cocktail as above. Following each incubation, supernatants were added to HBSS medium (Invitrogen) supplemented with 2% (v/v) FBS, 10mM HEPES and 1% (v/v) penicillin-streptomycin. To further retrieve endosteal stromal cells, remaining bone fragments were gently crushed in supplemented HBSS medium using a pestle and mortar (5 x 50 gentle taps) and supernatants were pooled to previous ones. Red blood cell lysis was then performed on the resulting cell suspension prior to its filtration and resuspension in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). (Skin MCs) Mouse trunk and dorsal skin (~12 cm2 / mouse) was aseptically dissected and incubated for 45 minutes in 0.01% (w/v) liberase. Dermis was then mechanically isolated and incubated with agitation (80 RPM) at 37oC for 2x30 minutes in the same enzymatic cocktail as above. Post-incubation, supernatants were filtered and pooled to 25 mL of PBS supplemented with 1% FBS and 5mM EDTA. Final cell suspension was then centrifuged and resuspended in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen). Transcriptome librairies were generated from total RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina) following the manufacturer’s protocol. Enrichment of RNA-seq stranded libraries with adapter molecules on both ends was done using 15 cycles of PCR amplification using the Illumina PCR mix and primers cocktail. Paired-end (2 x 100 bp) sequencing was peformed using the Illumina HiSeq 2000 running TruSeq v3 chemistry. Three RNA-seq librairies were sequenced per lane (8 lanes per flow cell).	Illumina HiSeq 2000	age;;3 to 4 wks-old|cell type;;Mesenchymal cells (Lin- SCA1+ cells)|source_name;;Thymus|strain;;C57BL/6|tissue;;Thymus	GEO Accession;;GSM1888158		GSM1888158	Thymus_SCA1p_3	5213010400	26065052	2016-02-26 22:54:03	3572742825	5213010400	26065052	2	26065052	index:0,count:26065052,average:100,stdev:0|index:1,count:26065052,average:100,stdev:0	GSM1888158_r3				in_mesa	27183606	2.57	3.14	0.06	3118127469	3116464404	2955975453	2968588215	99.95	100.43	22825375	20689501	173.615	749.808	106	177732	89.76	94.92	24986091	20488394	24986091	20488394	91.23	91.78	24986091	20822468	24986091	19809002	140625169	4.51	1.25	0	4.76	0	0.26	0	0.06	0	0.00	0	12.11	0	22825375	0	200	0	191.29	0	1.53	0	0.01	0	1.19	0	0.00	0	302.69	0	0.19	0	324578	0	26065052	0	1241177	0	67484	0	15706	0	0	0	3156487	0	5147	0	0	0	76778	0	12210625	0	13019	0	12305569	0	82.81	0	21584198	0	147530	9607089	65.119562122958	26065052.0	22825375.0	324578.0	1241177.0	67484.0	15706.0	0.0	3156487.0	21584198.0	87.6	1.2	4.8	0.3	0.1	0.0	12.1	82.8	100	100	100.00	38	2606505200	22.3	22.7	23.5	24.6	6.8	35.6	20.5	bulk
1803119	SRR2936836	SRP065767	SRS1145944	SRX1411331	SRA309283	GEO		Recruitment of Rod Photoreceptors from Short Wavelength Sensitive Cones during the Evolution of Nocturnal Vision in Mammals	Vertebrate ancestors had only cone-like photoreceptors. The duplex retina evolved in jawless vertebrates with the advent of highly photosensitive rod-like photoreceptors. Despite cones being the arbiters of high-resolution color vision, rods emerged as the dominant photoreceptor in mammals during a nocturnal phase early in their evolution. We investigated the evolutionary and developmental origins of rods in two divergent vertebrate retinae. In mice, we discovered genetic and epigenetic vestiges of short wavelength cones in developing rods and cell lineage tracing validated the genesis of rods from S-cones. Curiously, rods did not derive from S-cones in zebrafish. Our study illuminates several questions regarding the evolution of duplex retina and supports the hypothesis that, in mammals, the S-cone lineage was recruited via the Maf-family transcription factor NRL to augment rod photoreceptors. We propose that this developmental mechanism allowed the adaptive exploitation of scotopic niches during the nocturnal bottleneck early in mammalian evolution. Overall design: GFP positive cells from Nrlp-GFP or Nrlp-GFP;Nrl-KO mouse retinas at post-natal ages P2, P4, P6, P10, P14, and P28 were isolated by flow sorting by FACSAria II (Becton Dickinson). Total RNA was extracted by Trizol LS (Life Technologies) and analyzed by 2100 Bioanalyzer (Agilent Technologies Genomics). High quality of total RNA (RIN: >7.0) was subjected to sequencing library construction using 20 ng of total RNA as input. Libraries were constructed using a stranded modification of the Illumina TruSeq mRNA (Brooks, et al. Meth Mol Biol 2012). Each library was single-end sequenced in an independent lane of a GAIIx at a length of 76 bases.  Fastq files were generated from reads passing chastity filter.		GSM1924968: P2_rep1_seq; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Total RNA was extracted by Trizol LS (Life Tech). Libraries were constructed using a stranded modification of the Illumina TruSeq mRNA (Brooks, et al. Meth Mol Biol 2012). Each library was single-end sequenced in an independent lane of a GAIIx at a length of 76 bases.  Fastq files were generated from reads passing chastity filter. Stranded mRNA-seq (dUTP method)	Illumina Genome Analyzer IIx	cell type;;GFP positive retina cells|genotype;;Nrlp-GFP|source_name;;retina|strain;;C57BL/6	GEO Accession;;GSM1924968		GSM1924968	P2_rep1_seq	2416487640	31795890	2016-06-21 16:03:06	1012972120	2416487640	31795890	1	31795890	index:0,count:31795890,average:76,stdev:0	GSM1924968_r1				in_mesa	27326930	2.61	3.43	0.08	2345980264	2311697683	2125175466	2116746585	98.54	99.6	0	0	0	0	0	0	75.49	83.31	36804878	23492321	36804878	23492321	79.2	79.53	36804878	24645403	36804878	22424764	337439337	14.38	0.34	0	9.19	0	0.53	0	0.32	0	0.00	0	1.28	0	31119584	0	76	0	75.37	0	1.64	0	0.01	0	1.21	0	0.01	0	1090.14	0	0.37	0	107517	0	31795890	0	2922079	0	167076	0	103138	0	0	0	406092	0	3117	0	0	0	24403	0	3613151	0	8321	0	3648992	0	88.68	0	28197505	0	179688	3804610	21.173422821780	31795890.0	31119584.0	107517.0	2922079.0	167076.0	103138.0	0.0	406092.0	28197505.0	97.9	0.3	9.2	0.5	0.3	0.0	1.3	88.7	76	76	76.00	39	2416487640	25.8	24.1	23.8	26.2	0.2	35.1	16.8	bulk
1803135	SRR2936837	SRP065767	SRS1145943	SRX1411332	SRA309283	GEO		Recruitment of Rod Photoreceptors from Short Wavelength Sensitive Cones during the Evolution of Nocturnal Vision in Mammals	Vertebrate ancestors had only cone-like photoreceptors. The duplex retina evolved in jawless vertebrates with the advent of highly photosensitive rod-like photoreceptors. Despite cones being the arbiters of high-resolution color vision, rods emerged as the dominant photoreceptor in mammals during a nocturnal phase early in their evolution. We investigated the evolutionary and developmental origins of rods in two divergent vertebrate retinae. In mice, we discovered genetic and epigenetic vestiges of short wavelength cones in developing rods and cell lineage tracing validated the genesis of rods from S-cones. Curiously, rods did not derive from S-cones in zebrafish. Our study illuminates several questions regarding the evolution of duplex retina and supports the hypothesis that, in mammals, the S-cone lineage was recruited via the Maf-family transcription factor NRL to augment rod photoreceptors. We propose that this developmental mechanism allowed the adaptive exploitation of scotopic niches during the nocturnal bottleneck early in mammalian evolution. Overall design: GFP positive cells from Nrlp-GFP or Nrlp-GFP;Nrl-KO mouse retinas at post-natal ages P2, P4, P6, P10, P14, and P28 were isolated by flow sorting by FACSAria II (Becton Dickinson). Total RNA was extracted by Trizol LS (Life Technologies) and analyzed by 2100 Bioanalyzer (Agilent Technologies Genomics). High quality of total RNA (RIN: >7.0) was subjected to sequencing library construction using 20 ng of total RNA as input. Libraries were constructed using a stranded modification of the Illumina TruSeq mRNA (Brooks, et al. Meth Mol Biol 2012). Each library was single-end sequenced in an independent lane of a GAIIx at a length of 76 bases.  Fastq files were generated from reads passing chastity filter.		GSM1924969: P2_rep2_seq; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Total RNA was extracted by Trizol LS (Life Tech). Libraries were constructed using a stranded modification of the Illumina TruSeq mRNA (Brooks, et al. Meth Mol Biol 2012). Each library was single-end sequenced in an independent lane of a GAIIx at a length of 76 bases.  Fastq files were generated from reads passing chastity filter. Stranded mRNA-seq (dUTP method)	Illumina Genome Analyzer IIx	cell type;;GFP positive retina cells|genotype;;Nrlp-GFP|source_name;;retina|strain;;C57BL/6	GEO Accession;;GSM1924969		GSM1924969	P2_rep2_seq	2572243408	33845308	2016-06-21 16:03:06	1209172974	2572243408	33845308	1	33845308	index:0,count:33845308,average:76,stdev:0	GSM1924969_r1				in_mesa	27326930	2.81	3.53	0.09	2491059056	2419272643	2266799714	2223702849	97.12	98.1	0	0	0	0	0	0	74.26	81.59	38794840	24541411	38794840	24541411	77.97	78.22	38794840	25766410	38794840	23528130	370860952	14.89	0.45	0	8.77	0	0.56	0	0.36	0	0.00	0	1.44	0	33046125	0	76	0	75.36	0	1.52	0	0.00	0	1.19	0	0.00	0	1032.57	0	0.41	0	151360	0	33845308	0	2968074	0	190474	0	122521	0	0	0	486188	0	3487	0	0	0	27595	0	4067732	0	8929	0	4107743	0	88.87	0	30078051	0	183357	4279206	23.338110898411	33845308.0	33046125.0	151360.0	2968074.0	190474.0	122521.0	0.0	486188.0	30078051.0	97.6	0.4	8.8	0.6	0.4	0.0	1.4	88.9	76	76	76.00	39	2572243408	26.1	23.8	23.6	26.5	0.0	33.6	15.8	bulk
1803150	SRR2936838	SRP065767	SRS1145942	SRX1411333	SRA309283	GEO		Recruitment of Rod Photoreceptors from Short Wavelength Sensitive Cones during the Evolution of Nocturnal Vision in Mammals	Vertebrate ancestors had only cone-like photoreceptors. The duplex retina evolved in jawless vertebrates with the advent of highly photosensitive rod-like photoreceptors. Despite cones being the arbiters of high-resolution color vision, rods emerged as the dominant photoreceptor in mammals during a nocturnal phase early in their evolution. We investigated the evolutionary and developmental origins of rods in two divergent vertebrate retinae. In mice, we discovered genetic and epigenetic vestiges of short wavelength cones in developing rods and cell lineage tracing validated the genesis of rods from S-cones. Curiously, rods did not derive from S-cones in zebrafish. Our study illuminates several questions regarding the evolution of duplex retina and supports the hypothesis that, in mammals, the S-cone lineage was recruited via the Maf-family transcription factor NRL to augment rod photoreceptors. We propose that this developmental mechanism allowed the adaptive exploitation of scotopic niches during the nocturnal bottleneck early in mammalian evolution. Overall design: GFP positive cells from Nrlp-GFP or Nrlp-GFP;Nrl-KO mouse retinas at post-natal ages P2, P4, P6, P10, P14, and P28 were isolated by flow sorting by FACSAria II (Becton Dickinson). Total RNA was extracted by Trizol LS (Life Technologies) and analyzed by 2100 Bioanalyzer (Agilent Technologies Genomics). High quality of total RNA (RIN: >7.0) was subjected to sequencing library construction using 20 ng of total RNA as input. Libraries were constructed using a stranded modification of the Illumina TruSeq mRNA (Brooks, et al. Meth Mol Biol 2012). Each library was single-end sequenced in an independent lane of a GAIIx at a length of 76 bases.  Fastq files were generated from reads passing chastity filter.		GSM1924970: P4_rep1_seq; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Total RNA was extracted by Trizol LS (Life Tech). Libraries were constructed using a stranded modification of the Illumina TruSeq mRNA (Brooks, et al. Meth Mol Biol 2012). Each library was single-end sequenced in an independent lane of a GAIIx at a length of 76 bases.  Fastq files were generated from reads passing chastity filter. Stranded mRNA-seq (dUTP method)	Illumina Genome Analyzer IIx	cell type;;GFP positive retina cells|genotype;;Nrlp-GFP|source_name;;retina|strain;;C57BL/6	GEO Accession;;GSM1924970		GSM1924970	P4_rep1_seq	2463295888	32411788	2016-06-21 16:03:06	1265476179	2463295888	32411788	1	32411788	index:0,count:32411788,average:76,stdev:0	GSM1924970_r1				in_mesa	27326930	3.42	3.36	0.1	2364645001	2313735917	2146407277	2125690867	97.85	99.03	0	0	0	0	0	0	74.98	82.59	36794157	23526479	36794157	23526479	78.63	79.14	36794157	24672147	36794157	22543655	348524385	14.74	0.34	0	8.91	0	0.45	0	0.32	0	0.00	0	2.43	0	31376235	0	76	0	75.35	0	1.96	0	0.01	0	1.37	0	0.00	0	833.45	0	0.44	0	111497	0	32411788	0	2888645	0	145103	0	103320	0	0	0	787130	0	2924	0	0	0	25222	0	3670979	0	7190	0	3706315	0	87.89	0	28487590	0	153117	3857986	25.196326991778	32411788.0	31376235.0	111497.0	2888645.0	145103.0	103320.0	0.0	787130.0	28487590.0	96.8	0.3	8.9	0.4	0.3	0.0	2.4	87.9	76	76	76.00	38	2463295888	26.1	23.5	23.5	26.9	0.0	34.7	18.4	bulk
1803165	SRR2936839	SRP065767	SRS1145941	SRX1411334	SRA309283	GEO		Recruitment of Rod Photoreceptors from Short Wavelength Sensitive Cones during the Evolution of Nocturnal Vision in Mammals	Vertebrate ancestors had only cone-like photoreceptors. The duplex retina evolved in jawless vertebrates with the advent of highly photosensitive rod-like photoreceptors. Despite cones being the arbiters of high-resolution color vision, rods emerged as the dominant photoreceptor in mammals during a nocturnal phase early in their evolution. We investigated the evolutionary and developmental origins of rods in two divergent vertebrate retinae. In mice, we discovered genetic and epigenetic vestiges of short wavelength cones in developing rods and cell lineage tracing validated the genesis of rods from S-cones. Curiously, rods did not derive from S-cones in zebrafish. Our study illuminates several questions regarding the evolution of duplex retina and supports the hypothesis that, in mammals, the S-cone lineage was recruited via the Maf-family transcription factor NRL to augment rod photoreceptors. We propose that this developmental mechanism allowed the adaptive exploitation of scotopic niches during the nocturnal bottleneck early in mammalian evolution. Overall design: GFP positive cells from Nrlp-GFP or Nrlp-GFP;Nrl-KO mouse retinas at post-natal ages P2, P4, P6, P10, P14, and P28 were isolated by flow sorting by FACSAria II (Becton Dickinson). Total RNA was extracted by Trizol LS (Life Technologies) and analyzed by 2100 Bioanalyzer (Agilent Technologies Genomics). High quality of total RNA (RIN: >7.0) was subjected to sequencing library construction using 20 ng of total RNA as input. Libraries were constructed using a stranded modification of the Illumina TruSeq mRNA (Brooks, et al. Meth Mol Biol 2012). Each library was single-end sequenced in an independent lane of a GAIIx at a length of 76 bases.  Fastq files were generated from reads passing chastity filter.		GSM1924971: P4_rep2_seq; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Total RNA was extracted by Trizol LS (Life Tech). Libraries were constructed using a stranded modification of the Illumina TruSeq mRNA (Brooks, et al. Meth Mol Biol 2012). Each library was single-end sequenced in an independent lane of a GAIIx at a length of 76 bases.  Fastq files were generated from reads passing chastity filter. Stranded mRNA-seq (dUTP method)	Illumina Genome Analyzer IIx	cell type;;GFP positive retina cells|genotype;;Nrlp-GFP|source_name;;retina|strain;;C57BL/6	GEO Accession;;GSM1924971		GSM1924971	P4_rep2_seq	2317622812	30495037	2016-06-21 16:03:06	1176812774	2317622812	30495037	1	30495037	index:0,count:30495037,average:76,stdev:0	GSM1924971_r1				in_mesa	27326930	4.07	3.55	0.09	2172753011	2107667494	1969288836	1929625201	97.0	97.99	0	0	0	0	0	0	72.66	80.14	33765323	20941578	33765323	20941578	76.89	76.94	33765323	22162682	33765323	20104941	349225583	16.07	0.33	0	8.83	0	0.52	0	0.38	0	0.00	0	4.59	0	28823091	0	76	0	75.36	0	1.60	0	0.00	0	1.23	0	0.00	0	741.77	0	0.40	0	99855	0	30495037	0	2692926	0	157096	0	115784	0	0	0	1399066	0	2612	0	0	0	22662	0	3269587	0	6930	0	3301791	0	85.69	0	26130165	0	148584	3441269	23.160427771496	30495037.0	28823091.0	99855.0	2692926.0	157096.0	115784.0	0.0	1399066.0	26130165.0	94.5	0.3	8.8	0.5	0.4	0.0	4.6	85.7	76	76	76.00	38	2317622812	26.2	23.2	23.6	26.9	0.0	34.7	17.8	bulk
1803275	SRR2936840	SRP065767	SRS1145940	SRX1411335	SRA309283	GEO		Recruitment of Rod Photoreceptors from Short Wavelength Sensitive Cones during the Evolution of Nocturnal Vision in Mammals	Vertebrate ancestors had only cone-like photoreceptors. The duplex retina evolved in jawless vertebrates with the advent of highly photosensitive rod-like photoreceptors. Despite cones being the arbiters of high-resolution color vision, rods emerged as the dominant photoreceptor in mammals during a nocturnal phase early in their evolution. We investigated the evolutionary and developmental origins of rods in two divergent vertebrate retinae. In mice, we discovered genetic and epigenetic vestiges of short wavelength cones in developing rods and cell lineage tracing validated the genesis of rods from S-cones. Curiously, rods did not derive from S-cones in zebrafish. Our study illuminates several questions regarding the evolution of duplex retina and supports the hypothesis that, in mammals, the S-cone lineage was recruited via the Maf-family transcription factor NRL to augment rod photoreceptors. We propose that this developmental mechanism allowed the adaptive exploitation of scotopic niches during the nocturnal bottleneck early in mammalian evolution. Overall design: GFP positive cells from Nrlp-GFP or Nrlp-GFP;Nrl-KO mouse retinas at post-natal ages P2, P4, P6, P10, P14, and P28 were isolated by flow sorting by FACSAria II (Becton Dickinson). Total RNA was extracted by Trizol LS (Life Technologies) and analyzed by 2100 Bioanalyzer (Agilent Technologies Genomics). High quality of total RNA (RIN: >7.0) was subjected to sequencing library construction using 20 ng of total RNA as input. Libraries were constructed using a stranded modification of the Illumina TruSeq mRNA (Brooks, et al. Meth Mol Biol 2012). Each library was single-end sequenced in an independent lane of a GAIIx at a length of 76 bases.  Fastq files were generated from reads passing chastity filter.		GSM1924972: P6_rep1_seq; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Total RNA was extracted by Trizol LS (Life Tech). Libraries were constructed using a stranded modification of the Illumina TruSeq mRNA (Brooks, et al. Meth Mol Biol 2012). Each library was single-end sequenced in an independent lane of a GAIIx at a length of 76 bases.  Fastq files were generated from reads passing chastity filter. Stranded mRNA-seq (dUTP method)	Illumina Genome Analyzer IIx	cell type;;GFP positive retina cells|genotype;;Nrlp-GFP|source_name;;retina|strain;;C57BL/6	GEO Accession;;GSM1924972		GSM1924972	P6_rep1_seq	2562943896	33722946	2016-06-21 16:03:06	1047041896	2562943896	33722946	1	33722946	index:0,count:33722946,average:76,stdev:0	GSM1924972_r1				in_mesa	27326930	5.79	3.12	0.09	2244570143	2113335426	1969195596	1887114497	94.15	95.83	0	0	0	0	0	0	67.38	76.79	36435400	20054162	36435400	20054162	71.66	72.32	36435400	21330515	36435400	18887968	360942297	16.08	0.70	0	10.82	0	0.50	0	0.36	0	0.00	0	10.88	0	29764466	0	76	0	75.40	0	2.88	0	0.01	0	1.71	0	0.01	0	697.72	0	0.30	0	235045	0	33722946	0	3648071	0	167866	0	120962	0	0	0	3669652	0	3076	0	0	0	22803	0	3205788	0	10581	0	3242248	0	77.44	0	26116395	0	158890	3377478	21.256705897162	33722946.0	29764466.0	235045.0	3648071.0	167866.0	120962.0	0.0	3669652.0	26116395.0	88.3	0.7	10.8	0.5	0.4	0.0	10.9	77.4	76	76	76.00	39	2562943896	25.6	24.3	23.7	26.4	0.0	36.0	18.0	bulk
1803295	SRR2936841	SRP065767	SRS1145939	SRX1411336	SRA309283	GEO		Recruitment of Rod Photoreceptors from Short Wavelength Sensitive Cones during the Evolution of Nocturnal Vision in Mammals	Vertebrate ancestors had only cone-like photoreceptors. The duplex retina evolved in jawless vertebrates with the advent of highly photosensitive rod-like photoreceptors. Despite cones being the arbiters of high-resolution color vision, rods emerged as the dominant photoreceptor in mammals during a nocturnal phase early in their evolution. We investigated the evolutionary and developmental origins of rods in two divergent vertebrate retinae. In mice, we discovered genetic and epigenetic vestiges of short wavelength cones in developing rods and cell lineage tracing validated the genesis of rods from S-cones. Curiously, rods did not derive from S-cones in zebrafish. Our study illuminates several questions regarding the evolution of duplex retina and supports the hypothesis that, in mammals, the S-cone lineage was recruited via the Maf-family transcription factor NRL to augment rod photoreceptors. We propose that this developmental mechanism allowed the adaptive exploitation of scotopic niches during the nocturnal bottleneck early in mammalian evolution. Overall design: GFP positive cells from Nrlp-GFP or Nrlp-GFP;Nrl-KO mouse retinas at post-natal ages P2, P4, P6, P10, P14, and P28 were isolated by flow sorting by FACSAria II (Becton Dickinson). Total RNA was extracted by Trizol LS (Life Technologies) and analyzed by 2100 Bioanalyzer (Agilent Technologies Genomics). High quality of total RNA (RIN: >7.0) was subjected to sequencing library construction using 20 ng of total RNA as input. Libraries were constructed using a stranded modification of the Illumina TruSeq mRNA (Brooks, et al. Meth Mol Biol 2012). Each library was single-end sequenced in an independent lane of a GAIIx at a length of 76 bases.  Fastq files were generated from reads passing chastity filter.		GSM1924973: P6_rep2_seq; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Total RNA was extracted by Trizol LS (Life Tech). Libraries were constructed using a stranded modification of the Illumina TruSeq mRNA (Brooks, et al. Meth Mol Biol 2012). Each library was single-end sequenced in an independent lane of a GAIIx at a length of 76 bases.  Fastq files were generated from reads passing chastity filter. Stranded mRNA-seq (dUTP method)	Illumina Genome Analyzer IIx	cell type;;GFP positive retina cells|genotype;;Nrlp-GFP|source_name;;retina|strain;;C57BL/6	GEO Accession;;GSM1924973		GSM1924973	P6_rep2_seq	2292969780	30170655	2016-06-21 16:03:06	1043581397	2292969780	30170655	1	30170655	index:0,count:30170655,average:76,stdev:0	GSM1924973_r1				in_mesa	27326930	3.35	3.25	0.08	2190244929	2152509460	1987194453	1974344637	98.28	99.35	0	0	0	0	0	0	75.88	83.61	34076021	22060150	34076021	22060150	79.65	80.02	34076021	23156431	34076021	21111558	307234334	14.03	0.42	0	8.91	0	0.45	0	0.27	0	0.00	0	2.92	0	29073057	0	76	0	75.32	0	1.67	0	0.01	0	1.22	0	0.01	0	1015.09	0	0.50	0	127243	0	30170655	0	2689199	0	134636	0	82814	0	0	0	880148	0	3114	0	0	0	23156	0	3373598	0	7492	0	3407360	0	87.45	0	26383858	0	160122	3546530	22.148923945492	30170655.0	29073057.0	127243.0	2689199.0	134636.0	82814.0	0.0	880148.0	26383858.0	96.4	0.4	8.9	0.4	0.3	0.0	2.9	87.4	76	76	76.00	39	2292969780	26.2	24.0	23.5	26.3	0.0	33.0	14.1	bulk
1803311	SRR2936842	SRP065767	SRS1145938	SRX1411337	SRA309283	GEO		Recruitment of Rod Photoreceptors from Short Wavelength Sensitive Cones during the Evolution of Nocturnal Vision in Mammals	Vertebrate ancestors had only cone-like photoreceptors. The duplex retina evolved in jawless vertebrates with the advent of highly photosensitive rod-like photoreceptors. Despite cones being the arbiters of high-resolution color vision, rods emerged as the dominant photoreceptor in mammals during a nocturnal phase early in their evolution. We investigated the evolutionary and developmental origins of rods in two divergent vertebrate retinae. In mice, we discovered genetic and epigenetic vestiges of short wavelength cones in developing rods and cell lineage tracing validated the genesis of rods from S-cones. Curiously, rods did not derive from S-cones in zebrafish. Our study illuminates several questions regarding the evolution of duplex retina and supports the hypothesis that, in mammals, the S-cone lineage was recruited via the Maf-family transcription factor NRL to augment rod photoreceptors. We propose that this developmental mechanism allowed the adaptive exploitation of scotopic niches during the nocturnal bottleneck early in mammalian evolution. Overall design: GFP positive cells from Nrlp-GFP or Nrlp-GFP;Nrl-KO mouse retinas at post-natal ages P2, P4, P6, P10, P14, and P28 were isolated by flow sorting by FACSAria II (Becton Dickinson). Total RNA was extracted by Trizol LS (Life Technologies) and analyzed by 2100 Bioanalyzer (Agilent Technologies Genomics). High quality of total RNA (RIN: >7.0) was subjected to sequencing library construction using 20 ng of total RNA as input. Libraries were constructed using a stranded modification of the Illumina TruSeq mRNA (Brooks, et al. Meth Mol Biol 2012). Each library was single-end sequenced in an independent lane of a GAIIx at a length of 76 bases.  Fastq files were generated from reads passing chastity filter.		GSM1924974: P6_rep3_seq; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Total RNA was extracted by Trizol LS (Life Tech). Libraries were constructed using a stranded modification of the Illumina TruSeq mRNA (Brooks, et al. Meth Mol Biol 2012). Each library was single-end sequenced in an independent lane of a GAIIx at a length of 76 bases.  Fastq files were generated from reads passing chastity filter. Stranded mRNA-seq (dUTP method)	Illumina Genome Analyzer IIx	cell type;;GFP positive retina cells|genotype;;Nrlp-GFP|source_name;;retina|strain;;C57BL/6	GEO Accession;;GSM1924974		GSM1924974	P6_rep3_seq	2327749280	30628280	2016-06-21 16:03:06	1206382927	2327749280	30628280	1	30628280	index:0,count:30628280,average:76,stdev:0	GSM1924974_r1				in_mesa	27326930	3.68	3.42	0.06	2206549843	2167286745	2009454946	1994138077	98.22	99.24	0	0	0	0	0	0	77.17	84.72	34017040	22596012	34017040	22596012	80.98	81.38	34017040	23710191	34017040	21705370	283753555	12.86	0.34	0	8.52	0	0.43	0	0.29	0	0.00	0	3.69	0	29280742	0	76	0	75.34	0	1.75	0	0.00	0	1.24	0	0.00	0	1081.00	0	0.41	0	102843	0	30628280	0	2608557	0	130486	0	87875	0	0	0	1129177	0	2930	0	0	0	24930	0	3548292	0	6797	0	3582949	0	87.08	0	26672185	0	148926	3716799	24.957354659361	30628280.0	29280742.0	102843.0	2608557.0	130486.0	87875.0	0.0	1129177.0	26672185.0	95.6	0.3	8.5	0.4	0.3	0.0	3.7	87.1	76	76	76.00	38	2327749280	26.2	23.3	23.6	26.9	0.0	34.4	17.8	bulk
1803327	SRR2936843	SRP065767	SRS1145967	SRX1411338	SRA309283	GEO		Recruitment of Rod Photoreceptors from Short Wavelength Sensitive Cones during the Evolution of Nocturnal Vision in Mammals	Vertebrate ancestors had only cone-like photoreceptors. The duplex retina evolved in jawless vertebrates with the advent of highly photosensitive rod-like photoreceptors. Despite cones being the arbiters of high-resolution color vision, rods emerged as the dominant photoreceptor in mammals during a nocturnal phase early in their evolution. We investigated the evolutionary and developmental origins of rods in two divergent vertebrate retinae. In mice, we discovered genetic and epigenetic vestiges of short wavelength cones in developing rods and cell lineage tracing validated the genesis of rods from S-cones. Curiously, rods did not derive from S-cones in zebrafish. Our study illuminates several questions regarding the evolution of duplex retina and supports the hypothesis that, in mammals, the S-cone lineage was recruited via the Maf-family transcription factor NRL to augment rod photoreceptors. We propose that this developmental mechanism allowed the adaptive exploitation of scotopic niches during the nocturnal bottleneck early in mammalian evolution. Overall design: GFP positive cells from Nrlp-GFP or Nrlp-GFP;Nrl-KO mouse retinas at post-natal ages P2, P4, P6, P10, P14, and P28 were isolated by flow sorting by FACSAria II (Becton Dickinson). Total RNA was extracted by Trizol LS (Life Technologies) and analyzed by 2100 Bioanalyzer (Agilent Technologies Genomics). High quality of total RNA (RIN: >7.0) was subjected to sequencing library construction using 20 ng of total RNA as input. Libraries were constructed using a stranded modification of the Illumina TruSeq mRNA (Brooks, et al. Meth Mol Biol 2012). Each library was single-end sequenced in an independent lane of a GAIIx at a length of 76 bases.  Fastq files were generated from reads passing chastity filter.		GSM1924975: P10_rep1_seq; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Total RNA was extracted by Trizol LS (Life Tech). Libraries were constructed using a stranded modification of the Illumina TruSeq mRNA (Brooks, et al. Meth Mol Biol 2012). Each library was single-end sequenced in an independent lane of a GAIIx at a length of 76 bases.  Fastq files were generated from reads passing chastity filter. Stranded mRNA-seq (dUTP method)	Illumina Genome Analyzer IIx	cell type;;GFP positive retina cells|genotype;;Nrlp-GFP|source_name;;retina|strain;;C57BL/6	GEO Accession;;GSM1924975		GSM1924975	P10_rep1_seq	2807803052	36944777	2016-06-21 16:03:06	1097981821	2807803052	36944777	1	36944777	index:0,count:36944777,average:76,stdev:0	GSM1924975_r1				in_mesa	27326930	8.73	2.55	0.02	2643318700	2588342090	2270862557	2262982036	97.92	99.65	0	0	0	0	0	0	75.0	87.27	43261262	26297394	43261262	26297394	81.48	82.43	43261262	28567935	43261262	24838498	247787086	9.37	0.73	0	13.34	0	0.47	0	0.18	0	0.00	0	4.45	0	35063358	0	76	0	75.36	0	3.11	0	0.02	0	1.67	0	0.01	0	1047.25	0	0.29	0	270527	0	36944777	0	4929934	0	173549	0	64872	0	0	0	1642998	0	4034	0	0	0	28393	0	4275017	0	11015	0	4318459	0	81.56	0	30133424	0	155314	4485181	28.878150070180	36944777.0	35063358.0	270527.0	4929934.0	173549.0	64872.0	0.0	1642998.0	30133424.0	94.9	0.7	13.3	0.5	0.2	0.0	4.4	81.6	76	76	76.00	39	2807803052	25.2	24.0	24.4	26.4	0.0	36.1	18.4	bulk
1803359	SRR2936845	SRP065767	SRS1145965	SRX1411340	SRA309283	GEO		Recruitment of Rod Photoreceptors from Short Wavelength Sensitive Cones during the Evolution of Nocturnal Vision in Mammals	Vertebrate ancestors had only cone-like photoreceptors. The duplex retina evolved in jawless vertebrates with the advent of highly photosensitive rod-like photoreceptors. Despite cones being the arbiters of high-resolution color vision, rods emerged as the dominant photoreceptor in mammals during a nocturnal phase early in their evolution. We investigated the evolutionary and developmental origins of rods in two divergent vertebrate retinae. In mice, we discovered genetic and epigenetic vestiges of short wavelength cones in developing rods and cell lineage tracing validated the genesis of rods from S-cones. Curiously, rods did not derive from S-cones in zebrafish. Our study illuminates several questions regarding the evolution of duplex retina and supports the hypothesis that, in mammals, the S-cone lineage was recruited via the Maf-family transcription factor NRL to augment rod photoreceptors. We propose that this developmental mechanism allowed the adaptive exploitation of scotopic niches during the nocturnal bottleneck early in mammalian evolution. Overall design: GFP positive cells from Nrlp-GFP or Nrlp-GFP;Nrl-KO mouse retinas at post-natal ages P2, P4, P6, P10, P14, and P28 were isolated by flow sorting by FACSAria II (Becton Dickinson). Total RNA was extracted by Trizol LS (Life Technologies) and analyzed by 2100 Bioanalyzer (Agilent Technologies Genomics). High quality of total RNA (RIN: >7.0) was subjected to sequencing library construction using 20 ng of total RNA as input. Libraries were constructed using a stranded modification of the Illumina TruSeq mRNA (Brooks, et al. Meth Mol Biol 2012). Each library was single-end sequenced in an independent lane of a GAIIx at a length of 76 bases.  Fastq files were generated from reads passing chastity filter.		GSM1924977: P10_rep3_seq; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Total RNA was extracted by Trizol LS (Life Tech). Libraries were constructed using a stranded modification of the Illumina TruSeq mRNA (Brooks, et al. Meth Mol Biol 2012). Each library was single-end sequenced in an independent lane of a GAIIx at a length of 76 bases.  Fastq files were generated from reads passing chastity filter. Stranded mRNA-seq (dUTP method)	Illumina Genome Analyzer IIx	cell type;;GFP positive retina cells|genotype;;Nrlp-GFP|source_name;;retina|strain;;C57BL/6	GEO Accession;;GSM1924977		GSM1924977	P10_rep3_seq	2741119512	36067362	2016-06-21 16:03:06	1193260359	2741119512	36067362	1	36067362	index:0,count:36067362,average:76,stdev:0	GSM1924977_r1				in_mesa	27326930	8.78	2.63	0.02	2548785084	2504168898	2188331145	2176938983	98.25	99.48	0	0	0	0	0	0	79.63	92.7	41795337	26946377	41795337	26946377	88.1	89.11	41795337	29811246	41795337	25904181	139074299	5.46	0.37	0	13.22	0	0.52	0	0.13	0	0.00	0	5.53	0	33838877	0	76	0	75.28	0	1.84	0	0.01	0	1.41	0	0.01	0	843.13	0	0.37	0	132464	0	36067362	0	4769629	0	186679	0	48210	0	0	0	1993596	0	4275	0	0	0	29027	0	4522569	0	9065	0	4564936	0	80.60	0	29069248	0	117739	4768500	40.500598782052	36067362.0	33838877.0	132464.0	4769629.0	186679.0	48210.0	0.0	1993596.0	29069248.0	93.8	0.4	13.2	0.5	0.1	0.0	5.5	80.6	76	76	76.00	39	2741119512	25.0	24.0	24.8	26.2	0.0	34.7	16.6	bulk
1803391	SRR2936847	SRP065767	SRS1145963	SRX1411342	SRA309283	GEO		Recruitment of Rod Photoreceptors from Short Wavelength Sensitive Cones during the Evolution of Nocturnal Vision in Mammals	Vertebrate ancestors had only cone-like photoreceptors. The duplex retina evolved in jawless vertebrates with the advent of highly photosensitive rod-like photoreceptors. Despite cones being the arbiters of high-resolution color vision, rods emerged as the dominant photoreceptor in mammals during a nocturnal phase early in their evolution. We investigated the evolutionary and developmental origins of rods in two divergent vertebrate retinae. In mice, we discovered genetic and epigenetic vestiges of short wavelength cones in developing rods and cell lineage tracing validated the genesis of rods from S-cones. Curiously, rods did not derive from S-cones in zebrafish. Our study illuminates several questions regarding the evolution of duplex retina and supports the hypothesis that, in mammals, the S-cone lineage was recruited via the Maf-family transcription factor NRL to augment rod photoreceptors. We propose that this developmental mechanism allowed the adaptive exploitation of scotopic niches during the nocturnal bottleneck early in mammalian evolution. Overall design: GFP positive cells from Nrlp-GFP or Nrlp-GFP;Nrl-KO mouse retinas at post-natal ages P2, P4, P6, P10, P14, and P28 were isolated by flow sorting by FACSAria II (Becton Dickinson). Total RNA was extracted by Trizol LS (Life Technologies) and analyzed by 2100 Bioanalyzer (Agilent Technologies Genomics). High quality of total RNA (RIN: >7.0) was subjected to sequencing library construction using 20 ng of total RNA as input. Libraries were constructed using a stranded modification of the Illumina TruSeq mRNA (Brooks, et al. Meth Mol Biol 2012). Each library was single-end sequenced in an independent lane of a GAIIx at a length of 76 bases.  Fastq files were generated from reads passing chastity filter.		GSM1924979: P14_rep2_seq; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Total RNA was extracted by Trizol LS (Life Tech). Libraries were constructed using a stranded modification of the Illumina TruSeq mRNA (Brooks, et al. Meth Mol Biol 2012). Each library was single-end sequenced in an independent lane of a GAIIx at a length of 76 bases.  Fastq files were generated from reads passing chastity filter. Stranded mRNA-seq (dUTP method)	Illumina Genome Analyzer IIx	cell type;;GFP positive retina cells|genotype;;Nrlp-GFP|source_name;;retina|strain;;C57BL/6	GEO Accession;;GSM1924979		GSM1924979	P14_rep2_seq	2717536104	35757054	2016-06-21 16:03:06	1096634767	2717536104	35757054	1	35757054	index:0,count:35757054,average:76,stdev:0	GSM1924979_r1				in_mesa	27326930	6.29	2.7	0.02	2586557248	2554692203	2291570601	2286427282	98.77	99.78	0	0	0	0	0	0	84.36	95.18	40859900	28962240	40859900	28962240	90.97	92.06	40859900	31232146	40859900	28014988	94049342	3.64	0.35	0	10.91	0	0.59	0	0.14	0	0.00	0	3.26	0	34332747	0	76	0	75.31	0	1.60	0	0.00	0	1.33	0	0.01	0	1100.22	0	0.31	0	125294	0	35757054	0	3902602	0	209638	0	48662	0	0	0	1166007	0	4276	0	0	0	31483	0	4949056	0	8937	0	4993752	0	85.10	0	30430145	0	112071	5190786	46.316941938592	35757054.0	34332747.0	125294.0	3902602.0	209638.0	48662.0	0.0	1166007.0	30430145.0	96.0	0.4	10.9	0.6	0.1	0.0	3.3	85.1	76	76	76.00	39	2717536104	24.8	24.4	24.9	25.9	0.0	35.6	17.9	bulk
1803407	SRR2936848	SRP065767	SRS1145962	SRX1411343	SRA309283	GEO		Recruitment of Rod Photoreceptors from Short Wavelength Sensitive Cones during the Evolution of Nocturnal Vision in Mammals	Vertebrate ancestors had only cone-like photoreceptors. The duplex retina evolved in jawless vertebrates with the advent of highly photosensitive rod-like photoreceptors. Despite cones being the arbiters of high-resolution color vision, rods emerged as the dominant photoreceptor in mammals during a nocturnal phase early in their evolution. We investigated the evolutionary and developmental origins of rods in two divergent vertebrate retinae. In mice, we discovered genetic and epigenetic vestiges of short wavelength cones in developing rods and cell lineage tracing validated the genesis of rods from S-cones. Curiously, rods did not derive from S-cones in zebrafish. Our study illuminates several questions regarding the evolution of duplex retina and supports the hypothesis that, in mammals, the S-cone lineage was recruited via the Maf-family transcription factor NRL to augment rod photoreceptors. We propose that this developmental mechanism allowed the adaptive exploitation of scotopic niches during the nocturnal bottleneck early in mammalian evolution. Overall design: GFP positive cells from Nrlp-GFP or Nrlp-GFP;Nrl-KO mouse retinas at post-natal ages P2, P4, P6, P10, P14, and P28 were isolated by flow sorting by FACSAria II (Becton Dickinson). Total RNA was extracted by Trizol LS (Life Technologies) and analyzed by 2100 Bioanalyzer (Agilent Technologies Genomics). High quality of total RNA (RIN: >7.0) was subjected to sequencing library construction using 20 ng of total RNA as input. Libraries were constructed using a stranded modification of the Illumina TruSeq mRNA (Brooks, et al. Meth Mol Biol 2012). Each library was single-end sequenced in an independent lane of a GAIIx at a length of 76 bases.  Fastq files were generated from reads passing chastity filter.		GSM1924980: P28_rep1_seq; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Total RNA was extracted by Trizol LS (Life Tech). Libraries were constructed using a stranded modification of the Illumina TruSeq mRNA (Brooks, et al. Meth Mol Biol 2012). Each library was single-end sequenced in an independent lane of a GAIIx at a length of 76 bases.  Fastq files were generated from reads passing chastity filter. Stranded mRNA-seq (dUTP method)	Illumina Genome Analyzer IIx	cell type;;GFP positive retina cells|genotype;;Nrlp-GFP|source_name;;retina|strain;;C57BL/6	GEO Accession;;GSM1924980		GSM1924980	P28_rep1_seq	2582699412	33982887	2016-06-21 16:03:06	1176097095	2582699412	33982887	1	33982887	index:0,count:33982887,average:76,stdev:0	GSM1924980_r1				in_mesa	27326930	10.06	2.74	0.02	2501657332	2453039516	2177765051	2173675754	98.06	99.81	0	0	0	0	0	0	82.31	94.52	39787156	27281382	39787156	27281382	88.59	90.6	39787156	29359901	39787156	26147771	90099389	3.60	0.54	0	12.60	0	0.45	0	0.16	0	0.00	0	1.86	0	33142784	0	76	0	75.45	0	3.16	0	0.01	0	1.59	0	0.01	0	955.77	0	0.32	0	182837	0	33982887	0	4280535	0	154364	0	54447	0	0	0	631292	0	3028	0	0	0	28126	0	4485429	0	7682	0	4524265	0	84.93	0	28862249	0	133799	4678263	34.964857734363	33982887.0	33142784.0	182837.0	4280535.0	154364.0	54447.0	0.0	631292.0	28862249.0	97.5	0.5	12.6	0.5	0.2	0.0	1.9	84.9	76	76	76.00	39	2582699412	26.2	23.4	23.9	26.4	0.1	34.1	16.5	bulk
1803535	SRR2936850	SRP065767	SRS1145960	SRX1411345	SRA309283	GEO		Recruitment of Rod Photoreceptors from Short Wavelength Sensitive Cones during the Evolution of Nocturnal Vision in Mammals	Vertebrate ancestors had only cone-like photoreceptors. The duplex retina evolved in jawless vertebrates with the advent of highly photosensitive rod-like photoreceptors. Despite cones being the arbiters of high-resolution color vision, rods emerged as the dominant photoreceptor in mammals during a nocturnal phase early in their evolution. We investigated the evolutionary and developmental origins of rods in two divergent vertebrate retinae. In mice, we discovered genetic and epigenetic vestiges of short wavelength cones in developing rods and cell lineage tracing validated the genesis of rods from S-cones. Curiously, rods did not derive from S-cones in zebrafish. Our study illuminates several questions regarding the evolution of duplex retina and supports the hypothesis that, in mammals, the S-cone lineage was recruited via the Maf-family transcription factor NRL to augment rod photoreceptors. We propose that this developmental mechanism allowed the adaptive exploitation of scotopic niches during the nocturnal bottleneck early in mammalian evolution. Overall design: GFP positive cells from Nrlp-GFP or Nrlp-GFP;Nrl-KO mouse retinas at post-natal ages P2, P4, P6, P10, P14, and P28 were isolated by flow sorting by FACSAria II (Becton Dickinson). Total RNA was extracted by Trizol LS (Life Technologies) and analyzed by 2100 Bioanalyzer (Agilent Technologies Genomics). High quality of total RNA (RIN: >7.0) was subjected to sequencing library construction using 20 ng of total RNA as input. Libraries were constructed using a stranded modification of the Illumina TruSeq mRNA (Brooks, et al. Meth Mol Biol 2012). Each library was single-end sequenced in an independent lane of a GAIIx at a length of 76 bases.  Fastq files were generated from reads passing chastity filter.		GSM1924982: P28_rep3_seq; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Total RNA was extracted by Trizol LS (Life Tech). Libraries were constructed using a stranded modification of the Illumina TruSeq mRNA (Brooks, et al. Meth Mol Biol 2012). Each library was single-end sequenced in an independent lane of a GAIIx at a length of 76 bases.  Fastq files were generated from reads passing chastity filter. Stranded mRNA-seq (dUTP method)	Illumina Genome Analyzer IIx	cell type;;GFP positive retina cells|genotype;;Nrlp-GFP|source_name;;retina|strain;;C57BL/6	GEO Accession;;GSM1924982		GSM1924982	P28_rep3_seq	2461084060	32382685	2016-06-21 16:03:06	982246065	2461084060	32382685	1	32382685	index:0,count:32382685,average:76,stdev:0	GSM1924982_r1				in_mesa	27326930	8.18	2.59	0.02	2382498172	2361979768	2115061079	2115791731	99.14	100.03	0	0	0	0	0	0	86.26	97.12	37119070	27290083	37119070	27290083	93.4	94.42	37119070	29549869	37119070	26531260	52026070	2.18	0.37	0	10.93	0	0.65	0	0.13	0	0.00	0	1.52	0	31637258	0	76	0	75.27	0	1.63	0	0.00	0	1.30	0	0.01	0	1050.25	0	0.38	0	120024	0	32382685	0	3537930	0	210923	0	42650	0	0	0	491854	0	3506	0	0	0	27772	0	4788850	0	8126	0	4828254	0	86.77	0	28099328	0	120627	4990454	41.370953434969	32382685.0	31637258.0	120024.0	3537930.0	210923.0	42650.0	0.0	491854.0	28099328.0	97.7	0.4	10.9	0.7	0.1	0.0	1.5	86.8	76	76	76.00	39	2461084060	24.4	24.2	25.5	25.8	0.1	35.1	16.2	bulk
1803550	SRR2936851	SRP065767	SRS1145959	SRX1411346	SRA309283	GEO		Recruitment of Rod Photoreceptors from Short Wavelength Sensitive Cones during the Evolution of Nocturnal Vision in Mammals	Vertebrate ancestors had only cone-like photoreceptors. The duplex retina evolved in jawless vertebrates with the advent of highly photosensitive rod-like photoreceptors. Despite cones being the arbiters of high-resolution color vision, rods emerged as the dominant photoreceptor in mammals during a nocturnal phase early in their evolution. We investigated the evolutionary and developmental origins of rods in two divergent vertebrate retinae. In mice, we discovered genetic and epigenetic vestiges of short wavelength cones in developing rods and cell lineage tracing validated the genesis of rods from S-cones. Curiously, rods did not derive from S-cones in zebrafish. Our study illuminates several questions regarding the evolution of duplex retina and supports the hypothesis that, in mammals, the S-cone lineage was recruited via the Maf-family transcription factor NRL to augment rod photoreceptors. We propose that this developmental mechanism allowed the adaptive exploitation of scotopic niches during the nocturnal bottleneck early in mammalian evolution. Overall design: GFP positive cells from Nrlp-GFP or Nrlp-GFP;Nrl-KO mouse retinas at post-natal ages P2, P4, P6, P10, P14, and P28 were isolated by flow sorting by FACSAria II (Becton Dickinson). Total RNA was extracted by Trizol LS (Life Technologies) and analyzed by 2100 Bioanalyzer (Agilent Technologies Genomics). High quality of total RNA (RIN: >7.0) was subjected to sequencing library construction using 20 ng of total RNA as input. Libraries were constructed using a stranded modification of the Illumina TruSeq mRNA (Brooks, et al. Meth Mol Biol 2012). Each library was single-end sequenced in an independent lane of a GAIIx at a length of 76 bases.  Fastq files were generated from reads passing chastity filter.		GSM1924983: P28_rep4_seq; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Total RNA was extracted by Trizol LS (Life Tech). Libraries were constructed using a stranded modification of the Illumina TruSeq mRNA (Brooks, et al. Meth Mol Biol 2012). Each library was single-end sequenced in an independent lane of a GAIIx at a length of 76 bases.  Fastq files were generated from reads passing chastity filter. Stranded mRNA-seq (dUTP method)	Illumina Genome Analyzer IIx	cell type;;GFP positive retina cells|genotype;;Nrlp-GFP|source_name;;retina|strain;;C57BL/6	GEO Accession;;GSM1924983		GSM1924983	P28_rep4_seq	2419871312	31840412	2016-06-21 16:03:06	937351772	2419871312	31840412	1	31840412	index:0,count:31840412,average:76,stdev:0	GSM1924983_r1				in_mesa	27326930	7.82	2.63	0.02	2336384543	2313149782	2081467645	2079857760	99.01	99.92	0	0	0	0	0	0	86.31	96.84	36299207	26777590	36299207	26777590	93.02	94.1	36299207	28859119	36299207	26020262	54030400	2.31	0.38	0	10.59	0	0.62	0	0.14	0	0.00	0	1.81	0	31023381	0	76	0	75.28	0	1.66	0	0.00	0	1.34	0	0.01	0	947.32	0	0.33	0	122438	0	31840412	0	3373043	0	198740	0	43338	0	0	0	574953	0	3604	0	0	0	28134	0	4645862	0	8059	0	4685659	0	86.84	0	27650338	0	114367	4834934	42.275603976672	31840412.0	31023381.0	122438.0	3373043.0	198740.0	43338.0	0.0	574953.0	27650338.0	97.4	0.4	10.6	0.6	0.1	0.0	1.8	86.8	76	76	76.00	39	2419871312	24.5	24.2	25.5	25.8	0.0	35.4	16.7	bulk
3606674	SRR2936844	SRP065767	SRS1145966	SRX1411339	SRA309283	GEO		Recruitment of Rod Photoreceptors from Short Wavelength Sensitive Cones during the Evolution of Nocturnal Vision in Mammals	Vertebrate ancestors had only cone-like photoreceptors. The duplex retina evolved in jawless vertebrates with the advent of highly photosensitive rod-like photoreceptors. Despite cones being the arbiters of high-resolution color vision, rods emerged as the dominant photoreceptor in mammals during a nocturnal phase early in their evolution. We investigated the evolutionary and developmental origins of rods in two divergent vertebrate retinae. In mice, we discovered genetic and epigenetic vestiges of short wavelength cones in developing rods and cell lineage tracing validated the genesis of rods from S-cones. Curiously, rods did not derive from S-cones in zebrafish. Our study illuminates several questions regarding the evolution of duplex retina and supports the hypothesis that, in mammals, the S-cone lineage was recruited via the Maf-family transcription factor NRL to augment rod photoreceptors. We propose that this developmental mechanism allowed the adaptive exploitation of scotopic niches during the nocturnal bottleneck early in mammalian evolution. Overall design: GFP positive cells from Nrlp-GFP or Nrlp-GFP;Nrl-KO mouse retinas at post-natal ages P2, P4, P6, P10, P14, and P28 were isolated by flow sorting by FACSAria II (Becton Dickinson). Total RNA was extracted by Trizol LS (Life Technologies) and analyzed by 2100 Bioanalyzer (Agilent Technologies Genomics). High quality of total RNA (RIN: >7.0) was subjected to sequencing library construction using 20 ng of total RNA as input. Libraries were constructed using a stranded modification of the Illumina TruSeq mRNA (Brooks, et al. Meth Mol Biol 2012). Each library was single-end sequenced in an independent lane of a GAIIx at a length of 76 bases.  Fastq files were generated from reads passing chastity filter.		GSM1924976: P10_rep2_seq; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Total RNA was extracted by Trizol LS (Life Tech). Libraries were constructed using a stranded modification of the Illumina TruSeq mRNA (Brooks, et al. Meth Mol Biol 2012). Each library was single-end sequenced in an independent lane of a GAIIx at a length of 76 bases.  Fastq files were generated from reads passing chastity filter. Stranded mRNA-seq (dUTP method)	Illumina Genome Analyzer IIx	cell type;;GFP positive retina cells|genotype;;Nrlp-GFP|source_name;;retina|strain;;C57BL/6	GEO Accession;;GSM1924976		GSM1924976	P10_rep2_seq	2639848904	34734854	2016-06-21 16:03:06	1039159983	2639848904	34734854	1	34734854	index:0,count:34734854,average:76,stdev:0	GSM1924976_r1				in_mesa	27326930	14.5	2.45	0.02	2539891111	2517675482	2101768683	2105107985	99.13	100.16	0	0	0	0	0	0	79.2	95.63	42524360	26680944	42524360	26680944	91.76	92.34	42524360	30912447	42524360	25761988	85520203	3.37	0.42	0	16.67	0	0.57	0	0.11	0	0.00	0	2.33	0	33689884	0	76	0	75.34	0	1.44	0	0.00	0	1.22	0	0.01	0	811.98	0	0.31	0	145726	0	34734854	0	5791120	0	197274	0	39742	0	0	0	807954	0	4219	0	0	0	29283	0	4588809	0	9603	0	4631914	0	80.32	0	27898764	0	155649	4836063	31.070312048262	34734854.0	33689884.0	145726.0	5791120.0	197274.0	39742.0	0.0	807954.0	27898764.0	97.0	0.4	16.7	0.6	0.1	0.0	2.3	80.3	76	76	76.00	39	2639848904	25.0	23.1	24.9	27.0	0.0	35.8	17.9	bulk
3606736	SRR2936846	SRP065767	SRS1145964	SRX1411341	SRA309283	GEO		Recruitment of Rod Photoreceptors from Short Wavelength Sensitive Cones during the Evolution of Nocturnal Vision in Mammals	Vertebrate ancestors had only cone-like photoreceptors. The duplex retina evolved in jawless vertebrates with the advent of highly photosensitive rod-like photoreceptors. Despite cones being the arbiters of high-resolution color vision, rods emerged as the dominant photoreceptor in mammals during a nocturnal phase early in their evolution. We investigated the evolutionary and developmental origins of rods in two divergent vertebrate retinae. In mice, we discovered genetic and epigenetic vestiges of short wavelength cones in developing rods and cell lineage tracing validated the genesis of rods from S-cones. Curiously, rods did not derive from S-cones in zebrafish. Our study illuminates several questions regarding the evolution of duplex retina and supports the hypothesis that, in mammals, the S-cone lineage was recruited via the Maf-family transcription factor NRL to augment rod photoreceptors. We propose that this developmental mechanism allowed the adaptive exploitation of scotopic niches during the nocturnal bottleneck early in mammalian evolution. Overall design: GFP positive cells from Nrlp-GFP or Nrlp-GFP;Nrl-KO mouse retinas at post-natal ages P2, P4, P6, P10, P14, and P28 were isolated by flow sorting by FACSAria II (Becton Dickinson). Total RNA was extracted by Trizol LS (Life Technologies) and analyzed by 2100 Bioanalyzer (Agilent Technologies Genomics). High quality of total RNA (RIN: >7.0) was subjected to sequencing library construction using 20 ng of total RNA as input. Libraries were constructed using a stranded modification of the Illumina TruSeq mRNA (Brooks, et al. Meth Mol Biol 2012). Each library was single-end sequenced in an independent lane of a GAIIx at a length of 76 bases.  Fastq files were generated from reads passing chastity filter.		GSM1924978: P14_rep1_seq; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Total RNA was extracted by Trizol LS (Life Tech). Libraries were constructed using a stranded modification of the Illumina TruSeq mRNA (Brooks, et al. Meth Mol Biol 2012). Each library was single-end sequenced in an independent lane of a GAIIx at a length of 76 bases.  Fastq files were generated from reads passing chastity filter. Stranded mRNA-seq (dUTP method)	Illumina Genome Analyzer IIx	cell type;;GFP positive retina cells|genotype;;Nrlp-GFP|source_name;;retina|strain;;C57BL/6	GEO Accession;;GSM1924978		GSM1924978	P14_rep1_seq	2864154848	37686248	2016-06-21 16:03:06	1173467332	2864154848	37686248	1	37686248	index:0,count:37686248,average:76,stdev:0	GSM1924978_r1				in_mesa	27326930	7.59	2.67	0.02	2718907242	2660717929	2365869337	2356381576	97.86	99.6	0	0	0	0	0	0	79.22	91.01	43809706	28564260	43809706	28564260	84.82	86.4	43809706	30585484	43809706	27118688	165776304	6.10	0.70	0	12.40	0	0.51	0	0.17	0	0.00	0	3.64	0	36058494	0	76	0	75.38	0	3.25	0	0.02	0	1.64	0	0.01	0	976.05	0	0.29	0	265395	0	37686248	0	4671943	0	191697	0	63144	0	0	0	1372913	0	3812	0	0	0	30458	0	4619674	0	10572	0	4664516	0	83.28	0	31386551	0	147150	4836015	32.864525993884	37686248.0	36058494.0	265395.0	4671943.0	191697.0	63144.0	0.0	1372913.0	31386551.0	95.7	0.7	12.4	0.5	0.2	0.0	3.6	83.3	76	76	76.00	39	2864154848	25.3	23.9	24.4	26.4	0.1	35.6	18.0	bulk
3606832	SRR2936849	SRP065767	SRS1145961	SRX1411344	SRA309283	GEO		Recruitment of Rod Photoreceptors from Short Wavelength Sensitive Cones during the Evolution of Nocturnal Vision in Mammals	Vertebrate ancestors had only cone-like photoreceptors. The duplex retina evolved in jawless vertebrates with the advent of highly photosensitive rod-like photoreceptors. Despite cones being the arbiters of high-resolution color vision, rods emerged as the dominant photoreceptor in mammals during a nocturnal phase early in their evolution. We investigated the evolutionary and developmental origins of rods in two divergent vertebrate retinae. In mice, we discovered genetic and epigenetic vestiges of short wavelength cones in developing rods and cell lineage tracing validated the genesis of rods from S-cones. Curiously, rods did not derive from S-cones in zebrafish. Our study illuminates several questions regarding the evolution of duplex retina and supports the hypothesis that, in mammals, the S-cone lineage was recruited via the Maf-family transcription factor NRL to augment rod photoreceptors. We propose that this developmental mechanism allowed the adaptive exploitation of scotopic niches during the nocturnal bottleneck early in mammalian evolution. Overall design: GFP positive cells from Nrlp-GFP or Nrlp-GFP;Nrl-KO mouse retinas at post-natal ages P2, P4, P6, P10, P14, and P28 were isolated by flow sorting by FACSAria II (Becton Dickinson). Total RNA was extracted by Trizol LS (Life Technologies) and analyzed by 2100 Bioanalyzer (Agilent Technologies Genomics). High quality of total RNA (RIN: >7.0) was subjected to sequencing library construction using 20 ng of total RNA as input. Libraries were constructed using a stranded modification of the Illumina TruSeq mRNA (Brooks, et al. Meth Mol Biol 2012). Each library was single-end sequenced in an independent lane of a GAIIx at a length of 76 bases.  Fastq files were generated from reads passing chastity filter.		GSM1924981: P28_rep2_seq; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	single			Total RNA was extracted by Trizol LS (Life Tech). Libraries were constructed using a stranded modification of the Illumina TruSeq mRNA (Brooks, et al. Meth Mol Biol 2012). Each library was single-end sequenced in an independent lane of a GAIIx at a length of 76 bases.  Fastq files were generated from reads passing chastity filter. Stranded mRNA-seq (dUTP method)	Illumina Genome Analyzer IIx	cell type;;GFP positive retina cells|genotype;;Nrlp-GFP|source_name;;retina|strain;;C57BL/6	GEO Accession;;GSM1924981		GSM1924981	P28_rep2_seq	2634483684	34664259	2016-06-21 16:03:06	1063721295	2634483684	34664259	1	34664259	index:0,count:34664259,average:76,stdev:0	GSM1924981_r1				in_mesa	27326930	9.9	2.5	0.02	2543569880	2520155301	2233112017	2233533076	99.08	100.02	0	0	0	0	0	0	85.45	97.28	39917468	28841501	39917468	28841501	93.78	94.73	39917468	31653774	39917468	28085178	53151818	2.09	0.49	0	11.84	0	0.66	0	0.11	0	0.00	0	1.85	0	33753922	0	76	0	75.32	0	1.40	0	0.00	0	1.26	0	0.01	0	1014.56	0	0.35	0	168831	0	34664259	0	4104946	0	228738	0	38911	0	0	0	642688	0	3504	0	0	0	28399	0	4987726	0	9056	0	5028685	0	85.53	0	29648976	0	126836	5194310	40.952962881201	34664259.0	33753922.0	168831.0	4104946.0	228738.0	38911.0	0.0	642688.0	29648976.0	97.4	0.5	11.8	0.7	0.1	0.0	1.9	85.5	76	76	76.00	39	2634483684	24.6	23.7	25.5	26.2	0.0	35.5	17.6	bulk
2786547	SRR2971427	SRP066961	SRS1188248	SRX1460802	SRA314788	GEO		Loss of motoneuron-specific microRNA-218 causes systemic neuromuscular failure [RNA-seq]	We investigated microRNA expression in motoneurons by performing small RNA sequencing of fluorescence-activated cell sorting (FACS)-isolated motoneurons labelled with the Hb9:gfp transgenic reporter and Hb9:gfp negative non-motoneurons including spinal interneurons.  We find that one microRNA, microRNA-218, is highly enriched and abundantly expressed in motoneurons.  Furthermore, we find that miR-218 is transcribed from alternative, motoneuron-specific alternative promoters embedded within the Slit2 and Slit3 genes by performing RNA sequencing of FACS-isolated motoneurons and a dissected embryonic floor plate cells which served as a control.  Next, we performed RNA sequencing of FACS-isolated wild type (WT) motoneurons and motoneurons lacking miR-218 expression (218DKO motoneurons), and find that a large set of genes (named ''TARGET218'' genes) with predicted miR-218 binding sites are de-repressed in the absence of miR-218 expression.  Finally, we examine the expression of TARGET218 genes in other neuronal subpopulations by FACS-isolating  V1, V2a, and V3 interneurons expressing Cre-inducible fluorescent reporters and performing RNA sequencing.  We find that the TARGET218 network of genes is depleted in wild-type motoneurons versus these interneuron types.  Additionally, these genes are expressed at similar levels in 218DKO motoneurons compared with interneuron subtypes, suggesting that this genetic network. Overall design: Examination of mRNA expression in spinal progenitor, glial, and neuronal subpopulations.		GSM1961584: mRNA_Hb9:gfp_WT_rep_1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Isolated cells were collected directly into RNA lysis buffer (miRvana kit) and the total RNA isolation protocol was followed. mRNA sequencing libraries were prepared using the TruSeq RNA Library Preparation Kit (v2) according to the manufacturer’s instructions (Illumina). Briefly, RNA with polyA+ tails was selected using oligo-dT beads. mRNA was then fragmented and reverse-transcribed into cDNA. cDNA was end-repaired, index adapter-ligated and PCR amplified. AMPure XP beads (Beckman Coulter) were used to purify nucleic acids after each step.	Illumina HiSeq 2000	background mutation;;wild type|cell type;;motoneurons|developmental stage;;E12.5|genetic reporter;;Hb9::gfp|sorted fraction;;GFP positive|source_name;;WT_motoneurons	GEO Accession;;GSM1961584		GSM1961584	mRNA_Hb9:gfp_WT_rep_1	6825811200	34129056	2015-12-18 16:31:10	4626011786	6825811200	34129056	2	34129056	index:0,count:34129056,average:100,stdev:0|index:1,count:34129056,average:100,stdev:0	GSM1961584_r1				in_mesa	26680198	1.58	3.79	0.06	5047125332	5022893472	4779940391	4780012694	99.52	100.0	33476830	31385663	171.337	650.776	135	385508	84.88	89.72	36508165	28415120	36508165	28415120	85.72	86.01	36508165	28694939	36508165	27237615	476713445	9.45	1.15	0	5.30	0	0.22	0	0.13	0	0.00	0	1.57	0	33476830	0	200	0	198.37	0	1.94	0	0.01	0	1.73	0	0.01	0	267.68	0	0.29	0	392430	0	34129056	0	1807226	0	73453	0	42813	0	0	0	535960	0	10512	0	0	0	94953	0	13723297	0	31561	0	13860323	0	92.79	0	31669604	0	216989	11512386	53.055159478130	34129056.0	33476830.0	392430.0	1807226.0	73453.0	42813.0	0.0	535960.0	31669604.0	98.1	1.1	5.3	0.2	0.1	0.0	1.6	92.8	100	100	100.00	38	3412905600	25.1	24.9	24.9	25.2	0.0	35.6	21.3	bulk
2786834	SRR2971430	SRP066961	SRS1188245	SRX1460805	SRA314788	GEO		Loss of motoneuron-specific microRNA-218 causes systemic neuromuscular failure [RNA-seq]	We investigated microRNA expression in motoneurons by performing small RNA sequencing of fluorescence-activated cell sorting (FACS)-isolated motoneurons labelled with the Hb9:gfp transgenic reporter and Hb9:gfp negative non-motoneurons including spinal interneurons.  We find that one microRNA, microRNA-218, is highly enriched and abundantly expressed in motoneurons.  Furthermore, we find that miR-218 is transcribed from alternative, motoneuron-specific alternative promoters embedded within the Slit2 and Slit3 genes by performing RNA sequencing of FACS-isolated motoneurons and a dissected embryonic floor plate cells which served as a control.  Next, we performed RNA sequencing of FACS-isolated wild type (WT) motoneurons and motoneurons lacking miR-218 expression (218DKO motoneurons), and find that a large set of genes (named ''TARGET218'' genes) with predicted miR-218 binding sites are de-repressed in the absence of miR-218 expression.  Finally, we examine the expression of TARGET218 genes in other neuronal subpopulations by FACS-isolating  V1, V2a, and V3 interneurons expressing Cre-inducible fluorescent reporters and performing RNA sequencing.  We find that the TARGET218 network of genes is depleted in wild-type motoneurons versus these interneuron types.  Additionally, these genes are expressed at similar levels in 218DKO motoneurons compared with interneuron subtypes, suggesting that this genetic network. Overall design: Examination of mRNA expression in spinal progenitor, glial, and neuronal subpopulations.		GSM1961589: mRNA_Hb9:gfp_WT_rep_4; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Isolated cells were collected directly into RNA lysis buffer (miRvana kit) and the total RNA isolation protocol was followed. mRNA sequencing libraries were prepared using the TruSeq RNA Library Preparation Kit (v2) according to the manufacturer’s instructions (Illumina). Briefly, RNA with polyA+ tails was selected using oligo-dT beads. mRNA was then fragmented and reverse-transcribed into cDNA. cDNA was end-repaired, index adapter-ligated and PCR amplified. AMPure XP beads (Beckman Coulter) were used to purify nucleic acids after each step.	Illumina HiSeq 2000	background mutation;;wild type|cell type;;motoneurons|developmental stage;;E12.5|genetic reporter;;Hb9::gfp|sorted fraction;;GFP positive|source_name;;WT_motoneurons	GEO Accession;;GSM1961589		GSM1961589	mRNA_Hb9:gfp_WT_rep_4	4693044588	23232894	2015-12-18 16:31:10	2990100728	4693044588	23232894	2	23232894	index:0,count:23232894,average:101,stdev:0|index:1,count:23232894,average:101,stdev:0	GSM1961589_r1				in_mesa	26680198	3.03	3.94	0.03	3454448515	3434424202	3229164299	3229639890	99.42	100.01	22470948	21134910	169.907	615.851	146	301436	87.77	93.96	24856596	19722827	24856596	19722827	89.8	90.31	24856596	20178679	24856596	18956727	168617971	4.88	0.44	0	6.37	0	0.20	0	0.10	0	0.00	0	2.99	0	22470948	0	202	0	200.08	0	1.97	0	0.01	0	1.50	0	0.01	0	279.73	0	0.40	0	101895	0	23232894	0	1479884	0	45311	0	22354	0	0	0	694281	0	7686	0	0	0	66814	0	9758912	0	15934	0	9849346	0	90.35	0	20991064	0	178263	8312431	46.630153200608	23232894.0	22470948.0	101895.0	1479884.0	45311.0	22354.0	0.0	694281.0	20991064.0	96.7	0.4	6.4	0.2	0.1	0.0	3.0	90.4	101	101	101.00	38	2346522294	26.1	23.9	23.8	26.3	0.0	35.1	16.3	bulk
2786866	SRR2971431	SRP066961	SRS1188244	SRX1460806	SRA314788	GEO		Loss of motoneuron-specific microRNA-218 causes systemic neuromuscular failure [RNA-seq]	We investigated microRNA expression in motoneurons by performing small RNA sequencing of fluorescence-activated cell sorting (FACS)-isolated motoneurons labelled with the Hb9:gfp transgenic reporter and Hb9:gfp negative non-motoneurons including spinal interneurons.  We find that one microRNA, microRNA-218, is highly enriched and abundantly expressed in motoneurons.  Furthermore, we find that miR-218 is transcribed from alternative, motoneuron-specific alternative promoters embedded within the Slit2 and Slit3 genes by performing RNA sequencing of FACS-isolated motoneurons and a dissected embryonic floor plate cells which served as a control.  Next, we performed RNA sequencing of FACS-isolated wild type (WT) motoneurons and motoneurons lacking miR-218 expression (218DKO motoneurons), and find that a large set of genes (named ''TARGET218'' genes) with predicted miR-218 binding sites are de-repressed in the absence of miR-218 expression.  Finally, we examine the expression of TARGET218 genes in other neuronal subpopulations by FACS-isolating  V1, V2a, and V3 interneurons expressing Cre-inducible fluorescent reporters and performing RNA sequencing.  We find that the TARGET218 network of genes is depleted in wild-type motoneurons versus these interneuron types.  Additionally, these genes are expressed at similar levels in 218DKO motoneurons compared with interneuron subtypes, suggesting that this genetic network. Overall design: Examination of mRNA expression in spinal progenitor, glial, and neuronal subpopulations.		GSM1961591: mRNA_Hb9:gfp_WT_rep_5; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Isolated cells were collected directly into RNA lysis buffer (miRvana kit) and the total RNA isolation protocol was followed. mRNA sequencing libraries were prepared using the TruSeq RNA Library Preparation Kit (v2) according to the manufacturer’s instructions (Illumina). Briefly, RNA with polyA+ tails was selected using oligo-dT beads. mRNA was then fragmented and reverse-transcribed into cDNA. cDNA was end-repaired, index adapter-ligated and PCR amplified. AMPure XP beads (Beckman Coulter) were used to purify nucleic acids after each step.	Illumina HiSeq 2000	background mutation;;wild type|cell type;;motoneurons|developmental stage;;E12.5|genetic reporter;;Hb9::gfp|sorted fraction;;GFP positive|source_name;;WT_motoneurons	GEO Accession;;GSM1961591		GSM1961591	mRNA_Hb9:gfp_WT_rep_5	2759926606	13663003	2015-12-18 16:31:10	1796249987	2759926606	13663003	2	13663003	index:0,count:13663003,average:101,stdev:0|index:1,count:13663003,average:101,stdev:0	GSM1961591_r1				in_mesa	26680198	1.78	3.51	0.03	2135971329	2144480119	2006618197	2023984603	100.4	100.87	13050684	12136513	188.741	727.955	146	132180	89.68	95.54	14373126	11703863	14373126	11703863	90.63	91.11	14373126	11827808	14373126	11161193	72743361	3.41	0.38	0	5.86	0	0.20	0	0.07	0	0.00	0	4.21	0	13050684	0	202	0	199.77	0	2.21	0	0.01	0	1.58	0	0.01	0	190.65	0	0.48	0	52056	0	13663003	0	800605	0	27413	0	9653	0	0	0	575253	0	4633	0	0	0	43596	0	6091634	0	9950	0	6149813	0	89.66	0	12250079	0	161213	5504952	34.147072506560	13663003.0	13050684.0	52056.0	800605.0	27413.0	9653.0	0.0	575253.0	12250079.0	95.5	0.4	5.9	0.2	0.1	0.0	4.2	89.7	101	101	101.00	38	1379963303	24.5	25.6	25.5	24.5	0.0	34.1	15.1	bulk
2786897	SRR2971432	SRP066961	SRS1188243	SRX1460807	SRA314788	GEO		Loss of motoneuron-specific microRNA-218 causes systemic neuromuscular failure [RNA-seq]	We investigated microRNA expression in motoneurons by performing small RNA sequencing of fluorescence-activated cell sorting (FACS)-isolated motoneurons labelled with the Hb9:gfp transgenic reporter and Hb9:gfp negative non-motoneurons including spinal interneurons.  We find that one microRNA, microRNA-218, is highly enriched and abundantly expressed in motoneurons.  Furthermore, we find that miR-218 is transcribed from alternative, motoneuron-specific alternative promoters embedded within the Slit2 and Slit3 genes by performing RNA sequencing of FACS-isolated motoneurons and a dissected embryonic floor plate cells which served as a control.  Next, we performed RNA sequencing of FACS-isolated wild type (WT) motoneurons and motoneurons lacking miR-218 expression (218DKO motoneurons), and find that a large set of genes (named ''TARGET218'' genes) with predicted miR-218 binding sites are de-repressed in the absence of miR-218 expression.  Finally, we examine the expression of TARGET218 genes in other neuronal subpopulations by FACS-isolating  V1, V2a, and V3 interneurons expressing Cre-inducible fluorescent reporters and performing RNA sequencing.  We find that the TARGET218 network of genes is depleted in wild-type motoneurons versus these interneuron types.  Additionally, these genes are expressed at similar levels in 218DKO motoneurons compared with interneuron subtypes, suggesting that this genetic network. Overall design: Examination of mRNA expression in spinal progenitor, glial, and neuronal subpopulations.		GSM1961593: mRNA_Hb9:gfp_WT_rep_6; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Isolated cells were collected directly into RNA lysis buffer (miRvana kit) and the total RNA isolation protocol was followed. mRNA sequencing libraries were prepared using the TruSeq RNA Library Preparation Kit (v2) according to the manufacturer’s instructions (Illumina). Briefly, RNA with polyA+ tails was selected using oligo-dT beads. mRNA was then fragmented and reverse-transcribed into cDNA. cDNA was end-repaired, index adapter-ligated and PCR amplified. AMPure XP beads (Beckman Coulter) were used to purify nucleic acids after each step.	Illumina HiSeq 2000	background mutation;;wild type|cell type;;motoneurons|developmental stage;;E12.5|genetic reporter;;Hb9::gfp|sorted fraction;;GFP positive|source_name;;WT_motoneurons	GEO Accession;;GSM1961593		GSM1961593	mRNA_Hb9:gfp_WT_rep_6	3490927842	17281821	2015-12-18 16:31:10	2264079795	3490927842	17281821	2	17281821	index:0,count:17281821,average:101,stdev:0|index:1,count:17281821,average:101,stdev:0	GSM1961593_r1				in_mesa	26680198	1.81	3.67	0.02	2609419490	2617366933	2446310114	2465838974	100.3	100.8	16471819	15366598	179.696	698.876	146	184224	89.94	96.01	18203480	14814458	18203480	14814458	91.22	91.72	18203480	15024926	18203480	14153341	80542300	3.09	0.47	0	6.03	0	0.21	0	0.07	0	0.00	0	4.41	0	16471819	0	202	0	199.68	0	2.04	0	0.01	0	1.56	0	0.01	0	209.48	0	0.47	0	80842	0	17281821	0	1041328	0	35858	0	12303	0	0	0	761841	0	6160	0	0	0	53627	0	7799235	0	13142	0	7872164	0	89.29	0	15430491	0	168747	6838638	40.525982684137	17281821.0	16471819.0	80842.0	1041328.0	35858.0	12303.0	0.0	761841.0	15430491.0	95.3	0.5	6.0	0.2	0.1	0.0	4.4	89.3	101	101	101.00	38	1745463921	24.6	25.3	25.3	24.7	0.0	34.2	15.1	bulk
2786930	SRR2971433	SRP066961	SRS1188242	SRX1460808	SRA314788	GEO		Loss of motoneuron-specific microRNA-218 causes systemic neuromuscular failure [RNA-seq]	We investigated microRNA expression in motoneurons by performing small RNA sequencing of fluorescence-activated cell sorting (FACS)-isolated motoneurons labelled with the Hb9:gfp transgenic reporter and Hb9:gfp negative non-motoneurons including spinal interneurons.  We find that one microRNA, microRNA-218, is highly enriched and abundantly expressed in motoneurons.  Furthermore, we find that miR-218 is transcribed from alternative, motoneuron-specific alternative promoters embedded within the Slit2 and Slit3 genes by performing RNA sequencing of FACS-isolated motoneurons and a dissected embryonic floor plate cells which served as a control.  Next, we performed RNA sequencing of FACS-isolated wild type (WT) motoneurons and motoneurons lacking miR-218 expression (218DKO motoneurons), and find that a large set of genes (named ''TARGET218'' genes) with predicted miR-218 binding sites are de-repressed in the absence of miR-218 expression.  Finally, we examine the expression of TARGET218 genes in other neuronal subpopulations by FACS-isolating  V1, V2a, and V3 interneurons expressing Cre-inducible fluorescent reporters and performing RNA sequencing.  We find that the TARGET218 network of genes is depleted in wild-type motoneurons versus these interneuron types.  Additionally, these genes are expressed at similar levels in 218DKO motoneurons compared with interneuron subtypes, suggesting that this genetic network. Overall design: Examination of mRNA expression in spinal progenitor, glial, and neuronal subpopulations.		GSM1961595: mRNA_Floor_Plate_rep_1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Isolated cells were collected directly into RNA lysis buffer (miRvana kit) and the total RNA isolation protocol was followed. mRNA sequencing libraries were prepared using the TruSeq RNA Library Preparation Kit (v2) according to the manufacturer’s instructions (Illumina). Briefly, RNA with polyA+ tails was selected using oligo-dT beads. mRNA was then fragmented and reverse-transcribed into cDNA. cDNA was end-repaired, index adapter-ligated and PCR amplified. AMPure XP beads (Beckman Coulter) were used to purify nucleic acids after each step.	Illumina HiSeq 2000	background mutation;;wild type|cell type;;floor plate glial cells|developmental stage;;E12.5|genetic reporter;;none|sorted fraction;;unsorted|source_name;;WT_floor_plate_cells	GEO Accession;;GSM1961595		GSM1961595	mRNA_Floor_Plate_rep_1	6381127600	31905638	2015-12-18 16:31:10	4328161667	6381127600	31905638	2	31905638	index:0,count:31905638,average:100,stdev:0|index:1,count:31905638,average:100,stdev:0	GSM1961595_r1				in_mesa	26680198	3.7	3.39	0.05	4867033936	4854215707	4557284878	4566561380	99.74	100.2	31425407	29475655	176.103	592.705	145	354642	86.91	92.94	34673379	27312640	34673379	27312640	88.81	89.1	34673379	27908109	34673379	26184260	301051146	6.19	0.96	0	6.38	0	0.22	0	0.09	0	0.00	0	1.19	0	31425407	0	200	0	198.41	0	1.91	0	0.01	0	1.64	0	0.01	0	298.34	0	0.29	0	304953	0	31905638	0	2036897	0	71583	0	29697	0	0	0	378951	0	10217	0	0	0	87505	0	14071628	0	28039	0	14197389	0	92.11	0	29388510	0	224395	12299054	54.809839791439	31905638.0	31425407.0	304953.0	2036897.0	71583.0	29697.0	0.0	378951.0	29388510.0	98.5	1.0	6.4	0.2	0.1	0.0	1.2	92.1	100	100	100.00	38	3190563800	25.3	24.7	24.7	25.4	0.0	35.7	21.5	bulk
1644637	SRR3032185	SRP067565	SRS1212740	SRX1491265	SRA320716	GEO		Gene expression profiling of sensory epithelium of cochleas and vestibules of the inner ears of wild-type C57Bl/6J mice at post-natal day 0 (P0)	The sensory epithelium of cochleas and vestibules of mice were compared. The two tissues are quite similar in structure, but have distinct roles in hearing and balance. By comparing their gene expression, we hoped to identify key regulators of differentiation. Overall design: Cochlear and vestibular sensory epithelium was dissected from 20 inner ears of 10 P0 C57Bl/6J mice, generating 2.4 and 1.5 µg of total RNA, respectively. 450 ng RNA from each sample was used to create libraries with the TruSeq Stranded mRNA Sample Prep Kit (Illumina), followed by high-throughput sequencing at 100 bp paired end (PE) at the Technion Genome Center, Haifa, Israel. Six samples were generated, 3 cochlear and 3 vestibular, for sequencing in triplicate.		GSM1975057: WT_P0_Cochlea_SensoryEpithelium_1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Sensory epithelia from 20 cochlea or 20 vestibule were removed and RNA was harvested using QIAgen’s RNeasy micro kit. Illumina TruSeq® Stranded mRNA Sample Preparation Kit (Cat# RS-122-2101) was used with 450 ng of total RNA for the construction of sequencing libraries.	Illumina HiSeq 2500	age;;newborns (P0)|Sex;;pooled male and female|source_name;;Mouse P0 cochlear sensory epithelium|strain;;C57BL/6J|tissue;;cochlear sensory epithelium	GEO Accession;;GSM1975057		GSM1975057	WT_P0_Cochlea_SensoryEpithelium_1	5964299066	29526233	2017-04-13 14:09:16	2700402981	5964299066	29526233	2	29526233	index:0,count:29526233,average:101,stdev:0|index:1,count:29526233,average:101,stdev:0	GSM1975057_r1						6.91	3.18	0.02	4570804556	4527780048	4059779094	4045575753	99.06	99.65	28499220	26344235	191.891	661.729	139	225958	83.87	94.75	33530000	23903516	33530000	23903516	90.26	90.82	33530000	25722635	33530000	22912745	152432184	3.33	0.78	0	11.08	0	0.19	0	0.04	0	0.00	0	3.25	0	28499220	0	202	0	200.00	0	1.92	0	0.01	0	2.03	0	0.01	0	278.99	0	0.26	0	229802	0	29526233	0	3271464	0	56887	0	10689	0	0	0	959437	0	8999	0	0	0	90906	0	12877612	0	20625	0	12998142	0	85.44	0	25227756	0	208864	11680700	55.924908074154	29526233.0	28499220.0	229802.0	3271464.0	56887.0	10689.0	0.0	959437.0	25227756.0	96.5	0.8	11.1	0.2	0.0	0.0	3.2	85.4	101	101	101.00	8	2982149533	24.1	24.8	25.1	26.0	0.0	35.8	25.2	bulk
1644654	SRR3032186	SRP067565	SRS1212741	SRX1491266	SRA320716	GEO		Gene expression profiling of sensory epithelium of cochleas and vestibules of the inner ears of wild-type C57Bl/6J mice at post-natal day 0 (P0)	The sensory epithelium of cochleas and vestibules of mice were compared. The two tissues are quite similar in structure, but have distinct roles in hearing and balance. By comparing their gene expression, we hoped to identify key regulators of differentiation. Overall design: Cochlear and vestibular sensory epithelium was dissected from 20 inner ears of 10 P0 C57Bl/6J mice, generating 2.4 and 1.5 µg of total RNA, respectively. 450 ng RNA from each sample was used to create libraries with the TruSeq Stranded mRNA Sample Prep Kit (Illumina), followed by high-throughput sequencing at 100 bp paired end (PE) at the Technion Genome Center, Haifa, Israel. Six samples were generated, 3 cochlear and 3 vestibular, for sequencing in triplicate.		GSM1975058: WT_P0_Cochlea_SensoryEpithelium_2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Sensory epithelia from 20 cochlea or 20 vestibule were removed and RNA was harvested using QIAgen’s RNeasy micro kit. Illumina TruSeq® Stranded mRNA Sample Preparation Kit (Cat# RS-122-2101) was used with 450 ng of total RNA for the construction of sequencing libraries.	Illumina HiSeq 2500	age;;newborns (P0)|Sex;;pooled male and female|source_name;;Mouse P0 cochlear sensory epithelium|strain;;C57BL/6J|tissue;;cochlear sensory epithelium	GEO Accession;;GSM1975058		GSM1975058	WT_P0_Cochlea_SensoryEpithelium_2	7106887624	35182612	2017-04-13 14:09:16	3237020147	7106887624	35182612	2	35182612	index:0,count:35182612,average:101,stdev:0|index:1,count:35182612,average:101,stdev:0	GSM1975058_r1						5.4	3.12	0.02	5461454836	5400504155	4881181788	4855202600	98.88	99.47	33870607	31297290	193.008	672.338	148	269677	83.45	93.68	39751625	28265996	39751625	28265996	88.73	89.36	39751625	30052122	39751625	26962934	211765518	3.88	0.69	0	10.51	0	0.25	0	0.04	0	0.00	0	3.44	0	33870607	0	202	0	199.89	0	2.29	0	0.01	0	2.22	0	0.01	0	249.33	0	0.29	0	241389	0	35182612	0	3698402	0	87734	0	13455	0	0	0	1210816	0	9833	0	0	0	113117	0	15898576	0	24003	0	16045529	0	85.76	0	30172205	0	227152	14421487	63.488267767838	35182612.0	33870607.0	241389.0	3698402.0	87734.0	13455.0	0.0	1210816.0	30172205.0	96.3	0.7	10.5	0.2	0.0	0.0	3.4	85.8	101	101	101.00	8	3553443812	23.6	25.4	25.3	25.7	0.0	35.7	25.0	bulk
1644669	SRR3032187	SRP067565	SRS1212739	SRX1491267	SRA320716	GEO		Gene expression profiling of sensory epithelium of cochleas and vestibules of the inner ears of wild-type C57Bl/6J mice at post-natal day 0 (P0)	The sensory epithelium of cochleas and vestibules of mice were compared. The two tissues are quite similar in structure, but have distinct roles in hearing and balance. By comparing their gene expression, we hoped to identify key regulators of differentiation. Overall design: Cochlear and vestibular sensory epithelium was dissected from 20 inner ears of 10 P0 C57Bl/6J mice, generating 2.4 and 1.5 µg of total RNA, respectively. 450 ng RNA from each sample was used to create libraries with the TruSeq Stranded mRNA Sample Prep Kit (Illumina), followed by high-throughput sequencing at 100 bp paired end (PE) at the Technion Genome Center, Haifa, Israel. Six samples were generated, 3 cochlear and 3 vestibular, for sequencing in triplicate.		GSM1975059: WT_P0_Cochlea_SensoryEpithelium_3; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Sensory epithelia from 20 cochlea or 20 vestibule were removed and RNA was harvested using QIAgen’s RNeasy micro kit. Illumina TruSeq® Stranded mRNA Sample Preparation Kit (Cat# RS-122-2101) was used with 450 ng of total RNA for the construction of sequencing libraries.	Illumina HiSeq 2500	age;;newborns (P0)|Sex;;pooled male and female|source_name;;Mouse P0 cochlear sensory epithelium|strain;;C57BL/6J|tissue;;cochlear sensory epithelium	GEO Accession;;GSM1975059		GSM1975059	WT_P0_Cochlea_SensoryEpithelium_3	7334701002	36310401	2017-04-13 14:09:16	3328273344	7334701002	36310401	2	36310401	index:0,count:36310401,average:101,stdev:0|index:1,count:36310401,average:101,stdev:0	GSM1975059_r1						4.77	3.03	0.02	5608533389	5549849433	5128743648	5101114652	98.95	99.46	35060512	32547814	189.614	635.857	142	292260	83.45	91.52	39927002	29258247	39927002	29258247	86.97	87.43	39927002	30492340	39927002	27952182	347614354	6.20	0.73	0	8.51	0	0.20	0	0.05	0	0.00	0	3.19	0	35060512	0	202	0	200.04	0	2.14	0	0.01	0	2.06	0	0.01	0	312.72	0	0.27	0	264705	0	36310401	0	3089787	0	70974	0	19166	0	0	0	1159749	0	10276	0	0	0	108697	0	16152679	0	24883	0	16296535	0	88.05	0	31970725	0	229084	14409650	62.901162892214	36310401.0	35060512.0	264705.0	3089787.0	70974.0	19166.0	0.0	1159749.0	31970725.0	96.6	0.7	8.5	0.2	0.1	0.0	3.2	88.0	101	101	101.00	8	3667350501	23.9	25.2	25.3	25.5	0.0	35.8	25.1	bulk
1644685	SRR3032188	SRP067565	SRS1212738	SRX1491268	SRA320716	GEO		Gene expression profiling of sensory epithelium of cochleas and vestibules of the inner ears of wild-type C57Bl/6J mice at post-natal day 0 (P0)	The sensory epithelium of cochleas and vestibules of mice were compared. The two tissues are quite similar in structure, but have distinct roles in hearing and balance. By comparing their gene expression, we hoped to identify key regulators of differentiation. Overall design: Cochlear and vestibular sensory epithelium was dissected from 20 inner ears of 10 P0 C57Bl/6J mice, generating 2.4 and 1.5 µg of total RNA, respectively. 450 ng RNA from each sample was used to create libraries with the TruSeq Stranded mRNA Sample Prep Kit (Illumina), followed by high-throughput sequencing at 100 bp paired end (PE) at the Technion Genome Center, Haifa, Israel. Six samples were generated, 3 cochlear and 3 vestibular, for sequencing in triplicate.		GSM1975060: WT_P0_Vestibule_SensoryEpithelium_1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Sensory epithelia from 20 cochlea or 20 vestibule were removed and RNA was harvested using QIAgen’s RNeasy micro kit. Illumina TruSeq® Stranded mRNA Sample Preparation Kit (Cat# RS-122-2101) was used with 450 ng of total RNA for the construction of sequencing libraries.	Illumina HiSeq 2500	age;;newborns (P0)|Sex;;pooled male and female|source_name;;Mouse P0 vestibular sensory epithelium|strain;;C57BL/6J|tissue;;vestibular sensory epithelium	GEO Accession;;GSM1975060		GSM1975060	WT_P0_Vestibule_SensoryEpithelium_1	8310345650	41140325	2017-04-13 14:09:16	3765118951	8310345650	41140325	2	41140325	index:0,count:41140325,average:101,stdev:0|index:1,count:41140325,average:101,stdev:0	GSM1975060_r1						2.99	3.06	0.03	6363688581	6307329540	5946290450	5920375931	99.11	99.56	39763374	36607603	191.020	679.810	142	326394	86.59	92.86	44119846	34429241	44119846	34429241	88.66	89.18	44119846	35253611	44119846	33063934	342845331	5.39	0.78	0	6.53	0	0.20	0	0.06	0	0.00	0	3.09	0	39763374	0	202	0	200.03	0	1.80	0	0.01	0	1.86	0	0.01	0	248.08	0	0.24	0	320079	0	41140325	0	2687674	0	82359	0	24307	0	0	0	1270285	0	13628	0	0	0	135857	0	20241399	0	28708	0	20419592	0	90.12	0	37075700	0	261082	17935808	68.697987605427	41140325.0	39763374.0	320079.0	2687674.0	82359.0	24307.0	0.0	1270285.0	37075700.0	96.7	0.8	6.5	0.2	0.1	0.0	3.1	90.1	101	101	101.00	8	4155172825	23.8	25.4	25.2	25.5	0.0	35.8	25.2	bulk
1644702	SRR3032189	SRP067565	SRS1212737	SRX1491269	SRA320716	GEO		Gene expression profiling of sensory epithelium of cochleas and vestibules of the inner ears of wild-type C57Bl/6J mice at post-natal day 0 (P0)	The sensory epithelium of cochleas and vestibules of mice were compared. The two tissues are quite similar in structure, but have distinct roles in hearing and balance. By comparing their gene expression, we hoped to identify key regulators of differentiation. Overall design: Cochlear and vestibular sensory epithelium was dissected from 20 inner ears of 10 P0 C57Bl/6J mice, generating 2.4 and 1.5 µg of total RNA, respectively. 450 ng RNA from each sample was used to create libraries with the TruSeq Stranded mRNA Sample Prep Kit (Illumina), followed by high-throughput sequencing at 100 bp paired end (PE) at the Technion Genome Center, Haifa, Israel. Six samples were generated, 3 cochlear and 3 vestibular, for sequencing in triplicate.		GSM1975061: WT_P0_Vestibule_SensoryEpithelium_2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Sensory epithelia from 20 cochlea or 20 vestibule were removed and RNA was harvested using QIAgen’s RNeasy micro kit. Illumina TruSeq® Stranded mRNA Sample Preparation Kit (Cat# RS-122-2101) was used with 450 ng of total RNA for the construction of sequencing libraries.	Illumina HiSeq 2500	age;;newborns (P0)|Sex;;pooled male and female|source_name;;Mouse P0 vestibular sensory epithelium|strain;;C57BL/6J|tissue;;vestibular sensory epithelium	GEO Accession;;GSM1975061		GSM1975061	WT_P0_Vestibule_SensoryEpithelium_2	6436964926	31866163	2017-04-13 14:09:16	2922014709	6436964926	31866163	2	31866163	index:0,count:31866163,average:101,stdev:0|index:1,count:31866163,average:101,stdev:0	GSM1975061_r1						5.15	2.98	0.03	4951994132	4891555000	4531646741	4501176293	98.78	99.33	30693186	28549378	191.651	607.423	148	250737	84.05	92.09	34874313	25798757	34874313	25798757	87.68	88.17	34874313	26910995	34874313	24701849	282036831	5.70	0.77	0	8.40	0	0.21	0	0.05	0	0.00	0	3.42	0	30693186	0	202	0	200.01	0	1.92	0	0.01	0	2.02	0	0.01	0	261.91	0	0.26	0	246615	0	31866163	0	2677067	0	66194	0	15501	0	0	0	1091282	0	9800	0	0	0	92160	0	13656731	0	20483	0	13779174	0	87.92	0	28016119	0	228641	12302577	53.807396748615	31866163.0	30693186.0	246615.0	2677067.0	66194.0	15501.0	0.0	1091282.0	28016119.0	96.3	0.8	8.4	0.2	0.0	0.0	3.4	87.9	101	101	101.00	8	3218482463	24.2	25.0	25.2	25.6	0.0	35.8	25.0	bulk
1644814	SRR3032190	SRP067565	SRS1212736	SRX1491270	SRA320716	GEO		Gene expression profiling of sensory epithelium of cochleas and vestibules of the inner ears of wild-type C57Bl/6J mice at post-natal day 0 (P0)	The sensory epithelium of cochleas and vestibules of mice were compared. The two tissues are quite similar in structure, but have distinct roles in hearing and balance. By comparing their gene expression, we hoped to identify key regulators of differentiation. Overall design: Cochlear and vestibular sensory epithelium was dissected from 20 inner ears of 10 P0 C57Bl/6J mice, generating 2.4 and 1.5 µg of total RNA, respectively. 450 ng RNA from each sample was used to create libraries with the TruSeq Stranded mRNA Sample Prep Kit (Illumina), followed by high-throughput sequencing at 100 bp paired end (PE) at the Technion Genome Center, Haifa, Israel. Six samples were generated, 3 cochlear and 3 vestibular, for sequencing in triplicate.		GSM1975062: WT_P0_Vestibule_SensoryEpithelium_3; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Sensory epithelia from 20 cochlea or 20 vestibule were removed and RNA was harvested using QIAgen’s RNeasy micro kit. Illumina TruSeq® Stranded mRNA Sample Preparation Kit (Cat# RS-122-2101) was used with 450 ng of total RNA for the construction of sequencing libraries.	Illumina HiSeq 2500	age;;newborns (P0)|Sex;;pooled male and female|source_name;;Mouse P0 vestibular sensory epithelium|strain;;C57BL/6J|tissue;;vestibular sensory epithelium	GEO Accession;;GSM1975062		GSM1975062	WT_P0_Vestibule_SensoryEpithelium_3	6354499032	31457916	2017-04-13 14:09:16	2887062286	6354499032	31457916	2	31457916	index:0,count:31457916,average:101,stdev:0|index:1,count:31457916,average:101,stdev:0	GSM1975062_r1						5.54	3.01	0.03	4826304387	4769973620	4367499433	4342891230	98.83	99.44	30227638	27954022	190.412	651.786	134	243319	83.8	92.88	34857170	25330331	34857170	25330331	88.08	88.69	34857170	26623489	34857170	24189190	228850123	4.74	0.81	0	9.39	0	0.22	0	0.04	0	0.00	0	3.65	0	30227638	0	202	0	199.90	0	2.15	0	0.01	0	2.14	0	0.01	0	267.10	0	0.28	0	255205	0	31457916	0	2955258	0	68869	0	11973	0	0	0	1149436	0	10056	0	0	0	93703	0	13984324	0	22846	0	14110929	0	86.69	0	27272380	0	224526	12509940	55.717110713236	31457916.0	30227638.0	255205.0	2955258.0	68869.0	11973.0	0.0	1149436.0	27272380.0	96.1	0.8	9.4	0.2	0.0	0.0	3.7	86.7	101	101	101.00	8	3177249516	24.0	25.1	25.2	25.6	0.0	35.8	25.0	bulk
1511535	SRR3175106	SRP070433	SRS1305170	SRX1589664	SRA354792	GEO		Quantitative Analysis of Notch mutant (Notch1&2-null, Psen1&2-null, RBPjk-null) and wild-type hair follicle transcriptomes by NGS	The goals of this study is to test whether NICD presence protects the RBPjk-null Hair Follicles by altering gene expression via association with other DNA binding proteins at P3, just before the conversion to TSLP-producing keratin cysts. Overall design: Methods: Skin samples were embedded in OCT. Sectioned at 20µm thickness. Dehydrated in EtOH, and equilibrated to Xylene before the LCM procedure. Laser capture was performed with Arcturus Veritas. Methods: ~100 hair follicles from Notch-null, PS-null, RBPjk-null and wild-type samples were pooled into 3 biological replicates for each genotype and subjected to RNA isolation followed by RNA-Seq. Conclusions: A total of 2047 genes were differentially expressed (=1.5 fold) in three or more biological replicates of Notch mutant hair follicles compared to wild-type controls (p-value<0.05). Unsupervised hierarchical clustering analysis failed to distinguish between the mutants.		GSM2064357: Wildtype from Notch line; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Skin samples were embedded in OCT immediately after collecting and snap-frozen in liquid nitrogen before storing at -80°C Sectioned at 20μm thickness, tissue slices were placed on poly-lysine (Sigma-P8920; 1:10 dilution) treated PEN membrane glass slides (Arcturus, LCM0522), dehydrated in EtOH, and equilibrated to Xylene before the LCM procedure Laser capture was performed with Arcturus Veritas and Arcturus CapSure HS LCM Caps (Arcturus Engineering, Inc., Mountain View, CA) within 45 minutes to avoid degradation. 4 membrane with ~25-30 hair follicles each were pooled and stored in QIAzol (Qiagen) at -80°C. RNA extracted as described in methods was QCed for sequencing using an Agilent 2100 Bioanalyzer requiring integrity numbers >8 to pass. Libraries were prepared with the Nextera XT DNA Sample Preparation kit (Illumina Technologies). 1ng of cDNA was tagmented with the Amplicon Tagment Mix at 55°C for 10min. NT Buffer was added to neutralize the samples. Libraries were PCR amplified (Nextera PCR Master Mix) in the following program: one cycle of 72°C for 3min, one cycle of 98°C for 30s, 12 cycles of 95°C for 10s, 55°C for 30s, and 72°C for 1min, and one cycle of 72°C for 5min and (N7XX, and N5XX). The purified cDNA was captured on an Illumina flow cell for cluster generation and sequenced (75bp paired-end, 20 million reads, Illumina HiSeq2500) following the manufacturer's protocol.	Illumina HiSeq 2500	age;;Postnatal day (P) 3|genotype;;Wild-type|source_name;;Hair Follicle|strain;;Mixed background	GEO Accession;;GSM2064357		GSM2064357	Wildtype from Notch line	2689425000	17929500	2016-02-29 16:27:16	1627136343	2689425000	17929500	2	17929500	index:0,count:17929500,average:75,stdev:0|index:1,count:17929500,average:75,stdev:0	GSM2064357_r1				in_mesa	26940862	36.74	1.97	0.06	1961243068	1955770239	1858073370	1866220873	99.72	100.44	13964283	12876224	282.043	1069.620	281	52621	74.98	79.36	15244206	10470860	15244206	10470860	74.9	75.47	15244206	10458664	15244206	9956954	368343405	18.78	15.58	0	4.30	0	0.13	0	0.13	0	0.00	0	21.85	0	13964283	0	150	0	145.86	0	2.21	0	0.01	0	2.61	0	0.02	0	290.75	0	0.43	0	2793750	0	17929500	0	770309	0	23492	0	24038	0	0	0	3917687	0	987	0	0	0	8514	0	1187394	0	11825	0	1208720	0	73.59	0	13193974	0	116795	1220317	10.448366796524	17929500.0	13964283.0	2793750.0	770309.0	23492.0	24038.0	0.0	3917687.0	13193974.0	77.9	15.6	4.3	0.1	0.1	0.0	21.9	73.6	75	75	75.00	38	1344712500	28.3	21.1	21.7	29.0	0.0	37.5	20.5	bulk
1511550	SRR3175107	SRP070433	SRS1305169	SRX1589665	SRA354792	GEO		Quantitative Analysis of Notch mutant (Notch1&2-null, Psen1&2-null, RBPjk-null) and wild-type hair follicle transcriptomes by NGS	The goals of this study is to test whether NICD presence protects the RBPjk-null Hair Follicles by altering gene expression via association with other DNA binding proteins at P3, just before the conversion to TSLP-producing keratin cysts. Overall design: Methods: Skin samples were embedded in OCT. Sectioned at 20µm thickness. Dehydrated in EtOH, and equilibrated to Xylene before the LCM procedure. Laser capture was performed with Arcturus Veritas. Methods: ~100 hair follicles from Notch-null, PS-null, RBPjk-null and wild-type samples were pooled into 3 biological replicates for each genotype and subjected to RNA isolation followed by RNA-Seq. Conclusions: A total of 2047 genes were differentially expressed (=1.5 fold) in three or more biological replicates of Notch mutant hair follicles compared to wild-type controls (p-value<0.05). Unsupervised hierarchical clustering analysis failed to distinguish between the mutants.		GSM2064358: Wildtype from Preselin Line; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Skin samples were embedded in OCT immediately after collecting and snap-frozen in liquid nitrogen before storing at -80°C Sectioned at 20μm thickness, tissue slices were placed on poly-lysine (Sigma-P8920; 1:10 dilution) treated PEN membrane glass slides (Arcturus, LCM0522), dehydrated in EtOH, and equilibrated to Xylene before the LCM procedure Laser capture was performed with Arcturus Veritas and Arcturus CapSure HS LCM Caps (Arcturus Engineering, Inc., Mountain View, CA) within 45 minutes to avoid degradation. 4 membrane with ~25-30 hair follicles each were pooled and stored in QIAzol (Qiagen) at -80°C. RNA extracted as described in methods was QCed for sequencing using an Agilent 2100 Bioanalyzer requiring integrity numbers >8 to pass. Libraries were prepared with the Nextera XT DNA Sample Preparation kit (Illumina Technologies). 1ng of cDNA was tagmented with the Amplicon Tagment Mix at 55°C for 10min. NT Buffer was added to neutralize the samples. Libraries were PCR amplified (Nextera PCR Master Mix) in the following program: one cycle of 72°C for 3min, one cycle of 98°C for 30s, 12 cycles of 95°C for 10s, 55°C for 30s, and 72°C for 1min, and one cycle of 72°C for 5min and (N7XX, and N5XX). The purified cDNA was captured on an Illumina flow cell for cluster generation and sequenced (75bp paired-end, 20 million reads, Illumina HiSeq2500) following the manufacturer's protocol.	Illumina HiSeq 2500	age;;Postnatal day (P) 3|genotype;;Wild-type|source_name;;Hair Follicle|strain;;Mixed background	GEO Accession;;GSM2064358		GSM2064358	Wildtype from Preselin Line	2913640350	19424269	2016-02-29 16:27:16	1733699125	2913640350	19424269	2	19424269	index:0,count:19424269,average:75,stdev:0|index:1,count:19424269,average:75,stdev:0	GSM2064358_r1				in_mesa	26940862	41.48	2.21	0.03	2116066085	2084663776	2032536561	2012205051	98.52	99.0	15053422	14111344	283.522	1014.347	281	58577	73.52	76.71	16098462	11066864	16098462	11066864	74.28	74.57	16098462	11180986	16098462	10757297	456407429	21.57	18.05	0	3.23	0	0.12	0	0.18	0	0.00	0	22.21	0	15053422	0	150	0	145.85	0	1.87	0	0.01	0	2.32	0	0.01	0	279.71	0	0.37	0	3506850	0	19424269	0	627332	0	22760	0	34887	0	0	0	4313200	0	892	0	0	0	7910	0	1042339	0	11446	0	1062587	0	74.27	0	14426090	0	109920	1068977	9.725045487627	19424269.0	15053422.0	3506850.0	627332.0	22760.0	34887.0	0.0	4313200.0	14426090.0	77.5	18.1	3.2	0.1	0.2	0.0	22.2	74.3	75	75	75.00	38	1456820175	29.1	20.2	20.7	30.0	0.0	37.5	20.2	bulk
1511567	SRR3175108	SRP070433	SRS1305168	SRX1589666	SRA354792	GEO		Quantitative Analysis of Notch mutant (Notch1&2-null, Psen1&2-null, RBPjk-null) and wild-type hair follicle transcriptomes by NGS	The goals of this study is to test whether NICD presence protects the RBPjk-null Hair Follicles by altering gene expression via association with other DNA binding proteins at P3, just before the conversion to TSLP-producing keratin cysts. Overall design: Methods: Skin samples were embedded in OCT. Sectioned at 20µm thickness. Dehydrated in EtOH, and equilibrated to Xylene before the LCM procedure. Laser capture was performed with Arcturus Veritas. Methods: ~100 hair follicles from Notch-null, PS-null, RBPjk-null and wild-type samples were pooled into 3 biological replicates for each genotype and subjected to RNA isolation followed by RNA-Seq. Conclusions: A total of 2047 genes were differentially expressed (=1.5 fold) in three or more biological replicates of Notch mutant hair follicles compared to wild-type controls (p-value<0.05). Unsupervised hierarchical clustering analysis failed to distinguish between the mutants.		GSM2064359: Wildtype from RBPjk line; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Skin samples were embedded in OCT immediately after collecting and snap-frozen in liquid nitrogen before storing at -80°C Sectioned at 20μm thickness, tissue slices were placed on poly-lysine (Sigma-P8920; 1:10 dilution) treated PEN membrane glass slides (Arcturus, LCM0522), dehydrated in EtOH, and equilibrated to Xylene before the LCM procedure Laser capture was performed with Arcturus Veritas and Arcturus CapSure HS LCM Caps (Arcturus Engineering, Inc., Mountain View, CA) within 45 minutes to avoid degradation. 4 membrane with ~25-30 hair follicles each were pooled and stored in QIAzol (Qiagen) at -80°C. RNA extracted as described in methods was QCed for sequencing using an Agilent 2100 Bioanalyzer requiring integrity numbers >8 to pass. Libraries were prepared with the Nextera XT DNA Sample Preparation kit (Illumina Technologies). 1ng of cDNA was tagmented with the Amplicon Tagment Mix at 55°C for 10min. NT Buffer was added to neutralize the samples. Libraries were PCR amplified (Nextera PCR Master Mix) in the following program: one cycle of 72°C for 3min, one cycle of 98°C for 30s, 12 cycles of 95°C for 10s, 55°C for 30s, and 72°C for 1min, and one cycle of 72°C for 5min and (N7XX, and N5XX). The purified cDNA was captured on an Illumina flow cell for cluster generation and sequenced (75bp paired-end, 20 million reads, Illumina HiSeq2500) following the manufacturer's protocol.	Illumina HiSeq 2500	age;;Postnatal day (P) 3|genotype;;Wild-type|source_name;;Hair Follicle|strain;;Mixed background	GEO Accession;;GSM2064359		GSM2064359	Wildtype from RBPjk line	2948894550	19659297	2016-02-29 16:27:16	1801595005	2948894550	19659297	2	19659297	index:0,count:19659297,average:75,stdev:0|index:1,count:19659297,average:75,stdev:0	GSM2064359_r1				in_mesa	26940862	35.75	2.16	0.11	2102703115	2062944824	2010534693	1983639889	98.11	98.66	14992869	13956080	271.858	1086.778	258	58004	71.03	74.46	16195917	10649347	16195917	10649347	71.61	72.05	16195917	10736225	16195917	10305489	493554212	23.47	18.26	0	3.51	0	0.14	0	0.18	0	0.00	0	23.42	0	14992869	0	150	0	145.52	0	1.95	0	0.01	0	2.42	0	0.02	0	279.74	0	0.45	0	3589601	0	19659297	0	689848	0	26790	0	35267	0	0	0	4604371	0	1046	0	0	0	8949	0	1187163	0	13445	0	1210603	0	72.75	0	14303021	0	117319	1218275	10.384294104109	19659297.0	14992869.0	3589601.0	689848.0	26790.0	35267.0	0.0	4604371.0	14303021.0	76.3	18.3	3.5	0.1	0.2	0.0	23.4	72.8	75	75	75.00	38	1474447275	28.5	20.6	21.3	29.6	0.0	37.5	20.3	bulk
1511582	SRR3175109	SRP070433	SRS1305167	SRX1589667	SRA354792	GEO		Quantitative Analysis of Notch mutant (Notch1&2-null, Psen1&2-null, RBPjk-null) and wild-type hair follicle transcriptomes by NGS	The goals of this study is to test whether NICD presence protects the RBPjk-null Hair Follicles by altering gene expression via association with other DNA binding proteins at P3, just before the conversion to TSLP-producing keratin cysts. Overall design: Methods: Skin samples were embedded in OCT. Sectioned at 20µm thickness. Dehydrated in EtOH, and equilibrated to Xylene before the LCM procedure. Laser capture was performed with Arcturus Veritas. Methods: ~100 hair follicles from Notch-null, PS-null, RBPjk-null and wild-type samples were pooled into 3 biological replicates for each genotype and subjected to RNA isolation followed by RNA-Seq. Conclusions: A total of 2047 genes were differentially expressed (=1.5 fold) in three or more biological replicates of Notch mutant hair follicles compared to wild-type controls (p-value<0.05). Unsupervised hierarchical clustering analysis failed to distinguish between the mutants.		GSM2064360: Mixture of wildtypes from N, PS, and RBPj lines; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Skin samples were embedded in OCT immediately after collecting and snap-frozen in liquid nitrogen before storing at -80°C Sectioned at 20μm thickness, tissue slices were placed on poly-lysine (Sigma-P8920; 1:10 dilution) treated PEN membrane glass slides (Arcturus, LCM0522), dehydrated in EtOH, and equilibrated to Xylene before the LCM procedure Laser capture was performed with Arcturus Veritas and Arcturus CapSure HS LCM Caps (Arcturus Engineering, Inc., Mountain View, CA) within 45 minutes to avoid degradation. 4 membrane with ~25-30 hair follicles each were pooled and stored in QIAzol (Qiagen) at -80°C. RNA extracted as described in methods was QCed for sequencing using an Agilent 2100 Bioanalyzer requiring integrity numbers >8 to pass. Libraries were prepared with the Nextera XT DNA Sample Preparation kit (Illumina Technologies). 1ng of cDNA was tagmented with the Amplicon Tagment Mix at 55°C for 10min. NT Buffer was added to neutralize the samples. Libraries were PCR amplified (Nextera PCR Master Mix) in the following program: one cycle of 72°C for 3min, one cycle of 98°C for 30s, 12 cycles of 95°C for 10s, 55°C for 30s, and 72°C for 1min, and one cycle of 72°C for 5min and (N7XX, and N5XX). The purified cDNA was captured on an Illumina flow cell for cluster generation and sequenced (75bp paired-end, 20 million reads, Illumina HiSeq2500) following the manufacturer's protocol.	Illumina HiSeq 2500	age;;Postnatal day (P) 3|genotype;;Wild-type|source_name;;Hair Follicle|strain;;Mixed background	GEO Accession;;GSM2064360		GSM2064360	Mixture of wildtypes from N, PS, and RBPj lines	2979038400	19860256	2016-02-29 16:27:16	1754023801	2979038400	19860256	2	19860256	index:0,count:19860256,average:75,stdev:0|index:1,count:19860256,average:75,stdev:0	GSM2064360_r1				in_mesa	26940862	37.45	2.02	0.06	2181593828	2161804216	2077579605	2071778228	99.09	99.72	15570801	14581073	263.018	953.482	258	64169	72.99	76.84	16891460	11365013	16891460	11365013	72.82	73.37	16891460	11338880	16891460	10851779	457591093	20.98	16.61	0	3.93	0	0.12	0	0.16	0	0.00	0	21.32	0	15570801	0	150	0	145.71	0	2.09	0	0.01	0	2.53	0	0.02	0	308.18	0	0.40	0	3299107	0	19860256	0	781063	0	24618	0	31398	0	0	0	4233439	0	1083	0	0	0	8825	0	1192106	0	13139	0	1215153	0	74.47	0	14789738	0	117117	1221924	10.433361510285	19860256.0	15570801.0	3299107.0	781063.0	24618.0	31398.0	0.0	4233439.0	14789738.0	78.4	16.6	3.9	0.1	0.2	0.0	21.3	74.5	75	75	75.00	38	1489519200	28.4	20.8	21.4	29.3	0.0	37.5	20.4	bulk
2818195	SRR3212804	SRP071321	SRS1329181	SRX1620342	SRA382274	GEO		Extensive cryptic splicing upon loss of RBM17 and TDP43 in neurodegeneration models	Translating ribosome affinity purification technology was used to isolate mRNAs from cerebellar Purkinje neurons from control (Pcp2-BacTrap; Rbm17 f/+) and mutant (Pcp2-BacTRAP; Pcp2-Cre; Rbm17 f/-) mice. Overall design: RNA isolation was performed when animals were four-weeks-old (n=3 animals per genotype). Using NuGEN Ovation RNA-Seq System v2, purified double-stranded cDNA was generated from 10 ng of total RNA and amplified using both 3' poly (A) selection and random priming. 2 µg of each sample was sheared using the Covaris S2 focused-ultrasonicator following the manufacturer's protocol to obtain a final library with insert size of 400 bp. The sheared samples were quantified using the NanoDrop ND-1000 spectrophotometer and Invitrogen Qubit 2.0 DNA quantitation assay. The fragment sizes were confirmed on the Agilent Bioanalyzer to verify proper shearing. A double-stranded DNA library was produced using Illumina TruSeq DNA library preparation system and the sequencing was run on a HiSeq 2500 system.		GSM2083850: Control 1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			BacTRAP profiling was performed as previously described (Heiman et al. 2014) with the following modifications: One cerebellum was homogenized in 1.5 mL of homogenization buffer and 60 µg each of 19C8 and 19F7 was used for every immunoprecipitation experiment. Using NuGEN Ovation RNA-Seq System v2, purified double-stranded cDNA was generated from 10 ng of total RNA and amplified using both 3’ poly (A) selection and random priming. 2 µg of each sample was sheared using the Covaris S2 focused-ultrasonicator following the manufacturer’s protocol to obtain a final library with insert size of 400 bp. The sheared samples were quantified using the NanoDrop ND-1000 spectrophotometer and Invitrogen Qubit 2.0 DNA quantitation assay. The fragment sizes were confirmed on the Agilent Bioanalyzer to verify proper shearing. A double-stranded DNA library was produced using Illumina TruSeq DNA library preparation system and the sequencing was run on a HiSeq 2500 system.	Illumina HiSeq 2500	age;;4-weeks-old|genotype/variation;;Pcp2-BacTrap; Rbm17 f/+|source_name;;Cerebellar Purkinje neurons|strain;;C57BL/6|tissue;;brain	GEO Accession;;GSM2083850		GSM2083850	Control 1	6092170318	30159259	2016-10-31 08:44:35	4501508052	6092170318	30159259	2	30159259	index:0,count:30159259,average:101,stdev:0|index:1,count:30159259,average:101,stdev:0	GSM2083850_r1				in_mesa	28007900	0.08	2.63	0.03	4704025781	4813173511	4491803718	4631151594	102.32	103.1	26488926	23957760	226.231	1159.611	169	168175	86.94	91.23	28564698	23028431	28564698	23028431	80.64	82.22	28564698	21359365	28564698	20753952	274261378	5.83	7.23	0	4.14	0	0.36	0	0.03	0	0.00	0	11.77	0	26488926	0	202	0	196.70	0	3.50	0	0.02	0	2.49	0	0.02	0	208.79	0	0.50	0	2180137	0	30159259	0	1247634	0	109837	0	10057	0	0	0	3550439	0	8782	0	0	0	62338	0	9556989	0	32341	0	9660450	0	83.69	0	25241292	0	175518	9269627	52.812970749439	30159259.0	26488926.0	2180137.0	1247634.0	109837.0	10057.0	0.0	3550439.0	25241292.0	87.8	7.2	4.1	0.4	0.0	0.0	11.8	83.7	101	101	101.00	38	3046085159	24.8	25.2	25.4	24.6	0.0	34.1	21.5	bulk
2818227	SRR3212805	SRP071321	SRS1329181	SRX1620342	SRA382274	GEO		Extensive cryptic splicing upon loss of RBM17 and TDP43 in neurodegeneration models	Translating ribosome affinity purification technology was used to isolate mRNAs from cerebellar Purkinje neurons from control (Pcp2-BacTrap; Rbm17 f/+) and mutant (Pcp2-BacTRAP; Pcp2-Cre; Rbm17 f/-) mice. Overall design: RNA isolation was performed when animals were four-weeks-old (n=3 animals per genotype). Using NuGEN Ovation RNA-Seq System v2, purified double-stranded cDNA was generated from 10 ng of total RNA and amplified using both 3' poly (A) selection and random priming. 2 µg of each sample was sheared using the Covaris S2 focused-ultrasonicator following the manufacturer's protocol to obtain a final library with insert size of 400 bp. The sheared samples were quantified using the NanoDrop ND-1000 spectrophotometer and Invitrogen Qubit 2.0 DNA quantitation assay. The fragment sizes were confirmed on the Agilent Bioanalyzer to verify proper shearing. A double-stranded DNA library was produced using Illumina TruSeq DNA library preparation system and the sequencing was run on a HiSeq 2500 system.		GSM2083850: Control 1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			BacTRAP profiling was performed as previously described (Heiman et al. 2014) with the following modifications: One cerebellum was homogenized in 1.5 mL of homogenization buffer and 60 µg each of 19C8 and 19F7 was used for every immunoprecipitation experiment. Using NuGEN Ovation RNA-Seq System v2, purified double-stranded cDNA was generated from 10 ng of total RNA and amplified using both 3’ poly (A) selection and random priming. 2 µg of each sample was sheared using the Covaris S2 focused-ultrasonicator following the manufacturer’s protocol to obtain a final library with insert size of 400 bp. The sheared samples were quantified using the NanoDrop ND-1000 spectrophotometer and Invitrogen Qubit 2.0 DNA quantitation assay. The fragment sizes were confirmed on the Agilent Bioanalyzer to verify proper shearing. A double-stranded DNA library was produced using Illumina TruSeq DNA library preparation system and the sequencing was run on a HiSeq 2500 system.	Illumina HiSeq 2500	age;;4-weeks-old|genotype/variation;;Pcp2-BacTrap; Rbm17 f/+|source_name;;Cerebellar Purkinje neurons|strain;;C57BL/6|tissue;;brain	GEO Accession;;GSM2083850		GSM2083850	Control 1	6066532276	30032338	2016-10-31 08:44:35	4496586703	6066532276	30032338	2	30032338	index:0,count:30032338,average:101,stdev:0|index:1,count:30032338,average:101,stdev:0	GSM2083850_r2				in_mesa	28007900	0.08	2.64	0.03	4676244774	4783194983	4465761997	4602960767	102.29	103.07	26350859	23844503	225.866	1154.316	169	167801	86.93	91.22	28410236	22907315	28410236	22907315	80.65	82.23	28410236	21251918	28410236	20650575	273537884	5.85	7.21	0	4.12	0	0.36	0	0.03	0	0.00	0	11.87	0	26350859	0	202	0	196.63	0	3.51	0	0.02	0	2.48	0	0.02	0	218.86	0	0.52	0	2165153	0	30032338	0	1238059	0	108462	0	9643	0	0	0	3563374	0	8771	0	0	0	61627	0	9469260	0	31767	0	9571425	0	83.62	0	25112800	0	175478	9182229	52.326952666431	30032338.0	26350859.0	2165153.0	1238059.0	108462.0	9643.0	0.0	3563374.0	25112800.0	87.7	7.2	4.1	0.4	0.0	0.0	11.9	83.6	101	101	101.00	38	3033266138	24.8	25.2	25.4	24.6	0.0	34.0	21.3	bulk
2818258	SRR3212806	SRP071321	SRS1329181	SRX1620342	SRA382274	GEO		Extensive cryptic splicing upon loss of RBM17 and TDP43 in neurodegeneration models	Translating ribosome affinity purification technology was used to isolate mRNAs from cerebellar Purkinje neurons from control (Pcp2-BacTrap; Rbm17 f/+) and mutant (Pcp2-BacTRAP; Pcp2-Cre; Rbm17 f/-) mice. Overall design: RNA isolation was performed when animals were four-weeks-old (n=3 animals per genotype). Using NuGEN Ovation RNA-Seq System v2, purified double-stranded cDNA was generated from 10 ng of total RNA and amplified using both 3' poly (A) selection and random priming. 2 µg of each sample was sheared using the Covaris S2 focused-ultrasonicator following the manufacturer's protocol to obtain a final library with insert size of 400 bp. The sheared samples were quantified using the NanoDrop ND-1000 spectrophotometer and Invitrogen Qubit 2.0 DNA quantitation assay. The fragment sizes were confirmed on the Agilent Bioanalyzer to verify proper shearing. A double-stranded DNA library was produced using Illumina TruSeq DNA library preparation system and the sequencing was run on a HiSeq 2500 system.		GSM2083850: Control 1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			BacTRAP profiling was performed as previously described (Heiman et al. 2014) with the following modifications: One cerebellum was homogenized in 1.5 mL of homogenization buffer and 60 µg each of 19C8 and 19F7 was used for every immunoprecipitation experiment. Using NuGEN Ovation RNA-Seq System v2, purified double-stranded cDNA was generated from 10 ng of total RNA and amplified using both 3’ poly (A) selection and random priming. 2 µg of each sample was sheared using the Covaris S2 focused-ultrasonicator following the manufacturer’s protocol to obtain a final library with insert size of 400 bp. The sheared samples were quantified using the NanoDrop ND-1000 spectrophotometer and Invitrogen Qubit 2.0 DNA quantitation assay. The fragment sizes were confirmed on the Agilent Bioanalyzer to verify proper shearing. A double-stranded DNA library was produced using Illumina TruSeq DNA library preparation system and the sequencing was run on a HiSeq 2500 system.	Illumina HiSeq 2500	age;;4-weeks-old|genotype/variation;;Pcp2-BacTrap; Rbm17 f/+|source_name;;Cerebellar Purkinje neurons|strain;;C57BL/6|tissue;;brain	GEO Accession;;GSM2083850		GSM2083850	Control 1	6101425150	30205075	2016-10-31 08:44:35	4510719059	6101425150	30205075	2	30205075	index:0,count:30205075,average:101,stdev:0|index:1,count:30205075,average:101,stdev:0	GSM2083850_r3				in_mesa	28007900	0.08	2.63	0.03	4711010421	4820742770	4498299668	4638302141	102.33	103.11	26556866	24036655	225.557	1153.974	170	168355	86.86	91.16	28636398	23067822	28636398	23067822	80.5	82.08	28636398	21379507	28636398	20771165	276589774	5.87	7.30	0	4.15	0	0.36	0	0.03	0	0.00	0	11.69	0	26556866	0	202	0	196.64	0	3.53	0	0.02	0	2.50	0	0.03	0	225.60	0	0.51	0	2205908	0	30205075	0	1252034	0	108583	0	9838	0	0	0	3529788	0	8956	0	0	0	62106	0	9517183	0	32631	0	9620876	0	83.78	0	25304832	0	175225	9227670	52.661834783849	30205075.0	26556866.0	2205908.0	1252034.0	108583.0	9838.0	0.0	3529788.0	25304832.0	87.9	7.3	4.1	0.4	0.0	0.0	11.7	83.8	101	101	101.00	38	3050712575	24.8	25.2	25.4	24.6	0.0	34.1	21.7	bulk
2818291	SRR3212807	SRP071321	SRS1329181	SRX1620342	SRA382274	GEO		Extensive cryptic splicing upon loss of RBM17 and TDP43 in neurodegeneration models	Translating ribosome affinity purification technology was used to isolate mRNAs from cerebellar Purkinje neurons from control (Pcp2-BacTrap; Rbm17 f/+) and mutant (Pcp2-BacTRAP; Pcp2-Cre; Rbm17 f/-) mice. Overall design: RNA isolation was performed when animals were four-weeks-old (n=3 animals per genotype). Using NuGEN Ovation RNA-Seq System v2, purified double-stranded cDNA was generated from 10 ng of total RNA and amplified using both 3' poly (A) selection and random priming. 2 µg of each sample was sheared using the Covaris S2 focused-ultrasonicator following the manufacturer's protocol to obtain a final library with insert size of 400 bp. The sheared samples were quantified using the NanoDrop ND-1000 spectrophotometer and Invitrogen Qubit 2.0 DNA quantitation assay. The fragment sizes were confirmed on the Agilent Bioanalyzer to verify proper shearing. A double-stranded DNA library was produced using Illumina TruSeq DNA library preparation system and the sequencing was run on a HiSeq 2500 system.		GSM2083850: Control 1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			BacTRAP profiling was performed as previously described (Heiman et al. 2014) with the following modifications: One cerebellum was homogenized in 1.5 mL of homogenization buffer and 60 µg each of 19C8 and 19F7 was used for every immunoprecipitation experiment. Using NuGEN Ovation RNA-Seq System v2, purified double-stranded cDNA was generated from 10 ng of total RNA and amplified using both 3’ poly (A) selection and random priming. 2 µg of each sample was sheared using the Covaris S2 focused-ultrasonicator following the manufacturer’s protocol to obtain a final library with insert size of 400 bp. The sheared samples were quantified using the NanoDrop ND-1000 spectrophotometer and Invitrogen Qubit 2.0 DNA quantitation assay. The fragment sizes were confirmed on the Agilent Bioanalyzer to verify proper shearing. A double-stranded DNA library was produced using Illumina TruSeq DNA library preparation system and the sequencing was run on a HiSeq 2500 system.	Illumina HiSeq 2500	age;;4-weeks-old|genotype/variation;;Pcp2-BacTrap; Rbm17 f/+|source_name;;Cerebellar Purkinje neurons|strain;;C57BL/6|tissue;;brain	GEO Accession;;GSM2083850		GSM2083850	Control 1	6094645626	30171513	2016-10-31 08:44:35	4512482804	6094645626	30171513	2	30171513	index:0,count:30171513,average:101,stdev:0|index:1,count:30171513,average:101,stdev:0	GSM2083850_r4				in_mesa	28007900	0.08	2.63	0.03	4708613513	4819416491	4496662439	4637779119	102.35	103.14	26548588	24040167	225.392	1152.875	169	169729	86.84	91.13	28624258	23055294	28624258	23055294	80.43	82.01	28624258	21353243	28624258	20748379	277042802	5.88	7.35	0	4.14	0	0.36	0	0.03	0	0.00	0	11.62	0	26548588	0	202	0	196.63	0	3.57	0	0.02	0	2.50	0	0.03	0	196.06	0	0.49	0	2218901	0	30171513	0	1247927	0	107961	0	9920	0	0	0	3505044	0	8942	0	0	0	62285	0	9506801	0	32896	0	9610924	0	83.86	0	25300661	0	175511	9215074	52.504253294665	30171513.0	26548588.0	2218901.0	1247927.0	107961.0	9920.0	0.0	3505044.0	25300661.0	88.0	7.4	4.1	0.4	0.0	0.0	11.6	83.9	101	101	101.00	38	3047322813	24.8	25.2	25.4	24.7	0.0	34.1	21.8	bulk
2818323	SRR3212808	SRP071321	SRS1329181	SRX1620342	SRA382274	GEO		Extensive cryptic splicing upon loss of RBM17 and TDP43 in neurodegeneration models	Translating ribosome affinity purification technology was used to isolate mRNAs from cerebellar Purkinje neurons from control (Pcp2-BacTrap; Rbm17 f/+) and mutant (Pcp2-BacTRAP; Pcp2-Cre; Rbm17 f/-) mice. Overall design: RNA isolation was performed when animals were four-weeks-old (n=3 animals per genotype). Using NuGEN Ovation RNA-Seq System v2, purified double-stranded cDNA was generated from 10 ng of total RNA and amplified using both 3' poly (A) selection and random priming. 2 µg of each sample was sheared using the Covaris S2 focused-ultrasonicator following the manufacturer's protocol to obtain a final library with insert size of 400 bp. The sheared samples were quantified using the NanoDrop ND-1000 spectrophotometer and Invitrogen Qubit 2.0 DNA quantitation assay. The fragment sizes were confirmed on the Agilent Bioanalyzer to verify proper shearing. A double-stranded DNA library was produced using Illumina TruSeq DNA library preparation system and the sequencing was run on a HiSeq 2500 system.		GSM2083850: Control 1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			BacTRAP profiling was performed as previously described (Heiman et al. 2014) with the following modifications: One cerebellum was homogenized in 1.5 mL of homogenization buffer and 60 µg each of 19C8 and 19F7 was used for every immunoprecipitation experiment. Using NuGEN Ovation RNA-Seq System v2, purified double-stranded cDNA was generated from 10 ng of total RNA and amplified using both 3’ poly (A) selection and random priming. 2 µg of each sample was sheared using the Covaris S2 focused-ultrasonicator following the manufacturer’s protocol to obtain a final library with insert size of 400 bp. The sheared samples were quantified using the NanoDrop ND-1000 spectrophotometer and Invitrogen Qubit 2.0 DNA quantitation assay. The fragment sizes were confirmed on the Agilent Bioanalyzer to verify proper shearing. A double-stranded DNA library was produced using Illumina TruSeq DNA library preparation system and the sequencing was run on a HiSeq 2500 system.	Illumina HiSeq 2500	age;;4-weeks-old|genotype/variation;;Pcp2-BacTrap; Rbm17 f/+|source_name;;Cerebellar Purkinje neurons|strain;;C57BL/6|tissue;;brain	GEO Accession;;GSM2083850		GSM2083850	Control 1	6215821386	30771393	2016-10-31 08:44:35	4589569043	6215821386	30771393	2	30771393	index:0,count:30771393,average:101,stdev:0|index:1,count:30771393,average:101,stdev:0	GSM2083850_r5				in_mesa	28007900	0.08	2.63	0.03	4799270733	4911695196	4582874658	4726165073	102.34	103.13	27060315	24507430	225.317	1149.421	169	172363	86.83	91.12	29177965	23497535	29177965	23497535	80.43	82.01	29177965	21765443	29177965	21148448	282486418	5.89	7.29	0	4.14	0	0.36	0	0.03	0	0.00	0	11.67	0	27060315	0	202	0	196.66	0	3.53	0	0.02	0	2.51	0	0.03	0	198.88	0	0.50	0	2241947	0	30771393	0	1274098	0	110668	0	9872	0	0	0	3590538	0	8993	0	0	0	62593	0	9706892	0	33325	0	9811803	0	83.80	0	25786217	0	175987	9405088	53.441947416571	30771393.0	27060315.0	2241947.0	1274098.0	110668.0	9872.0	0.0	3590538.0	25786217.0	87.9	7.3	4.1	0.4	0.0	0.0	11.7	83.8	101	101	101.00	38	3107910693	24.8	25.2	25.4	24.6	0.0	34.2	21.9	bulk
2818354	SRR3212809	SRP071321	SRS1329181	SRX1620342	SRA382274	GEO		Extensive cryptic splicing upon loss of RBM17 and TDP43 in neurodegeneration models	Translating ribosome affinity purification technology was used to isolate mRNAs from cerebellar Purkinje neurons from control (Pcp2-BacTrap; Rbm17 f/+) and mutant (Pcp2-BacTRAP; Pcp2-Cre; Rbm17 f/-) mice. Overall design: RNA isolation was performed when animals were four-weeks-old (n=3 animals per genotype). Using NuGEN Ovation RNA-Seq System v2, purified double-stranded cDNA was generated from 10 ng of total RNA and amplified using both 3' poly (A) selection and random priming. 2 µg of each sample was sheared using the Covaris S2 focused-ultrasonicator following the manufacturer's protocol to obtain a final library with insert size of 400 bp. The sheared samples were quantified using the NanoDrop ND-1000 spectrophotometer and Invitrogen Qubit 2.0 DNA quantitation assay. The fragment sizes were confirmed on the Agilent Bioanalyzer to verify proper shearing. A double-stranded DNA library was produced using Illumina TruSeq DNA library preparation system and the sequencing was run on a HiSeq 2500 system.		GSM2083850: Control 1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			BacTRAP profiling was performed as previously described (Heiman et al. 2014) with the following modifications: One cerebellum was homogenized in 1.5 mL of homogenization buffer and 60 µg each of 19C8 and 19F7 was used for every immunoprecipitation experiment. Using NuGEN Ovation RNA-Seq System v2, purified double-stranded cDNA was generated from 10 ng of total RNA and amplified using both 3’ poly (A) selection and random priming. 2 µg of each sample was sheared using the Covaris S2 focused-ultrasonicator following the manufacturer’s protocol to obtain a final library with insert size of 400 bp. The sheared samples were quantified using the NanoDrop ND-1000 spectrophotometer and Invitrogen Qubit 2.0 DNA quantitation assay. The fragment sizes were confirmed on the Agilent Bioanalyzer to verify proper shearing. A double-stranded DNA library was produced using Illumina TruSeq DNA library preparation system and the sequencing was run on a HiSeq 2500 system.	Illumina HiSeq 2500	age;;4-weeks-old|genotype/variation;;Pcp2-BacTrap; Rbm17 f/+|source_name;;Cerebellar Purkinje neurons|strain;;C57BL/6|tissue;;brain	GEO Accession;;GSM2083850		GSM2083850	Control 1	6175813468	30573334	2016-10-31 08:44:35	4546309071	6175813468	30573334	2	30573334	index:0,count:30573334,average:101,stdev:0|index:1,count:30573334,average:101,stdev:0	GSM2083850_r6				in_mesa	28007900	0.08	2.63	0.03	4769680145	4881164979	4554827787	4697048522	102.34	103.12	26895733	24364464	225.216	1147.422	170	171455	86.85	91.14	29003283	23359022	29003283	23359022	80.45	82.03	29003283	21638205	29003283	21025511	280534854	5.88	7.32	0	4.14	0	0.36	0	0.03	0	0.00	0	11.64	0	26895733	0	202	0	196.68	0	3.55	0	0.02	0	2.50	0	0.03	0	175.54	0	0.49	0	2238166	0	30573334	0	1265189	0	109473	0	10444	0	0	0	3557684	0	9003	0	0	0	63181	0	9648870	0	33281	0	9754335	0	83.83	0	25630544	0	176084	9347022	53.082744599169	30573334.0	26895733.0	2238166.0	1265189.0	109473.0	10444.0	0.0	3557684.0	25630544.0	88.0	7.3	4.1	0.4	0.0	0.0	11.6	83.8	101	101	101.00	38	3087906734	24.8	25.2	25.4	24.6	0.0	34.3	22.0	bulk
2818578	SRR3212810	SRP071321	SRS1329180	SRX1620343	SRA382274	GEO		Extensive cryptic splicing upon loss of RBM17 and TDP43 in neurodegeneration models	Translating ribosome affinity purification technology was used to isolate mRNAs from cerebellar Purkinje neurons from control (Pcp2-BacTrap; Rbm17 f/+) and mutant (Pcp2-BacTRAP; Pcp2-Cre; Rbm17 f/-) mice. Overall design: RNA isolation was performed when animals were four-weeks-old (n=3 animals per genotype). Using NuGEN Ovation RNA-Seq System v2, purified double-stranded cDNA was generated from 10 ng of total RNA and amplified using both 3' poly (A) selection and random priming. 2 µg of each sample was sheared using the Covaris S2 focused-ultrasonicator following the manufacturer's protocol to obtain a final library with insert size of 400 bp. The sheared samples were quantified using the NanoDrop ND-1000 spectrophotometer and Invitrogen Qubit 2.0 DNA quantitation assay. The fragment sizes were confirmed on the Agilent Bioanalyzer to verify proper shearing. A double-stranded DNA library was produced using Illumina TruSeq DNA library preparation system and the sequencing was run on a HiSeq 2500 system.		GSM2083851: Control 2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			BacTRAP profiling was performed as previously described (Heiman et al. 2014) with the following modifications: One cerebellum was homogenized in 1.5 mL of homogenization buffer and 60 µg each of 19C8 and 19F7 was used for every immunoprecipitation experiment. Using NuGEN Ovation RNA-Seq System v2, purified double-stranded cDNA was generated from 10 ng of total RNA and amplified using both 3’ poly (A) selection and random priming. 2 µg of each sample was sheared using the Covaris S2 focused-ultrasonicator following the manufacturer’s protocol to obtain a final library with insert size of 400 bp. The sheared samples were quantified using the NanoDrop ND-1000 spectrophotometer and Invitrogen Qubit 2.0 DNA quantitation assay. The fragment sizes were confirmed on the Agilent Bioanalyzer to verify proper shearing. A double-stranded DNA library was produced using Illumina TruSeq DNA library preparation system and the sequencing was run on a HiSeq 2500 system.	Illumina HiSeq 2500	age;;4-weeks-old|genotype/variation;;Pcp2-BacTrap; Rbm17 f/+|source_name;;Cerebellar Purkinje neurons|strain;;C57BL/6|tissue;;brain	GEO Accession;;GSM2083851		GSM2083851	Control 2	6509761888	32226544	2016-10-31 08:44:35	4824118611	6509761888	32226544	2	32226544	index:0,count:32226544,average:101,stdev:0|index:1,count:32226544,average:101,stdev:0	GSM2083851_r1				in_mesa	28007900	0.09	2.56	0.03	5013205699	5145985245	4777287019	4944720592	102.65	103.5	28237519	25575721	226.821	1141.696	169	178458	86.17	90.62	30524207	24331103	30524207	24331103	79.19	80.92	30524207	22361417	30524207	21725853	313668233	6.26	7.14	0	4.31	0	0.33	0	0.03	0	0.00	0	12.01	0	28237519	0	202	0	196.55	0	3.64	0	0.02	0	2.58	0	0.03	0	203.18	0	0.53	0	2300089	0	32226544	0	1388691	0	107847	0	10689	0	0	0	3870489	0	9106	0	0	0	64581	0	9981248	0	34987	0	10089922	0	83.31	0	26848828	0	180812	9694099	53.614245735902	32226544.0	28237519.0	2300089.0	1388691.0	107847.0	10689.0	0.0	3870489.0	26848828.0	87.6	7.1	4.3	0.3	0.0	0.0	12.0	83.3	101	101	101.00	38	3254880944	24.5	25.5	25.6	24.4	0.0	33.9	21.4	bulk
2818609	SRR3212811	SRP071321	SRS1329180	SRX1620343	SRA382274	GEO		Extensive cryptic splicing upon loss of RBM17 and TDP43 in neurodegeneration models	Translating ribosome affinity purification technology was used to isolate mRNAs from cerebellar Purkinje neurons from control (Pcp2-BacTrap; Rbm17 f/+) and mutant (Pcp2-BacTRAP; Pcp2-Cre; Rbm17 f/-) mice. Overall design: RNA isolation was performed when animals were four-weeks-old (n=3 animals per genotype). Using NuGEN Ovation RNA-Seq System v2, purified double-stranded cDNA was generated from 10 ng of total RNA and amplified using both 3' poly (A) selection and random priming. 2 µg of each sample was sheared using the Covaris S2 focused-ultrasonicator following the manufacturer's protocol to obtain a final library with insert size of 400 bp. The sheared samples were quantified using the NanoDrop ND-1000 spectrophotometer and Invitrogen Qubit 2.0 DNA quantitation assay. The fragment sizes were confirmed on the Agilent Bioanalyzer to verify proper shearing. A double-stranded DNA library was produced using Illumina TruSeq DNA library preparation system and the sequencing was run on a HiSeq 2500 system.		GSM2083851: Control 2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			BacTRAP profiling was performed as previously described (Heiman et al. 2014) with the following modifications: One cerebellum was homogenized in 1.5 mL of homogenization buffer and 60 µg each of 19C8 and 19F7 was used for every immunoprecipitation experiment. Using NuGEN Ovation RNA-Seq System v2, purified double-stranded cDNA was generated from 10 ng of total RNA and amplified using both 3’ poly (A) selection and random priming. 2 µg of each sample was sheared using the Covaris S2 focused-ultrasonicator following the manufacturer’s protocol to obtain a final library with insert size of 400 bp. The sheared samples were quantified using the NanoDrop ND-1000 spectrophotometer and Invitrogen Qubit 2.0 DNA quantitation assay. The fragment sizes were confirmed on the Agilent Bioanalyzer to verify proper shearing. A double-stranded DNA library was produced using Illumina TruSeq DNA library preparation system and the sequencing was run on a HiSeq 2500 system.	Illumina HiSeq 2500	age;;4-weeks-old|genotype/variation;;Pcp2-BacTrap; Rbm17 f/+|source_name;;Cerebellar Purkinje neurons|strain;;C57BL/6|tissue;;brain	GEO Accession;;GSM2083851		GSM2083851	Control 2	6472485212	32042006	2016-10-31 08:44:35	4810186714	6472485212	32042006	2	32042006	index:0,count:32042006,average:101,stdev:0|index:1,count:32042006,average:101,stdev:0	GSM2083851_r2				in_mesa	28007900	0.09	2.57	0.03	4975915139	5105817854	4742264032	4906883288	102.61	103.47	28046975	25407978	226.446	1141.016	170	178220	86.18	90.63	30312328	24171025	30312328	24171025	79.24	80.96	30312328	22223381	30312328	21592116	311857408	6.27	7.12	0	4.30	0	0.33	0	0.03	0	0.00	0	12.10	0	28046975	0	202	0	196.47	0	3.66	0	0.02	0	2.56	0	0.03	0	221.40	0	0.54	0	2281224	0	32042006	0	1376346	0	106496	0	10430	0	0	0	3878105	0	9291	0	0	0	63767	0	9882660	0	34775	0	9990493	0	83.24	0	26670629	0	180182	9591921	53.234623880299	32042006.0	28046975.0	2281224.0	1376346.0	106496.0	10430.0	0.0	3878105.0	26670629.0	87.5	7.1	4.3	0.3	0.0	0.0	12.1	83.2	101	101	101.00	38	3236242606	24.5	25.5	25.6	24.4	0.0	33.8	21.2	bulk
2818641	SRR3212812	SRP071321	SRS1329180	SRX1620343	SRA382274	GEO		Extensive cryptic splicing upon loss of RBM17 and TDP43 in neurodegeneration models	Translating ribosome affinity purification technology was used to isolate mRNAs from cerebellar Purkinje neurons from control (Pcp2-BacTrap; Rbm17 f/+) and mutant (Pcp2-BacTRAP; Pcp2-Cre; Rbm17 f/-) mice. Overall design: RNA isolation was performed when animals were four-weeks-old (n=3 animals per genotype). Using NuGEN Ovation RNA-Seq System v2, purified double-stranded cDNA was generated from 10 ng of total RNA and amplified using both 3' poly (A) selection and random priming. 2 µg of each sample was sheared using the Covaris S2 focused-ultrasonicator following the manufacturer's protocol to obtain a final library with insert size of 400 bp. The sheared samples were quantified using the NanoDrop ND-1000 spectrophotometer and Invitrogen Qubit 2.0 DNA quantitation assay. The fragment sizes were confirmed on the Agilent Bioanalyzer to verify proper shearing. A double-stranded DNA library was produced using Illumina TruSeq DNA library preparation system and the sequencing was run on a HiSeq 2500 system.		GSM2083851: Control 2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			BacTRAP profiling was performed as previously described (Heiman et al. 2014) with the following modifications: One cerebellum was homogenized in 1.5 mL of homogenization buffer and 60 µg each of 19C8 and 19F7 was used for every immunoprecipitation experiment. Using NuGEN Ovation RNA-Seq System v2, purified double-stranded cDNA was generated from 10 ng of total RNA and amplified using both 3’ poly (A) selection and random priming. 2 µg of each sample was sheared using the Covaris S2 focused-ultrasonicator following the manufacturer’s protocol to obtain a final library with insert size of 400 bp. The sheared samples were quantified using the NanoDrop ND-1000 spectrophotometer and Invitrogen Qubit 2.0 DNA quantitation assay. The fragment sizes were confirmed on the Agilent Bioanalyzer to verify proper shearing. A double-stranded DNA library was produced using Illumina TruSeq DNA library preparation system and the sequencing was run on a HiSeq 2500 system.	Illumina HiSeq 2500	age;;4-weeks-old|genotype/variation;;Pcp2-BacTrap; Rbm17 f/+|source_name;;Cerebellar Purkinje neurons|strain;;C57BL/6|tissue;;brain	GEO Accession;;GSM2083851		GSM2083851	Control 2	6543175112	32391956	2016-10-31 08:44:35	4853081635	6543175112	32391956	2	32391956	index:0,count:32391956,average:101,stdev:0|index:1,count:32391956,average:101,stdev:0	GSM2083851_r3				in_mesa	28007900	0.09	2.56	0.03	5037619323	5172297925	4801164858	4970762296	102.67	103.53	28406871	25751254	226.066	1135.778	170	180814	86.1	90.54	30699104	24457873	30699104	24457873	79.05	80.77	30699104	22455692	30699104	21817999	318278558	6.32	7.21	0	4.30	0	0.33	0	0.03	0	0.00	0	11.94	0	28406871	0	202	0	196.49	0	3.68	0	0.02	0	2.58	0	0.03	0	240.93	0	0.54	0	2336783	0	32391956	0	1393522	0	106736	0	10462	0	0	0	3867887	0	9004	0	0	0	64162	0	9966300	0	35603	0	10075069	0	83.40	0	27013349	0	180790	9676338	53.522528900935	32391956.0	28406871.0	2336783.0	1393522.0	106736.0	10462.0	0.0	3867887.0	27013349.0	87.7	7.2	4.3	0.3	0.0	0.0	11.9	83.4	101	101	101.00	38	3271587556	24.5	25.5	25.6	24.4	0.0	34.0	21.6	bulk
2818673	SRR3212813	SRP071321	SRS1329180	SRX1620343	SRA382274	GEO		Extensive cryptic splicing upon loss of RBM17 and TDP43 in neurodegeneration models	Translating ribosome affinity purification technology was used to isolate mRNAs from cerebellar Purkinje neurons from control (Pcp2-BacTrap; Rbm17 f/+) and mutant (Pcp2-BacTRAP; Pcp2-Cre; Rbm17 f/-) mice. Overall design: RNA isolation was performed when animals were four-weeks-old (n=3 animals per genotype). Using NuGEN Ovation RNA-Seq System v2, purified double-stranded cDNA was generated from 10 ng of total RNA and amplified using both 3' poly (A) selection and random priming. 2 µg of each sample was sheared using the Covaris S2 focused-ultrasonicator following the manufacturer's protocol to obtain a final library with insert size of 400 bp. The sheared samples were quantified using the NanoDrop ND-1000 spectrophotometer and Invitrogen Qubit 2.0 DNA quantitation assay. The fragment sizes were confirmed on the Agilent Bioanalyzer to verify proper shearing. A double-stranded DNA library was produced using Illumina TruSeq DNA library preparation system and the sequencing was run on a HiSeq 2500 system.		GSM2083851: Control 2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			BacTRAP profiling was performed as previously described (Heiman et al. 2014) with the following modifications: One cerebellum was homogenized in 1.5 mL of homogenization buffer and 60 µg each of 19C8 and 19F7 was used for every immunoprecipitation experiment. Using NuGEN Ovation RNA-Seq System v2, purified double-stranded cDNA was generated from 10 ng of total RNA and amplified using both 3’ poly (A) selection and random priming. 2 µg of each sample was sheared using the Covaris S2 focused-ultrasonicator following the manufacturer’s protocol to obtain a final library with insert size of 400 bp. The sheared samples were quantified using the NanoDrop ND-1000 spectrophotometer and Invitrogen Qubit 2.0 DNA quantitation assay. The fragment sizes were confirmed on the Agilent Bioanalyzer to verify proper shearing. A double-stranded DNA library was produced using Illumina TruSeq DNA library preparation system and the sequencing was run on a HiSeq 2500 system.	Illumina HiSeq 2500	age;;4-weeks-old|genotype/variation;;Pcp2-BacTrap; Rbm17 f/+|source_name;;Cerebellar Purkinje neurons|strain;;C57BL/6|tissue;;brain	GEO Accession;;GSM2083851		GSM2083851	Control 2	6545452460	32403230	2016-10-31 08:44:35	4863251259	6545452460	32403230	2	32403230	index:0,count:32403230,average:101,stdev:0|index:1,count:32403230,average:101,stdev:0	GSM2083851_r4				in_mesa	28007900	0.09	2.56	0.03	5041890100	5176377991	4805417319	4974994201	102.67	103.53	28438884	25788310	225.885	1136.119	170	180898	86.05	90.48	30734123	24470519	30734123	24470519	78.95	80.66	30734123	22452069	30734123	21815383	318594705	6.32	7.26	0	4.30	0	0.33	0	0.03	0	0.00	0	11.87	0	28438884	0	202	0	196.48	0	3.72	0	0.02	0	2.59	0	0.03	0	208.31	0	0.52	0	2352769	0	32403230	0	1393945	0	107315	0	10595	0	0	0	3846436	0	9290	0	0	0	64315	0	9971822	0	35849	0	10081276	0	83.46	0	27044939	0	180640	9672312	53.544685562445	32403230.0	28438884.0	2352769.0	1393945.0	107315.0	10595.0	0.0	3846436.0	27044939.0	87.8	7.3	4.3	0.3	0.0	0.0	11.9	83.5	101	101	101.00	38	3272726230	24.5	25.5	25.6	24.4	0.0	33.9	21.6	bulk
2818705	SRR3212814	SRP071321	SRS1329180	SRX1620343	SRA382274	GEO		Extensive cryptic splicing upon loss of RBM17 and TDP43 in neurodegeneration models	Translating ribosome affinity purification technology was used to isolate mRNAs from cerebellar Purkinje neurons from control (Pcp2-BacTrap; Rbm17 f/+) and mutant (Pcp2-BacTRAP; Pcp2-Cre; Rbm17 f/-) mice. Overall design: RNA isolation was performed when animals were four-weeks-old (n=3 animals per genotype). Using NuGEN Ovation RNA-Seq System v2, purified double-stranded cDNA was generated from 10 ng of total RNA and amplified using both 3' poly (A) selection and random priming. 2 µg of each sample was sheared using the Covaris S2 focused-ultrasonicator following the manufacturer's protocol to obtain a final library with insert size of 400 bp. The sheared samples were quantified using the NanoDrop ND-1000 spectrophotometer and Invitrogen Qubit 2.0 DNA quantitation assay. The fragment sizes were confirmed on the Agilent Bioanalyzer to verify proper shearing. A double-stranded DNA library was produced using Illumina TruSeq DNA library preparation system and the sequencing was run on a HiSeq 2500 system.		GSM2083851: Control 2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			BacTRAP profiling was performed as previously described (Heiman et al. 2014) with the following modifications: One cerebellum was homogenized in 1.5 mL of homogenization buffer and 60 µg each of 19C8 and 19F7 was used for every immunoprecipitation experiment. Using NuGEN Ovation RNA-Seq System v2, purified double-stranded cDNA was generated from 10 ng of total RNA and amplified using both 3’ poly (A) selection and random priming. 2 µg of each sample was sheared using the Covaris S2 focused-ultrasonicator following the manufacturer’s protocol to obtain a final library with insert size of 400 bp. The sheared samples were quantified using the NanoDrop ND-1000 spectrophotometer and Invitrogen Qubit 2.0 DNA quantitation assay. The fragment sizes were confirmed on the Agilent Bioanalyzer to verify proper shearing. A double-stranded DNA library was produced using Illumina TruSeq DNA library preparation system and the sequencing was run on a HiSeq 2500 system.	Illumina HiSeq 2500	age;;4-weeks-old|genotype/variation;;Pcp2-BacTrap; Rbm17 f/+|source_name;;Cerebellar Purkinje neurons|strain;;C57BL/6|tissue;;brain	GEO Accession;;GSM2083851		GSM2083851	Control 2	6641689098	32879649	2016-10-31 08:44:35	4919685708	6641689098	32879649	2	32879649	index:0,count:32879649,average:101,stdev:0|index:1,count:32879649,average:101,stdev:0	GSM2083851_r5				in_mesa	28007900	0.09	2.56	0.03	5113854012	5250481333	4873477536	5045434828	102.67	103.53	28842874	26158570	225.778	1131.146	170	183995	86.06	90.51	31174681	24822423	31174681	24822423	78.99	80.71	31174681	22783832	31174681	22135384	323396572	6.32	7.20	0	4.31	0	0.33	0	0.03	0	0.00	0	11.92	0	28842874	0	202	0	196.51	0	3.66	0	0.02	0	2.58	0	0.03	0	200.28	0	0.53	0	2366797	0	32879649	0	1416833	0	108364	0	10775	0	0	0	3917636	0	9424	0	0	0	65698	0	10116702	0	36016	0	10227840	0	83.41	0	27426041	0	181166	9819458	54.201439563715	32879649.0	28842874.0	2366797.0	1416833.0	108364.0	10775.0	0.0	3917636.0	27426041.0	87.7	7.2	4.3	0.3	0.0	0.0	11.9	83.4	101	101	101.00	38	3320844549	24.5	25.5	25.6	24.4	0.0	34.0	21.7	bulk
2818737	SRR3212815	SRP071321	SRS1329180	SRX1620343	SRA382274	GEO		Extensive cryptic splicing upon loss of RBM17 and TDP43 in neurodegeneration models	Translating ribosome affinity purification technology was used to isolate mRNAs from cerebellar Purkinje neurons from control (Pcp2-BacTrap; Rbm17 f/+) and mutant (Pcp2-BacTRAP; Pcp2-Cre; Rbm17 f/-) mice. Overall design: RNA isolation was performed when animals were four-weeks-old (n=3 animals per genotype). Using NuGEN Ovation RNA-Seq System v2, purified double-stranded cDNA was generated from 10 ng of total RNA and amplified using both 3' poly (A) selection and random priming. 2 µg of each sample was sheared using the Covaris S2 focused-ultrasonicator following the manufacturer's protocol to obtain a final library with insert size of 400 bp. The sheared samples were quantified using the NanoDrop ND-1000 spectrophotometer and Invitrogen Qubit 2.0 DNA quantitation assay. The fragment sizes were confirmed on the Agilent Bioanalyzer to verify proper shearing. A double-stranded DNA library was produced using Illumina TruSeq DNA library preparation system and the sequencing was run on a HiSeq 2500 system.		GSM2083851: Control 2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			BacTRAP profiling was performed as previously described (Heiman et al. 2014) with the following modifications: One cerebellum was homogenized in 1.5 mL of homogenization buffer and 60 µg each of 19C8 and 19F7 was used for every immunoprecipitation experiment. Using NuGEN Ovation RNA-Seq System v2, purified double-stranded cDNA was generated from 10 ng of total RNA and amplified using both 3’ poly (A) selection and random priming. 2 µg of each sample was sheared using the Covaris S2 focused-ultrasonicator following the manufacturer’s protocol to obtain a final library with insert size of 400 bp. The sheared samples were quantified using the NanoDrop ND-1000 spectrophotometer and Invitrogen Qubit 2.0 DNA quantitation assay. The fragment sizes were confirmed on the Agilent Bioanalyzer to verify proper shearing. A double-stranded DNA library was produced using Illumina TruSeq DNA library preparation system and the sequencing was run on a HiSeq 2500 system.	Illumina HiSeq 2500	age;;4-weeks-old|genotype/variation;;Pcp2-BacTrap; Rbm17 f/+|source_name;;Cerebellar Purkinje neurons|strain;;C57BL/6|tissue;;brain	GEO Accession;;GSM2083851		GSM2083851	Control 2	6619386682	32769241	2016-10-31 08:44:35	4890049843	6619386682	32769241	2	32769241	index:0,count:32769241,average:101,stdev:0|index:1,count:32769241,average:101,stdev:0	GSM2083851_r6				in_mesa	28007900	0.09	2.56	0.03	5098308587	5233843000	4859323586	5030482679	102.66	103.52	28759291	26087131	225.710	1127.703	169	183879	86.08	90.52	31080540	24755705	31080540	24755705	79.01	80.73	31080540	22723365	31080540	22078949	322145006	6.32	7.22	0	4.30	0	0.33	0	0.03	0	0.00	0	11.87	0	28759291	0	202	0	196.52	0	3.69	0	0.02	0	2.58	0	0.03	0	182.05	0	0.52	0	2366140	0	32769241	0	1409629	0	108025	0	10584	0	0	0	3891341	0	9202	0	0	0	65585	0	10095932	0	36207	0	10206926	0	83.46	0	27349662	0	180742	9794163	54.188639054564	32769241.0	28759291.0	2366140.0	1409629.0	108025.0	10584.0	0.0	3891341.0	27349662.0	87.8	7.2	4.3	0.3	0.0	0.0	11.9	83.5	101	101	101.00	38	3309693341	24.5	25.5	25.6	24.4	0.0	34.1	21.8	bulk
2818769	SRR3212816	SRP071321	SRS1329179	SRX1620344	SRA382274	GEO		Extensive cryptic splicing upon loss of RBM17 and TDP43 in neurodegeneration models	Translating ribosome affinity purification technology was used to isolate mRNAs from cerebellar Purkinje neurons from control (Pcp2-BacTrap; Rbm17 f/+) and mutant (Pcp2-BacTRAP; Pcp2-Cre; Rbm17 f/-) mice. Overall design: RNA isolation was performed when animals were four-weeks-old (n=3 animals per genotype). Using NuGEN Ovation RNA-Seq System v2, purified double-stranded cDNA was generated from 10 ng of total RNA and amplified using both 3' poly (A) selection and random priming. 2 µg of each sample was sheared using the Covaris S2 focused-ultrasonicator following the manufacturer's protocol to obtain a final library with insert size of 400 bp. The sheared samples were quantified using the NanoDrop ND-1000 spectrophotometer and Invitrogen Qubit 2.0 DNA quantitation assay. The fragment sizes were confirmed on the Agilent Bioanalyzer to verify proper shearing. A double-stranded DNA library was produced using Illumina TruSeq DNA library preparation system and the sequencing was run on a HiSeq 2500 system.		GSM2083852: Control 3; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			BacTRAP profiling was performed as previously described (Heiman et al. 2014) with the following modifications: One cerebellum was homogenized in 1.5 mL of homogenization buffer and 60 µg each of 19C8 and 19F7 was used for every immunoprecipitation experiment. Using NuGEN Ovation RNA-Seq System v2, purified double-stranded cDNA was generated from 10 ng of total RNA and amplified using both 3’ poly (A) selection and random priming. 2 µg of each sample was sheared using the Covaris S2 focused-ultrasonicator following the manufacturer’s protocol to obtain a final library with insert size of 400 bp. The sheared samples were quantified using the NanoDrop ND-1000 spectrophotometer and Invitrogen Qubit 2.0 DNA quantitation assay. The fragment sizes were confirmed on the Agilent Bioanalyzer to verify proper shearing. A double-stranded DNA library was produced using Illumina TruSeq DNA library preparation system and the sequencing was run on a HiSeq 2500 system.	Illumina HiSeq 2500	age;;4-weeks-old|genotype/variation;;Pcp2-BacTrap; Rbm17 f/+|source_name;;Cerebellar Purkinje neurons|strain;;C57BL/6|tissue;;brain	GEO Accession;;GSM2083852		GSM2083852	Control 3	6027214794	29837697	2016-10-31 08:44:35	4484178982	6027214794	29837697	2	29837697	index:0,count:29837697,average:101,stdev:0|index:1,count:29837697,average:101,stdev:0	GSM2083852_r1				in_mesa	28007900	0.07	2.68	0.03	4665637298	4774874253	4454837847	4594630897	102.34	103.14	26286197	23756808	227.754	1164.281	169	163917	86.99	91.3	28341789	22867338	28341789	22867338	80.73	82.35	28341789	21220027	28341789	20624716	276218279	5.92	7.20	0	4.16	0	0.35	0	0.03	0	0.00	0	11.52	0	26286197	0	202	0	196.72	0	3.31	0	0.02	0	2.76	0	0.03	0	221.93	0	0.51	0	2147382	0	29837697	0	1240209	0	105182	0	10344	0	0	0	3435974	0	9426	0	0	0	60458	0	9447313	0	32556	0	9549753	0	83.94	0	25045988	0	178488	9154305	51.288069786204	29837697.0	26286197.0	2147382.0	1240209.0	105182.0	10344.0	0.0	3435974.0	25045988.0	88.1	7.2	4.2	0.4	0.0	0.0	11.5	83.9	101	101	101.00	38	3013607397	24.7	25.3	25.5	24.5	0.0	33.9	21.4	bulk
2818801	SRR3212817	SRP071321	SRS1329179	SRX1620344	SRA382274	GEO		Extensive cryptic splicing upon loss of RBM17 and TDP43 in neurodegeneration models	Translating ribosome affinity purification technology was used to isolate mRNAs from cerebellar Purkinje neurons from control (Pcp2-BacTrap; Rbm17 f/+) and mutant (Pcp2-BacTRAP; Pcp2-Cre; Rbm17 f/-) mice. Overall design: RNA isolation was performed when animals were four-weeks-old (n=3 animals per genotype). Using NuGEN Ovation RNA-Seq System v2, purified double-stranded cDNA was generated from 10 ng of total RNA and amplified using both 3' poly (A) selection and random priming. 2 µg of each sample was sheared using the Covaris S2 focused-ultrasonicator following the manufacturer's protocol to obtain a final library with insert size of 400 bp. The sheared samples were quantified using the NanoDrop ND-1000 spectrophotometer and Invitrogen Qubit 2.0 DNA quantitation assay. The fragment sizes were confirmed on the Agilent Bioanalyzer to verify proper shearing. A double-stranded DNA library was produced using Illumina TruSeq DNA library preparation system and the sequencing was run on a HiSeq 2500 system.		GSM2083852: Control 3; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			BacTRAP profiling was performed as previously described (Heiman et al. 2014) with the following modifications: One cerebellum was homogenized in 1.5 mL of homogenization buffer and 60 µg each of 19C8 and 19F7 was used for every immunoprecipitation experiment. Using NuGEN Ovation RNA-Seq System v2, purified double-stranded cDNA was generated from 10 ng of total RNA and amplified using both 3’ poly (A) selection and random priming. 2 µg of each sample was sheared using the Covaris S2 focused-ultrasonicator following the manufacturer’s protocol to obtain a final library with insert size of 400 bp. The sheared samples were quantified using the NanoDrop ND-1000 spectrophotometer and Invitrogen Qubit 2.0 DNA quantitation assay. The fragment sizes were confirmed on the Agilent Bioanalyzer to verify proper shearing. A double-stranded DNA library was produced using Illumina TruSeq DNA library preparation system and the sequencing was run on a HiSeq 2500 system.	Illumina HiSeq 2500	age;;4-weeks-old|genotype/variation;;Pcp2-BacTrap; Rbm17 f/+|source_name;;Cerebellar Purkinje neurons|strain;;C57BL/6|tissue;;brain	GEO Accession;;GSM2083852		GSM2083852	Control 3	6003478380	29720190	2016-10-31 08:44:35	4479127946	6003478380	29720190	2	29720190	index:0,count:29720190,average:101,stdev:0|index:1,count:29720190,average:101,stdev:0	GSM2083852_r2				in_mesa	28007900	0.08	2.69	0.03	4639706714	4746509478	4429944835	4567430853	102.3	103.1	26162115	23654981	227.342	1157.808	169	163002	86.98	91.29	28208164	22754897	28208164	22754897	80.74	82.36	28208164	21123315	28208164	20529141	275828551	5.94	7.19	0	4.16	0	0.35	0	0.03	0	0.00	0	11.59	0	26162115	0	202	0	196.65	0	3.33	0	0.02	0	2.76	0	0.03	0	212.29	0	0.53	0	2136546	0	29720190	0	1235315	0	103835	0	10181	0	0	0	3444059	0	9281	0	0	0	59906	0	9371459	0	32143	0	9472789	0	83.87	0	24926800	0	178213	9074026	50.916745691953	29720190.0	26162115.0	2136546.0	1235315.0	103835.0	10181.0	0.0	3444059.0	24926800.0	88.0	7.2	4.2	0.3	0.0	0.0	11.6	83.9	101	101	101.00	38	3001739190	24.7	25.3	25.5	24.6	0.0	33.8	21.2	bulk
2818833	SRR3212818	SRP071321	SRS1329179	SRX1620344	SRA382274	GEO		Extensive cryptic splicing upon loss of RBM17 and TDP43 in neurodegeneration models	Translating ribosome affinity purification technology was used to isolate mRNAs from cerebellar Purkinje neurons from control (Pcp2-BacTrap; Rbm17 f/+) and mutant (Pcp2-BacTRAP; Pcp2-Cre; Rbm17 f/-) mice. Overall design: RNA isolation was performed when animals were four-weeks-old (n=3 animals per genotype). Using NuGEN Ovation RNA-Seq System v2, purified double-stranded cDNA was generated from 10 ng of total RNA and amplified using both 3' poly (A) selection and random priming. 2 µg of each sample was sheared using the Covaris S2 focused-ultrasonicator following the manufacturer's protocol to obtain a final library with insert size of 400 bp. The sheared samples were quantified using the NanoDrop ND-1000 spectrophotometer and Invitrogen Qubit 2.0 DNA quantitation assay. The fragment sizes were confirmed on the Agilent Bioanalyzer to verify proper shearing. A double-stranded DNA library was produced using Illumina TruSeq DNA library preparation system and the sequencing was run on a HiSeq 2500 system.		GSM2083852: Control 3; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			BacTRAP profiling was performed as previously described (Heiman et al. 2014) with the following modifications: One cerebellum was homogenized in 1.5 mL of homogenization buffer and 60 µg each of 19C8 and 19F7 was used for every immunoprecipitation experiment. Using NuGEN Ovation RNA-Seq System v2, purified double-stranded cDNA was generated from 10 ng of total RNA and amplified using both 3’ poly (A) selection and random priming. 2 µg of each sample was sheared using the Covaris S2 focused-ultrasonicator following the manufacturer’s protocol to obtain a final library with insert size of 400 bp. The sheared samples were quantified using the NanoDrop ND-1000 spectrophotometer and Invitrogen Qubit 2.0 DNA quantitation assay. The fragment sizes were confirmed on the Agilent Bioanalyzer to verify proper shearing. A double-stranded DNA library was produced using Illumina TruSeq DNA library preparation system and the sequencing was run on a HiSeq 2500 system.	Illumina HiSeq 2500	age;;4-weeks-old|genotype/variation;;Pcp2-BacTrap; Rbm17 f/+|source_name;;Cerebellar Purkinje neurons|strain;;C57BL/6|tissue;;brain	GEO Accession;;GSM2083852		GSM2083852	Control 3	6043465492	29918146	2016-10-31 08:44:35	4497920223	6043465492	29918146	2	29918146	index:0,count:29918146,average:101,stdev:0|index:1,count:29918146,average:101,stdev:0	GSM2083852_r3				in_mesa	28007900	0.08	2.68	0.03	4679151984	4789336495	4467772244	4608890643	102.35	103.16	26392612	23880877	227.042	1154.767	169	165924	86.92	91.23	28453382	22940780	28453382	22940780	80.58	82.2	28453382	21268335	28453382	20670998	279294713	5.97	7.28	0	4.16	0	0.35	0	0.03	0	0.00	0	11.40	0	26392612	0	202	0	196.66	0	3.34	0	0.02	0	2.78	0	0.03	0	213.70	0	0.52	0	2176918	0	29918146	0	1245411	0	103990	0	10373	0	0	0	3411171	0	9177	0	0	0	60371	0	9414937	0	32818	0	9517303	0	84.05	0	25147201	0	178699	9116405	51.015422582107	29918146.0	26392612.0	2176918.0	1245411.0	103990.0	10373.0	0.0	3411171.0	25147201.0	88.2	7.3	4.2	0.3	0.0	0.0	11.4	84.1	101	101	101.00	38	3021732746	24.7	25.3	25.5	24.6	0.0	34.0	21.6	bulk
2818865	SRR3212819	SRP071321	SRS1329179	SRX1620344	SRA382274	GEO		Extensive cryptic splicing upon loss of RBM17 and TDP43 in neurodegeneration models	Translating ribosome affinity purification technology was used to isolate mRNAs from cerebellar Purkinje neurons from control (Pcp2-BacTrap; Rbm17 f/+) and mutant (Pcp2-BacTRAP; Pcp2-Cre; Rbm17 f/-) mice. Overall design: RNA isolation was performed when animals were four-weeks-old (n=3 animals per genotype). Using NuGEN Ovation RNA-Seq System v2, purified double-stranded cDNA was generated from 10 ng of total RNA and amplified using both 3' poly (A) selection and random priming. 2 µg of each sample was sheared using the Covaris S2 focused-ultrasonicator following the manufacturer's protocol to obtain a final library with insert size of 400 bp. The sheared samples were quantified using the NanoDrop ND-1000 spectrophotometer and Invitrogen Qubit 2.0 DNA quantitation assay. The fragment sizes were confirmed on the Agilent Bioanalyzer to verify proper shearing. A double-stranded DNA library was produced using Illumina TruSeq DNA library preparation system and the sequencing was run on a HiSeq 2500 system.		GSM2083852: Control 3; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			BacTRAP profiling was performed as previously described (Heiman et al. 2014) with the following modifications: One cerebellum was homogenized in 1.5 mL of homogenization buffer and 60 µg each of 19C8 and 19F7 was used for every immunoprecipitation experiment. Using NuGEN Ovation RNA-Seq System v2, purified double-stranded cDNA was generated from 10 ng of total RNA and amplified using both 3’ poly (A) selection and random priming. 2 µg of each sample was sheared using the Covaris S2 focused-ultrasonicator following the manufacturer’s protocol to obtain a final library with insert size of 400 bp. The sheared samples were quantified using the NanoDrop ND-1000 spectrophotometer and Invitrogen Qubit 2.0 DNA quantitation assay. The fragment sizes were confirmed on the Agilent Bioanalyzer to verify proper shearing. A double-stranded DNA library was produced using Illumina TruSeq DNA library preparation system and the sequencing was run on a HiSeq 2500 system.	Illumina HiSeq 2500	age;;4-weeks-old|genotype/variation;;Pcp2-BacTrap; Rbm17 f/+|source_name;;Cerebellar Purkinje neurons|strain;;C57BL/6|tissue;;brain	GEO Accession;;GSM2083852		GSM2083852	Control 3	6037519218	29888709	2016-10-31 08:44:35	4500658285	6037519218	29888709	2	29888709	index:0,count:29888709,average:101,stdev:0|index:1,count:29888709,average:101,stdev:0	GSM2083852_r4				in_mesa	28007900	0.08	2.67	0.03	4676963298	4787739621	4465800088	4607402553	102.37	103.17	26387494	23878518	226.833	1151.952	170	164938	86.87	91.17	28448512	22923187	28448512	22923187	80.49	82.1	28448512	21238093	28448512	20642472	280225567	5.99	7.32	0	4.16	0	0.35	0	0.03	0	0.00	0	11.33	0	26387494	0	202	0	196.66	0	3.39	0	0.02	0	2.79	0	0.03	0	191.80	0	0.50	0	2188700	0	29888709	0	1244394	0	104064	0	10439	0	0	0	3386712	0	9181	0	0	0	60454	0	9411494	0	32911	0	9514040	0	84.12	0	25143100	0	178508	9112614	51.048770923432	29888709.0	26387494.0	2188700.0	1244394.0	104064.0	10439.0	0.0	3386712.0	25143100.0	88.3	7.3	4.2	0.3	0.0	0.0	11.3	84.1	101	101	101.00	38	3018759609	24.7	25.3	25.4	24.6	0.0	33.9	21.6	bulk
2819090	SRR3212820	SRP071321	SRS1329179	SRX1620344	SRA382274	GEO		Extensive cryptic splicing upon loss of RBM17 and TDP43 in neurodegeneration models	Translating ribosome affinity purification technology was used to isolate mRNAs from cerebellar Purkinje neurons from control (Pcp2-BacTrap; Rbm17 f/+) and mutant (Pcp2-BacTRAP; Pcp2-Cre; Rbm17 f/-) mice. Overall design: RNA isolation was performed when animals were four-weeks-old (n=3 animals per genotype). Using NuGEN Ovation RNA-Seq System v2, purified double-stranded cDNA was generated from 10 ng of total RNA and amplified using both 3' poly (A) selection and random priming. 2 µg of each sample was sheared using the Covaris S2 focused-ultrasonicator following the manufacturer's protocol to obtain a final library with insert size of 400 bp. The sheared samples were quantified using the NanoDrop ND-1000 spectrophotometer and Invitrogen Qubit 2.0 DNA quantitation assay. The fragment sizes were confirmed on the Agilent Bioanalyzer to verify proper shearing. A double-stranded DNA library was produced using Illumina TruSeq DNA library preparation system and the sequencing was run on a HiSeq 2500 system.		GSM2083852: Control 3; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			BacTRAP profiling was performed as previously described (Heiman et al. 2014) with the following modifications: One cerebellum was homogenized in 1.5 mL of homogenization buffer and 60 µg each of 19C8 and 19F7 was used for every immunoprecipitation experiment. Using NuGEN Ovation RNA-Seq System v2, purified double-stranded cDNA was generated from 10 ng of total RNA and amplified using both 3’ poly (A) selection and random priming. 2 µg of each sample was sheared using the Covaris S2 focused-ultrasonicator following the manufacturer’s protocol to obtain a final library with insert size of 400 bp. The sheared samples were quantified using the NanoDrop ND-1000 spectrophotometer and Invitrogen Qubit 2.0 DNA quantitation assay. The fragment sizes were confirmed on the Agilent Bioanalyzer to verify proper shearing. A double-stranded DNA library was produced using Illumina TruSeq DNA library preparation system and the sequencing was run on a HiSeq 2500 system.	Illumina HiSeq 2500	age;;4-weeks-old|genotype/variation;;Pcp2-BacTrap; Rbm17 f/+|source_name;;Cerebellar Purkinje neurons|strain;;C57BL/6|tissue;;brain	GEO Accession;;GSM2083852		GSM2083852	Control 3	6146277432	30427116	2016-10-31 08:44:35	4570815129	6146277432	30427116	2	30427116	index:0,count:30427116,average:101,stdev:0|index:1,count:30427116,average:101,stdev:0	GSM2083852_r5				in_mesa	28007900	0.08	2.67	0.03	4758249777	4870772015	4542828454	4686837291	102.36	103.17	26844745	24298727	226.773	1151.253	169	168102	86.89	91.2	28946519	23325010	28946519	23325010	80.53	82.15	28946519	21617367	28946519	21009322	284640369	5.98	7.26	0	4.17	0	0.35	0	0.03	0	0.00	0	11.39	0	26844745	0	202	0	196.68	0	3.35	0	0.02	0	2.78	0	0.03	0	146.05	0	0.51	0	2208351	0	30427116	0	1269687	0	105778	0	10522	0	0	0	3466071	0	9502	0	0	0	61726	0	9585802	0	33447	0	9690477	0	84.05	0	25575058	0	179418	9284612	51.748497921056	30427116.0	26844745.0	2208351.0	1269687.0	105778.0	10522.0	0.0	3466071.0	25575058.0	88.2	7.3	4.2	0.3	0.0	0.0	11.4	84.1	101	101	101.00	38	3073138716	24.7	25.3	25.5	24.6	0.0	34.0	21.7	bulk
2819122	SRR3212821	SRP071321	SRS1329179	SRX1620344	SRA382274	GEO		Extensive cryptic splicing upon loss of RBM17 and TDP43 in neurodegeneration models	Translating ribosome affinity purification technology was used to isolate mRNAs from cerebellar Purkinje neurons from control (Pcp2-BacTrap; Rbm17 f/+) and mutant (Pcp2-BacTRAP; Pcp2-Cre; Rbm17 f/-) mice. Overall design: RNA isolation was performed when animals were four-weeks-old (n=3 animals per genotype). Using NuGEN Ovation RNA-Seq System v2, purified double-stranded cDNA was generated from 10 ng of total RNA and amplified using both 3' poly (A) selection and random priming. 2 µg of each sample was sheared using the Covaris S2 focused-ultrasonicator following the manufacturer's protocol to obtain a final library with insert size of 400 bp. The sheared samples were quantified using the NanoDrop ND-1000 spectrophotometer and Invitrogen Qubit 2.0 DNA quantitation assay. The fragment sizes were confirmed on the Agilent Bioanalyzer to verify proper shearing. A double-stranded DNA library was produced using Illumina TruSeq DNA library preparation system and the sequencing was run on a HiSeq 2500 system.		GSM2083852: Control 3; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			BacTRAP profiling was performed as previously described (Heiman et al. 2014) with the following modifications: One cerebellum was homogenized in 1.5 mL of homogenization buffer and 60 µg each of 19C8 and 19F7 was used for every immunoprecipitation experiment. Using NuGEN Ovation RNA-Seq System v2, purified double-stranded cDNA was generated from 10 ng of total RNA and amplified using both 3’ poly (A) selection and random priming. 2 µg of each sample was sheared using the Covaris S2 focused-ultrasonicator following the manufacturer’s protocol to obtain a final library with insert size of 400 bp. The sheared samples were quantified using the NanoDrop ND-1000 spectrophotometer and Invitrogen Qubit 2.0 DNA quantitation assay. The fragment sizes were confirmed on the Agilent Bioanalyzer to verify proper shearing. A double-stranded DNA library was produced using Illumina TruSeq DNA library preparation system and the sequencing was run on a HiSeq 2500 system.	Illumina HiSeq 2500	age;;4-weeks-old|genotype/variation;;Pcp2-BacTrap; Rbm17 f/+|source_name;;Cerebellar Purkinje neurons|strain;;C57BL/6|tissue;;brain	GEO Accession;;GSM2083852		GSM2083852	Control 3	6120877952	30301376	2016-10-31 08:44:35	4539068363	6120877952	30301376	2	30301376	index:0,count:30301376,average:101,stdev:0|index:1,count:30301376,average:101,stdev:0	GSM2083852_r6				in_mesa	28007900	0.08	2.68	0.03	4739485463	4850603447	4525517390	4668016125	102.34	103.15	26743135	24209238	226.600	1148.790	170	167672	86.88	91.18	28829923	23235359	28829923	23235359	80.53	82.14	28829923	21536525	28829923	20931465	283971771	5.99	7.29	0	4.16	0	0.35	0	0.04	0	0.00	0	11.36	0	26743135	0	202	0	196.70	0	3.37	0	0.02	0	2.78	0	0.03	0	215.16	0	0.50	0	2207567	0	30301376	0	1261442	0	105228	0	10663	0	0	0	3442350	0	9394	0	0	0	60711	0	9555370	0	33034	0	9658509	0	84.09	0	25481693	0	179115	9251123	51.649069033861	30301376.0	26743135.0	2207567.0	1261442.0	105228.0	10663.0	0.0	3442350.0	25481693.0	88.3	7.3	4.2	0.3	0.0	0.0	11.4	84.1	101	101	101.00	38	3060438976	24.7	25.3	25.5	24.6	0.0	34.1	21.9	bulk
1347944	SRR3370916	SRP073200	SRS1392418	SRX1700539	SRA410103	GEO		Multilayered control of alternative splicing regulatory networks by transcription factors (RNA-Seq)	Networks of coordinated alternative splicing (AS) events play critical roles in development and disease. However, a comprehensive knowledge of the factors that regulate these networks is lacking. We describe a high-throughput system for systematically linking trans-acting factors to endogenous RNA regulation events. Using this system, we identify hundreds of factors associated with diverse regulatory layers that positively or negatively control AS events linked to cell fate. Remarkably, more than one third of the new regulators are transcription factors. Further analyses of the zinc finger protein Zfp871 and BTB/POZ domain transcription factor Nacc1, which regulate neural and stem cell AS programs, respectively, reveal roles in controlling the expression of specific splicing regulators. Surprisingly, these proteins also appear to regulate target AS programs via binding RNA. Our results thus uncover a large ‘missing cache’ of splicing regulators among annotated transcription factors, some of which dually regulate AS through direct and indirect mechanisms. Overall design: RNA-Seq of N2A cells upon RNAi-mediated knockdown of Mbnl1/Mbnl2 or Nacc1, or control knockdown (1 replicate each), as well as upon knockdown of Srrm4 or Zfp871, or control knockdown (2 replicates each) vast-tools.AltSplicing_Mbnl.Nacc1.tab: Primary vast-tools output for Mbnl and Nacc1 knockdowns vast-tools.AltSplicing_Srrm4.Zfp871.tab: Primary vast-tools output for Srrm4 and Zfp871 knockdowns AltSplicing_Mbnl.Nacc1.tab: Filtered PSI values and differential AS annotation for Mbnl and Nacc1 knockdowns AltSplicing_Srrm4.Zfp871.tab: Filtered PSI values and differential AS annotation for Srrm4 and Zfp871 knockdowns Expression_Mbnl.Nacc1.tab: Raw and read counts per gene, normalized expression and fold-change for Mbnl and Nacc1 knockdowns Expression_Srrm4.Zfp871.tab: Raw read counts per gene, normalized expression and fold-change (edgeR analysis) for Srrm4 and Zfp871 knockdowns		GSM2120783: RNA-Seq of N2A cells after knockdown of Mbnl1 and Mbnl2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted either with TriZol (ThermoFisher) or the Qiagen RNasy kit. RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2500	cell line;;N2A|knockdown;;siMbnl1/Mbnl2|source_name;;Neuroblastoma cells	GEO Accession;;GSM2120783		GSM2120783	RNA-Seq of N2A cells after knockdown of Mbnl1 and Mbnl2	14974898600	74874493	2017-02-06 11:28:10	6309319953	14974898600	74874493	2	74874493	index:0,count:74874493,average:100,stdev:0|index:1,count:74874493,average:100,stdev:0	GSM2120783_r1						2.73	3.62	0.1	10686392267	10445849867	9667985013	9568995048	97.75	98.98	67950774	62648967	187.386	888.813	131	624385	80.29	88.87	80572882	54557802	80572882	54557802	84.33	85.44	80572882	57300916	80572882	52452323	1029246165	9.63	2.62	0	8.76	0	1.16	0	2.75	0	0.00	0	5.33	0	67950774	0	200	0	198.39	0	1.97	0	0.01	0	1.77	0	0.01	0	234.39	0	0.30	0	1961073	0	74874493	0	6558970	0	869252	0	2060681	0	0	0	3993786	0	26037	0	0	0	241577	0	32671599	0	83647	0	33022860	0	81.99	0	61391804	0	287981	28864257	100.229726961154	74874493.0	67950774.0	1961073.0	6558970.0	869252.0	2060681.0	0.0	3993786.0	61391804.0	90.8	2.6	8.8	1.2	2.8	0.0	5.3	82.0	100	100	100.00	23	7487449300	25.3	24.7	24.4	25.6	0.0	36.6	26.3	bulk
1348120	SRR3370921	SRP073200	SRS1392413	SRX1700544	SRA410103	GEO		Multilayered control of alternative splicing regulatory networks by transcription factors (RNA-Seq)	Networks of coordinated alternative splicing (AS) events play critical roles in development and disease. However, a comprehensive knowledge of the factors that regulate these networks is lacking. We describe a high-throughput system for systematically linking trans-acting factors to endogenous RNA regulation events. Using this system, we identify hundreds of factors associated with diverse regulatory layers that positively or negatively control AS events linked to cell fate. Remarkably, more than one third of the new regulators are transcription factors. Further analyses of the zinc finger protein Zfp871 and BTB/POZ domain transcription factor Nacc1, which regulate neural and stem cell AS programs, respectively, reveal roles in controlling the expression of specific splicing regulators. Surprisingly, these proteins also appear to regulate target AS programs via binding RNA. Our results thus uncover a large ‘missing cache’ of splicing regulators among annotated transcription factors, some of which dually regulate AS through direct and indirect mechanisms. Overall design: RNA-Seq of N2A cells upon RNAi-mediated knockdown of Mbnl1/Mbnl2 or Nacc1, or control knockdown (1 replicate each), as well as upon knockdown of Srrm4 or Zfp871, or control knockdown (2 replicates each) vast-tools.AltSplicing_Mbnl.Nacc1.tab: Primary vast-tools output for Mbnl and Nacc1 knockdowns vast-tools.AltSplicing_Srrm4.Zfp871.tab: Primary vast-tools output for Srrm4 and Zfp871 knockdowns AltSplicing_Mbnl.Nacc1.tab: Filtered PSI values and differential AS annotation for Mbnl and Nacc1 knockdowns AltSplicing_Srrm4.Zfp871.tab: Filtered PSI values and differential AS annotation for Srrm4 and Zfp871 knockdowns Expression_Mbnl.Nacc1.tab: Raw and read counts per gene, normalized expression and fold-change for Mbnl and Nacc1 knockdowns Expression_Srrm4.Zfp871.tab: Raw read counts per gene, normalized expression and fold-change (edgeR analysis) for Srrm4 and Zfp871 knockdowns		GSM2120788: RNA-Seq of N2A cells after knockdown of Zfp871, replicate 1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted either with TriZol (ThermoFisher) or the Qiagen RNasy kit. RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2500	cell line;;N2A|knockdown;;siZfp871|source_name;;Neuroblastoma cells	GEO Accession;;GSM2120788		GSM2120788	RNA-Seq of N2A cells after knockdown of Zfp871, replicate 1	18003687750	72014751	2017-02-06 11:28:10	8380048588	18003687750	72014751	2	72014751	index:0,count:72014751,average:125,stdev:0|index:1,count:72014751,average:125,stdev:0	GSM2120788_r1						2.83	3.66	0.06	10320477535	10201388124	9249523372	9258853254	98.85	100.1	63234702	55516860	195.303	1204.855	137	505197	85.64	95.74	75800091	54155348	75800091	54155348	89.86	91.36	75800091	56821453	75800091	51678039	347777308	3.37	1.71	0	9.26	0	0.97	0	1.26	0	0.00	0	9.96	0	63234702	0	250	0	243.84	0	2.12	0	0.01	0	2.12	0	0.01	0	171.58	0	0.28	0	1232521	0	72014751	0	6668154	0	699633	0	909783	0	0	0	7170633	0	40475	0	0	0	340823	0	44696635	0	88439	0	45166372	0	78.55	0	56566548	0	259156	33208305	128.140212844773	72014751.0	63234702.0	1232521.0	6668154.0	699633.0	909783.0	0.0	7170633.0	56566548.0	87.8	1.7	9.3	1.0	1.3	0.0	10.0	78.5	125	125	125.00	28	9001843875	23.6	24.9	25.1	26.4	0.0	36.2	28.5	bulk
1348137	SRR3370922	SRP073200	SRS1392412	SRX1700545	SRA410103	GEO		Multilayered control of alternative splicing regulatory networks by transcription factors (RNA-Seq)	Networks of coordinated alternative splicing (AS) events play critical roles in development and disease. However, a comprehensive knowledge of the factors that regulate these networks is lacking. We describe a high-throughput system for systematically linking trans-acting factors to endogenous RNA regulation events. Using this system, we identify hundreds of factors associated with diverse regulatory layers that positively or negatively control AS events linked to cell fate. Remarkably, more than one third of the new regulators are transcription factors. Further analyses of the zinc finger protein Zfp871 and BTB/POZ domain transcription factor Nacc1, which regulate neural and stem cell AS programs, respectively, reveal roles in controlling the expression of specific splicing regulators. Surprisingly, these proteins also appear to regulate target AS programs via binding RNA. Our results thus uncover a large ‘missing cache’ of splicing regulators among annotated transcription factors, some of which dually regulate AS through direct and indirect mechanisms. Overall design: RNA-Seq of N2A cells upon RNAi-mediated knockdown of Mbnl1/Mbnl2 or Nacc1, or control knockdown (1 replicate each), as well as upon knockdown of Srrm4 or Zfp871, or control knockdown (2 replicates each) vast-tools.AltSplicing_Mbnl.Nacc1.tab: Primary vast-tools output for Mbnl and Nacc1 knockdowns vast-tools.AltSplicing_Srrm4.Zfp871.tab: Primary vast-tools output for Srrm4 and Zfp871 knockdowns AltSplicing_Mbnl.Nacc1.tab: Filtered PSI values and differential AS annotation for Mbnl and Nacc1 knockdowns AltSplicing_Srrm4.Zfp871.tab: Filtered PSI values and differential AS annotation for Srrm4 and Zfp871 knockdowns Expression_Mbnl.Nacc1.tab: Raw and read counts per gene, normalized expression and fold-change for Mbnl and Nacc1 knockdowns Expression_Srrm4.Zfp871.tab: Raw read counts per gene, normalized expression and fold-change (edgeR analysis) for Srrm4 and Zfp871 knockdowns		GSM2120789: RNA-Seq of N2A cells after knockdown of Zfp871, replicate 2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted either with TriZol (ThermoFisher) or the Qiagen RNasy kit. RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2500	cell line;;N2A|knockdown;;siZfp871|source_name;;Neuroblastoma cells	GEO Accession;;GSM2120789		GSM2120789	RNA-Seq of N2A cells after knockdown of Zfp871, replicate 2	20593527250	82374109	2017-02-06 11:28:10	9640759334	20593527250	82374109	2	82374109	index:0,count:82374109,average:125,stdev:0|index:1,count:82374109,average:125,stdev:0	GSM2120789_r1						3.82	3.58	0.07	12257643427	12084562069	10982619665	10972069109	98.59	99.9	72103953	63753471	202.409	1162.913	137	523872	85.04	95.16	86336057	61319139	86336057	61319139	89.42	90.9	86336057	64474057	86336057	58573280	459027125	3.74	1.97	0	9.31	0	1.02	0	1.46	0	0.00	0	10.00	0	72103953	0	250	0	244.35	0	2.15	0	0.01	0	2.17	0	0.01	0	203.53	0	0.29	0	1623247	0	82374109	0	7665466	0	837493	0	1199056	0	0	0	8233607	0	45892	0	0	0	370739	0	49758174	0	104322	0	50279127	0	78.23	0	64438487	0	269668	38312968	142.074580595399	82374109.0	72103953.0	1623247.0	7665466.0	837493.0	1199056.0	0.0	8233607.0	64438487.0	87.5	2.0	9.3	1.0	1.5	0.0	10.0	78.2	125	125	125.00	28	10296763625	23.6	24.7	25.4	26.3	0.0	36.1	28.3	bulk
1348155	SRR3370923	SRP073200	SRS1392411	SRX1700546	SRA410103	GEO		Multilayered control of alternative splicing regulatory networks by transcription factors (RNA-Seq)	Networks of coordinated alternative splicing (AS) events play critical roles in development and disease. However, a comprehensive knowledge of the factors that regulate these networks is lacking. We describe a high-throughput system for systematically linking trans-acting factors to endogenous RNA regulation events. Using this system, we identify hundreds of factors associated with diverse regulatory layers that positively or negatively control AS events linked to cell fate. Remarkably, more than one third of the new regulators are transcription factors. Further analyses of the zinc finger protein Zfp871 and BTB/POZ domain transcription factor Nacc1, which regulate neural and stem cell AS programs, respectively, reveal roles in controlling the expression of specific splicing regulators. Surprisingly, these proteins also appear to regulate target AS programs via binding RNA. Our results thus uncover a large ‘missing cache’ of splicing regulators among annotated transcription factors, some of which dually regulate AS through direct and indirect mechanisms. Overall design: RNA-Seq of N2A cells upon RNAi-mediated knockdown of Mbnl1/Mbnl2 or Nacc1, or control knockdown (1 replicate each), as well as upon knockdown of Srrm4 or Zfp871, or control knockdown (2 replicates each) vast-tools.AltSplicing_Mbnl.Nacc1.tab: Primary vast-tools output for Mbnl and Nacc1 knockdowns vast-tools.AltSplicing_Srrm4.Zfp871.tab: Primary vast-tools output for Srrm4 and Zfp871 knockdowns AltSplicing_Mbnl.Nacc1.tab: Filtered PSI values and differential AS annotation for Mbnl and Nacc1 knockdowns AltSplicing_Srrm4.Zfp871.tab: Filtered PSI values and differential AS annotation for Srrm4 and Zfp871 knockdowns Expression_Mbnl.Nacc1.tab: Raw and read counts per gene, normalized expression and fold-change for Mbnl and Nacc1 knockdowns Expression_Srrm4.Zfp871.tab: Raw read counts per gene, normalized expression and fold-change (edgeR analysis) for Srrm4 and Zfp871 knockdowns		GSM2120790: RNA-Seq of N2A cells after non-targeting knockdown (control for Srrm4 and Zfp871 knockdowns), replicate 1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted either with TriZol (ThermoFisher) or the Qiagen RNasy kit. RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2500	cell line;;N2A|knockdown;;siNT|source_name;;Neuroblastoma cells	GEO Accession;;GSM2120790		GSM2120790	RNA-Seq of N2A cells after non-targeting knockdown (control for Srrm4 and Zfp871 knockdowns), replicate 1	18720842750	74883371	2017-02-06 11:28:10	9010530703	18720842750	74883371	2	74883371	index:0,count:74883371,average:125,stdev:0|index:1,count:74883371,average:125,stdev:0	GSM2120790_r1						3.1	3.61	0.06	10844003757	10744183704	9729647706	9751114028	99.08	100.22	66001365	58116355	196.030	1203.346	137	520026	85.68	95.69	78912389	56547949	78912389	56547949	90.02	91.32	78912389	59413375	78912389	53966004	377164860	3.48	1.73	0	9.22	0	0.87	0	0.91	0	0.00	0	10.09	0	66001365	0	250	0	243.75	0	2.15	0	0.01	0	2.16	0	0.01	0	185.79	0	0.30	0	1294232	0	74883371	0	6907206	0	648671	0	679479	0	0	0	7553856	0	38373	0	0	0	342828	0	45846255	0	87227	0	46314683	0	78.91	0	59094159	0	260366	34311394	131.781392347695	74883371.0	66001365.0	1294232.0	6907206.0	648671.0	679479.0	0.0	7553856.0	59094159.0	88.1	1.7	9.2	0.9	0.9	0.0	10.1	78.9	125	125	125.00	28	9360421375	23.5	24.8	25.6	26.1	0.0	35.7	27.4	bulk
1348170	SRR3370924	SRP073200	SRS1392408	SRX1700547	SRA410103	GEO		Multilayered control of alternative splicing regulatory networks by transcription factors (RNA-Seq)	Networks of coordinated alternative splicing (AS) events play critical roles in development and disease. However, a comprehensive knowledge of the factors that regulate these networks is lacking. We describe a high-throughput system for systematically linking trans-acting factors to endogenous RNA regulation events. Using this system, we identify hundreds of factors associated with diverse regulatory layers that positively or negatively control AS events linked to cell fate. Remarkably, more than one third of the new regulators are transcription factors. Further analyses of the zinc finger protein Zfp871 and BTB/POZ domain transcription factor Nacc1, which regulate neural and stem cell AS programs, respectively, reveal roles in controlling the expression of specific splicing regulators. Surprisingly, these proteins also appear to regulate target AS programs via binding RNA. Our results thus uncover a large ‘missing cache’ of splicing regulators among annotated transcription factors, some of which dually regulate AS through direct and indirect mechanisms. Overall design: RNA-Seq of N2A cells upon RNAi-mediated knockdown of Mbnl1/Mbnl2 or Nacc1, or control knockdown (1 replicate each), as well as upon knockdown of Srrm4 or Zfp871, or control knockdown (2 replicates each) vast-tools.AltSplicing_Mbnl.Nacc1.tab: Primary vast-tools output for Mbnl and Nacc1 knockdowns vast-tools.AltSplicing_Srrm4.Zfp871.tab: Primary vast-tools output for Srrm4 and Zfp871 knockdowns AltSplicing_Mbnl.Nacc1.tab: Filtered PSI values and differential AS annotation for Mbnl and Nacc1 knockdowns AltSplicing_Srrm4.Zfp871.tab: Filtered PSI values and differential AS annotation for Srrm4 and Zfp871 knockdowns Expression_Mbnl.Nacc1.tab: Raw and read counts per gene, normalized expression and fold-change for Mbnl and Nacc1 knockdowns Expression_Srrm4.Zfp871.tab: Raw read counts per gene, normalized expression and fold-change (edgeR analysis) for Srrm4 and Zfp871 knockdowns		GSM2120791: RNA-Seq of N2A cells after non-targeting knockdown (control for Srrm4 and Zfp871 knockdowns), replicate 2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted either with TriZol (ThermoFisher) or the Qiagen RNasy kit. RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2500	cell line;;N2A|knockdown;;siNT|source_name;;Neuroblastoma cells	GEO Accession;;GSM2120791		GSM2120791	RNA-Seq of N2A cells after non-targeting knockdown (control for Srrm4 and Zfp871 knockdowns), replicate 2	19736883500	78947534	2017-02-06 11:28:10	9172728772	19736883500	78947534	2	78947534	index:0,count:78947534,average:125,stdev:0|index:1,count:78947534,average:125,stdev:0	GSM2120791_r1						3.84	3.61	0.08	11839485270	11673256988	10670943387	10645068750	98.6	99.76	69948853	61956217	200.725	1153.668	142	522316	84.22	93.66	82930094	58908143	82930094	58908143	88.33	89.55	82930094	61783894	82930094	56327021	612156812	5.17	1.68	0	8.93	0	0.90	0	1.18	0	0.00	0	9.32	0	69948853	0	250	0	244.40	0	2.17	0	0.01	0	2.21	0	0.01	0	178.08	0	0.29	0	1327167	0	78947534	0	7051894	0	711694	0	931066	0	0	0	7355921	0	39018	0	0	0	365229	0	47076819	0	95258	0	47576324	0	79.67	0	62896959	0	266321	36050254	135.363917978680	78947534.0	69948853.0	1327167.0	7051894.0	711694.0	931066.0	0.0	7355921.0	62896959.0	88.6	1.7	8.9	0.9	1.2	0.0	9.3	79.7	125	125	125.00	28	9868441750	23.7	24.8	25.2	26.4	0.0	36.2	28.5	bulk
673981	SRR3370917	SRP073200	SRS1392410	SRX1700540	SRA410103	GEO		Multilayered control of alternative splicing regulatory networks by transcription factors (RNA-Seq)	Networks of coordinated alternative splicing (AS) events play critical roles in development and disease. However, a comprehensive knowledge of the factors that regulate these networks is lacking. We describe a high-throughput system for systematically linking trans-acting factors to endogenous RNA regulation events. Using this system, we identify hundreds of factors associated with diverse regulatory layers that positively or negatively control AS events linked to cell fate. Remarkably, more than one third of the new regulators are transcription factors. Further analyses of the zinc finger protein Zfp871 and BTB/POZ domain transcription factor Nacc1, which regulate neural and stem cell AS programs, respectively, reveal roles in controlling the expression of specific splicing regulators. Surprisingly, these proteins also appear to regulate target AS programs via binding RNA. Our results thus uncover a large ‘missing cache’ of splicing regulators among annotated transcription factors, some of which dually regulate AS through direct and indirect mechanisms. Overall design: RNA-Seq of N2A cells upon RNAi-mediated knockdown of Mbnl1/Mbnl2 or Nacc1, or control knockdown (1 replicate each), as well as upon knockdown of Srrm4 or Zfp871, or control knockdown (2 replicates each) vast-tools.AltSplicing_Mbnl.Nacc1.tab: Primary vast-tools output for Mbnl and Nacc1 knockdowns vast-tools.AltSplicing_Srrm4.Zfp871.tab: Primary vast-tools output for Srrm4 and Zfp871 knockdowns AltSplicing_Mbnl.Nacc1.tab: Filtered PSI values and differential AS annotation for Mbnl and Nacc1 knockdowns AltSplicing_Srrm4.Zfp871.tab: Filtered PSI values and differential AS annotation for Srrm4 and Zfp871 knockdowns Expression_Mbnl.Nacc1.tab: Raw and read counts per gene, normalized expression and fold-change for Mbnl and Nacc1 knockdowns Expression_Srrm4.Zfp871.tab: Raw read counts per gene, normalized expression and fold-change (edgeR analysis) for Srrm4 and Zfp871 knockdowns		GSM2120784: RNA-Seq of N2A cells after knockdown of Nacc1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted either with TriZol (ThermoFisher) or the Qiagen RNasy kit. RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2500	cell line;;N2A|knockdown;;siNacc1|source_name;;Neuroblastoma cells	GEO Accession;;GSM2120784		GSM2120784	RNA-Seq of N2A cells after knockdown of Nacc1	17918767600	89593838	2017-02-06 11:28:10	7386301276	17918767600	89593838	2	89593838	index:0,count:89593838,average:100,stdev:0|index:1,count:89593838,average:100,stdev:0	GSM2120784_r1						3.36	3.55	0.09	13009818386	12795507471	11747796263	11675456109	98.35	99.38	82592476	76269787	187.287	848.155	131	752275	80.21	88.97	97609019	66249427	97609019	66249427	84.8	85.57	97609019	70034926	97609019	63713899	1276398839	9.81	2.63	0	9.08	0	0.93	0	1.84	0	0.00	0	5.05	0	82592476	0	200	0	198.41	0	1.98	0	0.01	0	1.76	0	0.01	0	215.17	0	0.28	0	2358600	0	89593838	0	8132066	0	829885	0	1645271	0	0	0	4526206	0	32750	0	0	0	298982	0	39215329	0	99730	0	39646791	0	83.11	0	74460410	0	294983	34768012	117.864459985830	89593838.0	82592476.0	2358600.0	8132066.0	829885.0	1645271.0	0.0	4526206.0	74460410.0	92.2	2.6	9.1	0.9	1.8	0.0	5.1	83.1	100	100	100.00	23	8959383800	25.4	24.6	24.4	25.7	0.0	36.8	26.7	bulk
673989	SRR3370918	SRP073200	SRS1392414	SRX1700541	SRA410103	GEO		Multilayered control of alternative splicing regulatory networks by transcription factors (RNA-Seq)	Networks of coordinated alternative splicing (AS) events play critical roles in development and disease. However, a comprehensive knowledge of the factors that regulate these networks is lacking. We describe a high-throughput system for systematically linking trans-acting factors to endogenous RNA regulation events. Using this system, we identify hundreds of factors associated with diverse regulatory layers that positively or negatively control AS events linked to cell fate. Remarkably, more than one third of the new regulators are transcription factors. Further analyses of the zinc finger protein Zfp871 and BTB/POZ domain transcription factor Nacc1, which regulate neural and stem cell AS programs, respectively, reveal roles in controlling the expression of specific splicing regulators. Surprisingly, these proteins also appear to regulate target AS programs via binding RNA. Our results thus uncover a large ‘missing cache’ of splicing regulators among annotated transcription factors, some of which dually regulate AS through direct and indirect mechanisms. Overall design: RNA-Seq of N2A cells upon RNAi-mediated knockdown of Mbnl1/Mbnl2 or Nacc1, or control knockdown (1 replicate each), as well as upon knockdown of Srrm4 or Zfp871, or control knockdown (2 replicates each) vast-tools.AltSplicing_Mbnl.Nacc1.tab: Primary vast-tools output for Mbnl and Nacc1 knockdowns vast-tools.AltSplicing_Srrm4.Zfp871.tab: Primary vast-tools output for Srrm4 and Zfp871 knockdowns AltSplicing_Mbnl.Nacc1.tab: Filtered PSI values and differential AS annotation for Mbnl and Nacc1 knockdowns AltSplicing_Srrm4.Zfp871.tab: Filtered PSI values and differential AS annotation for Srrm4 and Zfp871 knockdowns Expression_Mbnl.Nacc1.tab: Raw and read counts per gene, normalized expression and fold-change for Mbnl and Nacc1 knockdowns Expression_Srrm4.Zfp871.tab: Raw read counts per gene, normalized expression and fold-change (edgeR analysis) for Srrm4 and Zfp871 knockdowns		GSM2120785: RNA-Seq of N2A cells after non-targeting knockdown (control for Mbnl and Nacc1 knockdowns); Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted either with TriZol (ThermoFisher) or the Qiagen RNasy kit. RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2500	cell line;;N2A|knockdown;;siNT|source_name;;Neuroblastoma cells	GEO Accession;;GSM2120785		GSM2120785	RNA-Seq of N2A cells after non-targeting knockdown (control for Mbnl and Nacc1 knockdowns)	18853236800	94266184	2017-02-06 11:28:10	7844553457	18853236800	94266184	2	94266184	index:0,count:94266184,average:100,stdev:0|index:1,count:94266184,average:100,stdev:0	GSM2120785_r1						3.13	3.58	0.09	13649436518	13417381332	12324834120	12244996935	98.3	99.35	86729432	79997375	187.829	870.989	131	802015	79.76	88.48	102550483	69176941	102550483	69176941	84.29	85.06	102550483	73105876	102550483	66507152	1400604667	10.26	2.67	0	9.06	0	0.93	0	1.95	0	0.00	0	5.11	0	86729432	0	200	0	198.43	0	2.00	0	0.01	0	1.80	0	0.01	0	254.39	0	0.28	0	2521329	0	94266184	0	8543334	0	876019	0	1840932	0	0	0	4819801	0	33637	0	0	0	304564	0	41044413	0	103957	0	41486571	0	82.94	0	78186098	0	301290	36292344	120.456516976999	94266184.0	86729432.0	2521329.0	8543334.0	876019.0	1840932.0	0.0	4819801.0	78186098.0	92.0	2.7	9.1	0.9	2.0	0.0	5.1	82.9	100	100	100.00	23	9426618400	25.3	24.7	24.5	25.5	0.0	36.7	26.4	bulk
673999	SRR3370919	SRP073200	SRS1392409	SRX1700542	SRA410103	GEO		Multilayered control of alternative splicing regulatory networks by transcription factors (RNA-Seq)	Networks of coordinated alternative splicing (AS) events play critical roles in development and disease. However, a comprehensive knowledge of the factors that regulate these networks is lacking. We describe a high-throughput system for systematically linking trans-acting factors to endogenous RNA regulation events. Using this system, we identify hundreds of factors associated with diverse regulatory layers that positively or negatively control AS events linked to cell fate. Remarkably, more than one third of the new regulators are transcription factors. Further analyses of the zinc finger protein Zfp871 and BTB/POZ domain transcription factor Nacc1, which regulate neural and stem cell AS programs, respectively, reveal roles in controlling the expression of specific splicing regulators. Surprisingly, these proteins also appear to regulate target AS programs via binding RNA. Our results thus uncover a large ‘missing cache’ of splicing regulators among annotated transcription factors, some of which dually regulate AS through direct and indirect mechanisms. Overall design: RNA-Seq of N2A cells upon RNAi-mediated knockdown of Mbnl1/Mbnl2 or Nacc1, or control knockdown (1 replicate each), as well as upon knockdown of Srrm4 or Zfp871, or control knockdown (2 replicates each) vast-tools.AltSplicing_Mbnl.Nacc1.tab: Primary vast-tools output for Mbnl and Nacc1 knockdowns vast-tools.AltSplicing_Srrm4.Zfp871.tab: Primary vast-tools output for Srrm4 and Zfp871 knockdowns AltSplicing_Mbnl.Nacc1.tab: Filtered PSI values and differential AS annotation for Mbnl and Nacc1 knockdowns AltSplicing_Srrm4.Zfp871.tab: Filtered PSI values and differential AS annotation for Srrm4 and Zfp871 knockdowns Expression_Mbnl.Nacc1.tab: Raw and read counts per gene, normalized expression and fold-change for Mbnl and Nacc1 knockdowns Expression_Srrm4.Zfp871.tab: Raw read counts per gene, normalized expression and fold-change (edgeR analysis) for Srrm4 and Zfp871 knockdowns		GSM2120786: RNA-Seq of N2A cells after knockdown of Srrm4, replicate 1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted either with TriZol (ThermoFisher) or the Qiagen RNasy kit. RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2500	cell line;;N2A|knockdown;;siSrrm4|source_name;;Neuroblastoma cells	GEO Accession;;GSM2120786		GSM2120786	RNA-Seq of N2A cells after knockdown of Srrm4, replicate 1	18026709250	72106837	2017-02-06 11:28:10	8387061626	18026709250	72106837	2	72106837	index:0,count:72106837,average:125,stdev:0|index:1,count:72106837,average:125,stdev:0	GSM2120786_r1						2.74	3.75	0.06	10743375590	10589590889	9617456907	9604359779	98.57	99.86	63176065	55615969	203.866	1228.072	137	449058	84.99	95.22	76122508	53695556	76122508	53695556	89.3	90.87	76122508	56416686	76122508	51243960	392211817	3.65	1.68	0	9.41	0	1.10	0	1.54	0	0.00	0	9.74	0	63176065	0	250	0	244.09	0	2.16	0	0.01	0	2.19	0	0.01	0	183.58	0	0.29	0	1209959	0	72106837	0	6785640	0	794597	0	1113780	0	0	0	7022395	0	38273	0	0	0	348458	0	44298027	0	87724	0	44772482	0	78.20	0	56390425	0	270136	34226878	126.702394349513	72106837.0	63176065.0	1209959.0	6785640.0	794597.0	1113780.0	0.0	7022395.0	56390425.0	87.6	1.7	9.4	1.1	1.5	0.0	9.7	78.2	125	125	125.00	28	9013354625	23.5	25.1	25.3	26.1	0.0	36.2	28.5	bulk
674054	SRR3370920	SRP073200	SRS1392415	SRX1700543	SRA410103	GEO		Multilayered control of alternative splicing regulatory networks by transcription factors (RNA-Seq)	Networks of coordinated alternative splicing (AS) events play critical roles in development and disease. However, a comprehensive knowledge of the factors that regulate these networks is lacking. We describe a high-throughput system for systematically linking trans-acting factors to endogenous RNA regulation events. Using this system, we identify hundreds of factors associated with diverse regulatory layers that positively or negatively control AS events linked to cell fate. Remarkably, more than one third of the new regulators are transcription factors. Further analyses of the zinc finger protein Zfp871 and BTB/POZ domain transcription factor Nacc1, which regulate neural and stem cell AS programs, respectively, reveal roles in controlling the expression of specific splicing regulators. Surprisingly, these proteins also appear to regulate target AS programs via binding RNA. Our results thus uncover a large ‘missing cache’ of splicing regulators among annotated transcription factors, some of which dually regulate AS through direct and indirect mechanisms. Overall design: RNA-Seq of N2A cells upon RNAi-mediated knockdown of Mbnl1/Mbnl2 or Nacc1, or control knockdown (1 replicate each), as well as upon knockdown of Srrm4 or Zfp871, or control knockdown (2 replicates each) vast-tools.AltSplicing_Mbnl.Nacc1.tab: Primary vast-tools output for Mbnl and Nacc1 knockdowns vast-tools.AltSplicing_Srrm4.Zfp871.tab: Primary vast-tools output for Srrm4 and Zfp871 knockdowns AltSplicing_Mbnl.Nacc1.tab: Filtered PSI values and differential AS annotation for Mbnl and Nacc1 knockdowns AltSplicing_Srrm4.Zfp871.tab: Filtered PSI values and differential AS annotation for Srrm4 and Zfp871 knockdowns Expression_Mbnl.Nacc1.tab: Raw and read counts per gene, normalized expression and fold-change for Mbnl and Nacc1 knockdowns Expression_Srrm4.Zfp871.tab: Raw read counts per gene, normalized expression and fold-change (edgeR analysis) for Srrm4 and Zfp871 knockdowns		GSM2120787: RNA-Seq of N2A cells after knockdown of Srrm4, replicate 2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted either with TriZol (ThermoFisher) or the Qiagen RNasy kit. RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2500	cell line;;N2A|knockdown;;siSrrm4|source_name;;Neuroblastoma cells	GEO Accession;;GSM2120787		GSM2120787	RNA-Seq of N2A cells after knockdown of Srrm4, replicate 2	25037140250	100148561	2017-02-06 11:28:10	11823553182	25037140250	100148561	2	100148561	index:0,count:100148561,average:125,stdev:0|index:1,count:100148561,average:125,stdev:0	GSM2120787_r1						4.19	3.77	0.07	14671017616	14364586419	13048765193	12972392243	97.91	99.41	87276752	77093036	199.484	1234.816	142	655153	83.97	94.6	105722791	73286555	105722791	73286555	88.6	90.34	105722791	77322895	105722791	69981824	580436780	3.96	1.62	0	9.80	0	1.24	0	1.97	0	0.00	0	9.64	0	87276752	0	250	0	244.28	0	2.14	0	0.01	0	2.19	0	0.01	0	170.95	0	0.30	0	1625768	0	100148561	0	9809609	0	1239639	0	1977089	0	0	0	9655081	0	51772	0	0	0	467782	0	59968844	0	118661	0	60607059	0	77.35	0	77467143	0	292860	45721904	156.122051492181	100148561.0	87276752.0	1625768.0	9809609.0	1239639.0	1977089.0	0.0	9655081.0	77467143.0	87.1	1.6	9.8	1.2	2.0	0.0	9.6	77.4	125	125	125.00	28	12518570125	23.6	24.8	25.1	26.5	0.0	36.1	28.3	bulk
1738248	SRR3666860	SRP076556	SRS1504100	SRX1845260	SRA433971	GEO		RNA-seq analysis of neonatal mouse cochlear supporting cells [NonTreated_JM]	This study examined transcripts that are enriched in neonatal mouse cochlear supporting cells at postnatal day 1 and postnatal day 6. Supporting cells were purified by FACS sorting for GFP fluorescence from the cochleas of transgenic mice in which a BAC including the LFng locus drives the expression of GFP. Two replicates of GFP+ supporting cells were compared with all other cochlear cell types that were GFP-. We performed this experiment at two different ages, postnatal day 1 and postnatal day 6. Overall design: mRNA profiles of supporting cells (GFP+) and all other cochlear cell types (GFP-), two replicates each, at P1 and P6 mice were generated by deep sequencing using Illumna TruSeq.		GSM2200199: P1 Cochlea GFP+ 2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted using Trizol (Thermo Fisher Scientific) and PelletPaint (Novagen EMD Millipore). Briefly, samples were homogenized in 300µl of Trizol and shaken with 60µl chloroform and 2µl PelletPaint and centrifuged for 15 minutes. The supernatant containing RNA was precipitated with 1 volume of isopropanol, centrifuged for 30 minutes, washed in 75% ethanol, resuspended in 100µl water and re-precipitated with 10µl 3M sodium acetate and 250µl ethanol. After a final wash in 75% ethanol, the pellet was allowed to dry, resuspended in 20µl RNAse-free water and stored at -80°C. cDNA libraries for RNAseq were generated using RNA Seq Truseq RNA sample preparation kit v2 (Illumina) following the “low sample” protocol according to the manufacturer's instructions for mRNA extraction, cDNA synthesis, indexing and amplification. cDNA generated from less than 20,000 cells received an initial amplification using the NuGen Ovation Kit.  The quality and integrity of RNA samples and the final quality of the sequencing libraries was checked by electrophenogram in an Agilent Bioanalyzer. paired end 100bp sequencing	Illumina HiSeq 2000	source_name;;Purified LFng-GFP+ cells from P1 mouse cochlea|strain;;LFng-GFP BAC Transgenic Mouse (B6; FVB-Tg(Lfng-EGFP)HM340Gsat/Mmucd)|tissue type;;P1 cochlea	GEO Accession;;GSM2200199		GSM2200199	P1 Cochlea GFP+ 2	8446404972	41813886	2016-07-01 15:42:32	5698030668	8446404972	41813886	2	41813886	index:0,count:41813886,average:101,stdev:0|index:1,count:41813886,average:101,stdev:0	GSM2200199_r1						3.16	2.92	0.11	5516993791	5399699945	5223511716	5135782963	97.87	98.32	37087566	35078570	169.468	633.279	126	409853	72.36	76.54	40328935	26837402	40328935	26837402	73.84	73.57	40328935	27384524	40328935	25798182	1192945972	21.62	1.61	0	4.84	0	0.23	0	0.17	0	0.00	0	10.91	0	37087566	0	202	0	199.19	0	2.07	0	0.02	0	1.76	0	0.02	0	194.73	0	0.41	0	674682	0	41813886	0	2022411	0	96775	0	69382	0	0	0	4560163	0	7951	0	0	0	79266	0	12487205	0	41801	0	12616223	0	83.86	0	35065155	0	230250	10385729	45.106314875136	41813886.0	37087566.0	674682.0	2022411.0	96775.0	69382.0	0.0	4560163.0	35065155.0	88.7	1.6	4.8	0.2	0.2	0.0	10.9	83.9	101	101	101.00	38	4223202486	26.1	24.5	24.0	25.4	0.0	34.5	16.0	bulk
1738265	SRR3666861	SRP076556	SRS1504101	SRX1845261	SRA433971	GEO		RNA-seq analysis of neonatal mouse cochlear supporting cells [NonTreated_JM]	This study examined transcripts that are enriched in neonatal mouse cochlear supporting cells at postnatal day 1 and postnatal day 6. Supporting cells were purified by FACS sorting for GFP fluorescence from the cochleas of transgenic mice in which a BAC including the LFng locus drives the expression of GFP. Two replicates of GFP+ supporting cells were compared with all other cochlear cell types that were GFP-. We performed this experiment at two different ages, postnatal day 1 and postnatal day 6. Overall design: mRNA profiles of supporting cells (GFP+) and all other cochlear cell types (GFP-), two replicates each, at P1 and P6 mice were generated by deep sequencing using Illumna TruSeq.		GSM2200200: P1 Cochlea GFP- 1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted using Trizol (Thermo Fisher Scientific) and PelletPaint (Novagen EMD Millipore). Briefly, samples were homogenized in 300µl of Trizol and shaken with 60µl chloroform and 2µl PelletPaint and centrifuged for 15 minutes. The supernatant containing RNA was precipitated with 1 volume of isopropanol, centrifuged for 30 minutes, washed in 75% ethanol, resuspended in 100µl water and re-precipitated with 10µl 3M sodium acetate and 250µl ethanol. After a final wash in 75% ethanol, the pellet was allowed to dry, resuspended in 20µl RNAse-free water and stored at -80°C. cDNA libraries for RNAseq were generated using RNA Seq Truseq RNA sample preparation kit v2 (Illumina) following the “low sample” protocol according to the manufacturer's instructions for mRNA extraction, cDNA synthesis, indexing and amplification. cDNA generated from less than 20,000 cells received an initial amplification using the NuGen Ovation Kit.  The quality and integrity of RNA samples and the final quality of the sequencing libraries was checked by electrophenogram in an Agilent Bioanalyzer. paired end 100bp sequencing	Illumina HiSeq 2000	source_name;;Purified LFng-GFP- cells from P1 mouse cochlea|strain;;LFng-GFP BAC Transgenic Mouse (B6; FVB-Tg(Lfng-EGFP)HM340Gsat/Mmucd)|tissue type;;P1 cochlea	GEO Accession;;GSM2200200		GSM2200200	P1 Cochlea GFP- 1	11805735470	58444235	2016-07-01 15:42:32	7902416835	11805735470	58444235	2	58444235	index:0,count:58444235,average:101,stdev:0|index:1,count:58444235,average:101,stdev:0	GSM2200200_r1						2.46	3.4	0.14	9123116141	8975847988	8643899635	8548384108	98.39	98.89	56360308	53328914	186.922	578.920	146	576764	73.39	77.54	61490160	41361050	61490160	41361050	74.36	74.26	61490160	41908540	61490160	39608540	1911045541	20.95	1.00	0	5.17	0	0.29	0	0.15	0	0.00	0	3.13	0	56360308	0	202	0	199.46	0	1.99	0	0.03	0	1.74	0	0.02	0	220.54	0	0.37	0	586563	0	58444235	0	3020369	0	168880	0	88218	0	0	0	1826829	0	13191	0	0	0	127918	0	20897476	0	67617	0	21106202	0	91.27	0	53339939	0	279920	18796545	67.149703486710	58444235.0	56360308.0	586563.0	3020369.0	168880.0	88218.0	0.0	1826829.0	53339939.0	96.4	1.0	5.2	0.3	0.2	0.0	3.1	91.3	101	101	101.00	38	5902867735	25.9	24.2	24.0	25.9	0.0	35.7	20.0	bulk
1738281	SRR3666862	SRP076556	SRS1504102	SRX1845262	SRA433971	GEO		RNA-seq analysis of neonatal mouse cochlear supporting cells [NonTreated_JM]	This study examined transcripts that are enriched in neonatal mouse cochlear supporting cells at postnatal day 1 and postnatal day 6. Supporting cells were purified by FACS sorting for GFP fluorescence from the cochleas of transgenic mice in which a BAC including the LFng locus drives the expression of GFP. Two replicates of GFP+ supporting cells were compared with all other cochlear cell types that were GFP-. We performed this experiment at two different ages, postnatal day 1 and postnatal day 6. Overall design: mRNA profiles of supporting cells (GFP+) and all other cochlear cell types (GFP-), two replicates each, at P1 and P6 mice were generated by deep sequencing using Illumna TruSeq.		GSM2200201: P1 Cochlea GFP- 2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted using Trizol (Thermo Fisher Scientific) and PelletPaint (Novagen EMD Millipore). Briefly, samples were homogenized in 300µl of Trizol and shaken with 60µl chloroform and 2µl PelletPaint and centrifuged for 15 minutes. The supernatant containing RNA was precipitated with 1 volume of isopropanol, centrifuged for 30 minutes, washed in 75% ethanol, resuspended in 100µl water and re-precipitated with 10µl 3M sodium acetate and 250µl ethanol. After a final wash in 75% ethanol, the pellet was allowed to dry, resuspended in 20µl RNAse-free water and stored at -80°C. cDNA libraries for RNAseq were generated using RNA Seq Truseq RNA sample preparation kit v2 (Illumina) following the “low sample” protocol according to the manufacturer's instructions for mRNA extraction, cDNA synthesis, indexing and amplification. cDNA generated from less than 20,000 cells received an initial amplification using the NuGen Ovation Kit.  The quality and integrity of RNA samples and the final quality of the sequencing libraries was checked by electrophenogram in an Agilent Bioanalyzer. paired end 100bp sequencing	Illumina HiSeq 2000	source_name;;Purified LFng-GFP- cells from P1 mouse cochlea|strain;;LFng-GFP BAC Transgenic Mouse (B6; FVB-Tg(Lfng-EGFP)HM340Gsat/Mmucd)|tissue type;;P1 cochlea	GEO Accession;;GSM2200201		GSM2200201	P1 Cochlea GFP- 2	18207186978	90134589	2016-07-01 15:42:32	12387365823	18207186978	90134589	2	90134589	index:0,count:90134589,average:101,stdev:0|index:1,count:90134589,average:101,stdev:0	GSM2200201_r1						2.58	3.39	0.11	14118019197	13967708889	13353838487	13277649010	98.94	99.43	87184698	82089224	187.433	586.989	146	911628	78.52	83.1	95170008	68457796	95170008	68457796	79.38	79.47	95170008	69203411	95170008	65462917	2186851025	15.49	1.01	0	5.34	0	0.28	0	0.14	0	0.00	0	2.86	0	87184698	0	202	0	199.64	0	2.09	0	0.02	0	1.80	0	0.02	0	313.81	0	0.43	0	906013	0	90134589	0	4809180	0	248002	0	122405	0	0	0	2579484	0	22984	0	0	0	211133	0	35321608	0	94982	0	35650707	0	91.39	0	82375518	0	293689	31726053	108.026017317639	90134589.0	87184698.0	906013.0	4809180.0	248002.0	122405.0	0.0	2579484.0	82375518.0	96.7	1.0	5.3	0.3	0.1	0.0	2.9	91.4	101	101	101.00	38	9103593489	25.5	24.6	24.4	25.6	0.0	35.0	17.4	bulk
1738297	SRR3666863	SRP076556	SRS1504103	SRX1845263	SRA433971	GEO		RNA-seq analysis of neonatal mouse cochlear supporting cells [NonTreated_JM]	This study examined transcripts that are enriched in neonatal mouse cochlear supporting cells at postnatal day 1 and postnatal day 6. Supporting cells were purified by FACS sorting for GFP fluorescence from the cochleas of transgenic mice in which a BAC including the LFng locus drives the expression of GFP. Two replicates of GFP+ supporting cells were compared with all other cochlear cell types that were GFP-. We performed this experiment at two different ages, postnatal day 1 and postnatal day 6. Overall design: mRNA profiles of supporting cells (GFP+) and all other cochlear cell types (GFP-), two replicates each, at P1 and P6 mice were generated by deep sequencing using Illumna TruSeq.		GSM2200202: P6 Cochlea GFP+ 1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted using Trizol (Thermo Fisher Scientific) and PelletPaint (Novagen EMD Millipore). Briefly, samples were homogenized in 300µl of Trizol and shaken with 60µl chloroform and 2µl PelletPaint and centrifuged for 15 minutes. The supernatant containing RNA was precipitated with 1 volume of isopropanol, centrifuged for 30 minutes, washed in 75% ethanol, resuspended in 100µl water and re-precipitated with 10µl 3M sodium acetate and 250µl ethanol. After a final wash in 75% ethanol, the pellet was allowed to dry, resuspended in 20µl RNAse-free water and stored at -80°C. cDNA libraries for RNAseq were generated using RNA Seq Truseq RNA sample preparation kit v2 (Illumina) following the “low sample” protocol according to the manufacturer's instructions for mRNA extraction, cDNA synthesis, indexing and amplification. cDNA generated from less than 20,000 cells received an initial amplification using the NuGen Ovation Kit.  The quality and integrity of RNA samples and the final quality of the sequencing libraries was checked by electrophenogram in an Agilent Bioanalyzer. paired end 100bp sequencing	Illumina HiSeq 2000	source_name;;Purified LFng-GFP+ cells from P6 mouse cochlea|strain;;LFng-GFP BAC Transgenic Mouse (B6; FVB-Tg(Lfng-EGFP)HM340Gsat/Mmucd)|tissue type;;P6 cochlea	GEO Accession;;GSM2200202		GSM2200202	P6 Cochlea GFP+ 1	5076894886	25133143	2016-07-01 15:42:32	3537776192	5076894886	25133143	2	25133143	index:0,count:25133143,average:101,stdev:0|index:1,count:25133143,average:101,stdev:0	GSM2200202_r1						6.31	2.59	0.09	3457531264	3411095674	3183768557	3158448399	98.66	99.2	23230039	21944545	170.006	543.455	125	263458	79.84	86.85	25974720	18547288	25974720	18547288	83.23	83.09	25974720	19333905	25974720	17745137	384935160	11.13	1.47	0	7.46	0	0.31	0	0.10	0	0.00	0	7.16	0	23230039	0	202	0	199.12	0	2.03	0	0.02	0	1.72	0	0.02	0	243.22	0	0.49	0	370182	0	25133143	0	1874792	0	77424	0	25798	0	0	0	1799882	0	5652	0	0	0	47818	0	8339525	0	22233	0	8415228	0	84.97	0	21355247	0	191771	6971821	36.354928534554	25133143.0	23230039.0	370182.0	1874792.0	77424.0	25798.0	0.0	1799882.0	21355247.0	92.4	1.5	7.5	0.3	0.1	0.0	7.2	85.0	101	101	101.00	38	2538447443	25.6	24.5	24.4	25.5	0.0	34.7	17.2	bulk
869071	SRR3666859	SRP076556	SRS1504099	SRX1845259	SRA433971	GEO		RNA-seq analysis of neonatal mouse cochlear supporting cells [NonTreated_JM]	This study examined transcripts that are enriched in neonatal mouse cochlear supporting cells at postnatal day 1 and postnatal day 6. Supporting cells were purified by FACS sorting for GFP fluorescence from the cochleas of transgenic mice in which a BAC including the LFng locus drives the expression of GFP. Two replicates of GFP+ supporting cells were compared with all other cochlear cell types that were GFP-. We performed this experiment at two different ages, postnatal day 1 and postnatal day 6. Overall design: mRNA profiles of supporting cells (GFP+) and all other cochlear cell types (GFP-), two replicates each, at P1 and P6 mice were generated by deep sequencing using Illumna TruSeq.		GSM2200198: P1 Cochlea GFP+ 1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted using Trizol (Thermo Fisher Scientific) and PelletPaint (Novagen EMD Millipore). Briefly, samples were homogenized in 300µl of Trizol and shaken with 60µl chloroform and 2µl PelletPaint and centrifuged for 15 minutes. The supernatant containing RNA was precipitated with 1 volume of isopropanol, centrifuged for 30 minutes, washed in 75% ethanol, resuspended in 100µl water and re-precipitated with 10µl 3M sodium acetate and 250µl ethanol. After a final wash in 75% ethanol, the pellet was allowed to dry, resuspended in 20µl RNAse-free water and stored at -80°C. cDNA libraries for RNAseq were generated using RNA Seq Truseq RNA sample preparation kit v2 (Illumina) following the “low sample” protocol according to the manufacturer's instructions for mRNA extraction, cDNA synthesis, indexing and amplification. cDNA generated from less than 20,000 cells received an initial amplification using the NuGen Ovation Kit.  The quality and integrity of RNA samples and the final quality of the sequencing libraries was checked by electrophenogram in an Agilent Bioanalyzer. paired end 100bp sequencing	Illumina HiSeq 2000	source_name;;Purified LFng-GFP+ cells from P1 mouse cochlea|strain;;LFng-GFP BAC Transgenic Mouse (B6; FVB-Tg(Lfng-EGFP)HM340Gsat/Mmucd)|tissue type;;P1 cochlea	GEO Accession;;GSM2200198		GSM2200198	P1 Cochlea GFP+ 1	14985195270	74184135	2016-07-01 15:42:32	9989612970	14985195270	74184135	2	74184135	index:0,count:74184135,average:101,stdev:0|index:1,count:74184135,average:101,stdev:0	GSM2200198_r1						4.6	2.93	0.11	9930462237	9710708246	9313681300	9154567237	97.79	98.29	67841408	64177925	166.704	655.113	125	731243	71.61	76.47	74511503	48580253	74511503	48580253	74.07	73.63	74511503	50249215	74511503	46775578	2138259574	21.53	2.03	0	5.81	0	0.26	0	0.15	0	0.00	0	8.14	0	67841408	0	202	0	198.66	0	2.00	0	0.02	0	1.81	0	0.02	0	230.43	0	0.34	0	1504336	0	74184135	0	4309779	0	190898	0	114533	0	0	0	6037296	0	14679	0	0	0	142501	0	22113962	0	78977	0	22350119	0	85.64	0	63531629	0	268480	18144033	67.580575834327	74184135.0	67841408.0	1504336.0	4309779.0	190898.0	114533.0	0.0	6037296.0	63531629.0	91.5	2.0	5.8	0.3	0.2	0.0	8.1	85.6	101	101	101.00	38	7492597635	26.3	23.9	23.9	25.9	0.0	35.6	19.3	bulk
869158	SRR3666864	SRP076556	SRS1504104	SRX1845264	SRA433971	GEO		RNA-seq analysis of neonatal mouse cochlear supporting cells [NonTreated_JM]	This study examined transcripts that are enriched in neonatal mouse cochlear supporting cells at postnatal day 1 and postnatal day 6. Supporting cells were purified by FACS sorting for GFP fluorescence from the cochleas of transgenic mice in which a BAC including the LFng locus drives the expression of GFP. Two replicates of GFP+ supporting cells were compared with all other cochlear cell types that were GFP-. We performed this experiment at two different ages, postnatal day 1 and postnatal day 6. Overall design: mRNA profiles of supporting cells (GFP+) and all other cochlear cell types (GFP-), two replicates each, at P1 and P6 mice were generated by deep sequencing using Illumna TruSeq.		GSM2200203: P6 Cochlea GFP+ 2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted using Trizol (Thermo Fisher Scientific) and PelletPaint (Novagen EMD Millipore). Briefly, samples were homogenized in 300µl of Trizol and shaken with 60µl chloroform and 2µl PelletPaint and centrifuged for 15 minutes. The supernatant containing RNA was precipitated with 1 volume of isopropanol, centrifuged for 30 minutes, washed in 75% ethanol, resuspended in 100µl water and re-precipitated with 10µl 3M sodium acetate and 250µl ethanol. After a final wash in 75% ethanol, the pellet was allowed to dry, resuspended in 20µl RNAse-free water and stored at -80°C. cDNA libraries for RNAseq were generated using RNA Seq Truseq RNA sample preparation kit v2 (Illumina) following the “low sample” protocol according to the manufacturer's instructions for mRNA extraction, cDNA synthesis, indexing and amplification. cDNA generated from less than 20,000 cells received an initial amplification using the NuGen Ovation Kit.  The quality and integrity of RNA samples and the final quality of the sequencing libraries was checked by electrophenogram in an Agilent Bioanalyzer. paired end 100bp sequencing	Illumina HiSeq 2000	source_name;;Purified LFng-GFP+ cells from P6 mouse cochlea|strain;;LFng-GFP BAC Transgenic Mouse (B6; FVB-Tg(Lfng-EGFP)HM340Gsat/Mmucd)|tissue type;;P6 cochlea	GEO Accession;;GSM2200203		GSM2200203	P6 Cochlea GFP+ 2	8796201302	43545551	2016-07-01 15:42:32	5884123398	8796201302	43545551	2	43545551	index:0,count:43545551,average:101,stdev:0|index:1,count:43545551,average:101,stdev:0	GSM2200203_r1						4.38	2.79	0.08	6089461779	6000926915	5737064817	5679198692	98.55	98.99	40616223	38088899	172.614	628.959	125	428938	77.75	82.64	44295959	31580291	44295959	31580291	79.67	79.51	44295959	32359924	44295959	30383934	962650013	15.81	1.55	0	5.51	0	0.30	0	0.13	0	0.00	0	6.30	0	40616223	0	202	0	199.28	0	1.99	0	0.02	0	1.79	0	0.01	0	280.44	0	0.38	0	676530	0	43545551	0	2401225	0	129951	0	56780	0	0	0	2742597	0	9696	0	0	0	93329	0	15758055	0	44832	0	15905912	0	87.76	0	38214998	0	241989	13093448	54.107616461905	43545551.0	40616223.0	676530.0	2401225.0	129951.0	56780.0	0.0	2742597.0	38214998.0	93.3	1.6	5.5	0.3	0.1	0.0	6.3	87.8	101	101	101.00	38	4398100651	25.6	24.4	24.3	25.6	0.1	35.3	17.8	bulk
869166	SRR3666865	SRP076556	SRS1504105	SRX1845265	SRA433971	GEO		RNA-seq analysis of neonatal mouse cochlear supporting cells [NonTreated_JM]	This study examined transcripts that are enriched in neonatal mouse cochlear supporting cells at postnatal day 1 and postnatal day 6. Supporting cells were purified by FACS sorting for GFP fluorescence from the cochleas of transgenic mice in which a BAC including the LFng locus drives the expression of GFP. Two replicates of GFP+ supporting cells were compared with all other cochlear cell types that were GFP-. We performed this experiment at two different ages, postnatal day 1 and postnatal day 6. Overall design: mRNA profiles of supporting cells (GFP+) and all other cochlear cell types (GFP-), two replicates each, at P1 and P6 mice were generated by deep sequencing using Illumna TruSeq.		GSM2200204: P6 Cochlea GFP- 1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted using Trizol (Thermo Fisher Scientific) and PelletPaint (Novagen EMD Millipore). Briefly, samples were homogenized in 300µl of Trizol and shaken with 60µl chloroform and 2µl PelletPaint and centrifuged for 15 minutes. The supernatant containing RNA was precipitated with 1 volume of isopropanol, centrifuged for 30 minutes, washed in 75% ethanol, resuspended in 100µl water and re-precipitated with 10µl 3M sodium acetate and 250µl ethanol. After a final wash in 75% ethanol, the pellet was allowed to dry, resuspended in 20µl RNAse-free water and stored at -80°C. cDNA libraries for RNAseq were generated using RNA Seq Truseq RNA sample preparation kit v2 (Illumina) following the “low sample” protocol according to the manufacturer's instructions for mRNA extraction, cDNA synthesis, indexing and amplification. cDNA generated from less than 20,000 cells received an initial amplification using the NuGen Ovation Kit.  The quality and integrity of RNA samples and the final quality of the sequencing libraries was checked by electrophenogram in an Agilent Bioanalyzer. paired end 100bp sequencing	Illumina HiSeq 2000	source_name;;Purified LFng-GFP- cells from P6 mouse cochlea|strain;;LFng-GFP BAC Transgenic Mouse (B6; FVB-Tg(Lfng-EGFP)HM340Gsat/Mmucd)|tissue type;;P6 cochlea	GEO Accession;;GSM2200204		GSM2200204	P6 Cochlea GFP- 1	16411281738	81243969	2016-07-01 15:42:32	11449259700	16411281738	81243969	2	81243969	index:0,count:81243969,average:101,stdev:0|index:1,count:81243969,average:101,stdev:0	GSM2200204_r1						2.08	3.01	0.06	12770663206	12729775230	12168064121	12182424922	99.68	100.12	78585588	73068860	193.081	638.538	146	769972	84.82	89.11	84804834	66656410	84804834	66656410	84.87	85.23	84804834	66699239	84804834	63752825	1238304453	9.70	0.93	0	4.66	0	0.28	0	0.09	0	0.00	0	2.90	0	78585588	0	202	0	199.35	0	2.13	0	0.02	0	1.77	0	0.02	0	239.15	0	0.50	0	754505	0	81243969	0	3783775	0	231052	0	74462	0	0	0	2352867	0	20728	0	0	0	186196	0	38080234	0	79417	0	38366575	0	92.07	0	74801813	0	284147	34079665	119.936740489958	81243969.0	78585588.0	754505.0	3783775.0	231052.0	74462.0	0.0	2352867.0	74801813.0	96.7	0.9	4.7	0.3	0.1	0.0	2.9	92.1	101	101	101.00	38	8205640869	25.0	25.0	24.9	25.1	0.0	34.7	17.4	bulk
869175	SRR3666866	SRP076556	SRS1504106	SRX1845266	SRA433971	GEO		RNA-seq analysis of neonatal mouse cochlear supporting cells [NonTreated_JM]	This study examined transcripts that are enriched in neonatal mouse cochlear supporting cells at postnatal day 1 and postnatal day 6. Supporting cells were purified by FACS sorting for GFP fluorescence from the cochleas of transgenic mice in which a BAC including the LFng locus drives the expression of GFP. Two replicates of GFP+ supporting cells were compared with all other cochlear cell types that were GFP-. We performed this experiment at two different ages, postnatal day 1 and postnatal day 6. Overall design: mRNA profiles of supporting cells (GFP+) and all other cochlear cell types (GFP-), two replicates each, at P1 and P6 mice were generated by deep sequencing using Illumna TruSeq.		GSM2200205: P6 Cochlea GFP- 2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted using Trizol (Thermo Fisher Scientific) and PelletPaint (Novagen EMD Millipore). Briefly, samples were homogenized in 300µl of Trizol and shaken with 60µl chloroform and 2µl PelletPaint and centrifuged for 15 minutes. The supernatant containing RNA was precipitated with 1 volume of isopropanol, centrifuged for 30 minutes, washed in 75% ethanol, resuspended in 100µl water and re-precipitated with 10µl 3M sodium acetate and 250µl ethanol. After a final wash in 75% ethanol, the pellet was allowed to dry, resuspended in 20µl RNAse-free water and stored at -80°C. cDNA libraries for RNAseq were generated using RNA Seq Truseq RNA sample preparation kit v2 (Illumina) following the “low sample” protocol according to the manufacturer's instructions for mRNA extraction, cDNA synthesis, indexing and amplification. cDNA generated from less than 20,000 cells received an initial amplification using the NuGen Ovation Kit.  The quality and integrity of RNA samples and the final quality of the sequencing libraries was checked by electrophenogram in an Agilent Bioanalyzer. paired end 100bp sequencing	Illumina HiSeq 2000	source_name;;Purified LFng-GFP- cells from P6 mouse cochlea|strain;;LFng-GFP BAC Transgenic Mouse (B6; FVB-Tg(Lfng-EGFP)HM340Gsat/Mmucd)|tissue type;;P6 cochlea	GEO Accession;;GSM2200205		GSM2200205	P6 Cochlea GFP- 2	19395834566	96018983	2016-07-01 15:42:32	13021642126	19395834566	96018983	2	96018983	index:0,count:96018983,average:101,stdev:0|index:1,count:96018983,average:101,stdev:0	GSM2200205_r1						2.32	2.94	0.09	14901293185	14792054806	14197531275	14160186412	99.27	99.74	92494062	86798450	189.185	594.456	146	928827	79.52	83.55	99890080	73550088	99890080	73550088	79.61	79.78	99890080	73632025	99890080	70237345	2277875647	15.29	0.98	0	4.64	0	0.27	0	0.13	0	0.00	0	3.27	0	92494062	0	202	0	199.56	0	2.11	0	0.02	0	1.78	0	0.02	0	264.47	0	0.42	0	944321	0	96018983	0	4457680	0	258814	0	126406	0	0	0	3139701	0	22273	0	0	0	201741	0	40967356	0	102538	0	41293908	0	91.69	0	88036382	0	300008	36369976	121.230020532786	96018983.0	92494062.0	944321.0	4457680.0	258814.0	126406.0	0.0	3139701.0	88036382.0	96.3	1.0	4.6	0.3	0.1	0.0	3.3	91.7	101	101	101.00	38	9697917283	25.2	24.8	24.6	25.3	0.1	35.2	17.7	bulk
1806463	SRR3901907	SRP078457	SRS1562164	SRX1944721	SRA440331	GEO		A Unique Twist-Dependent Progenitor Cell Contributes to Adult Skeletal Muscle [Tw2 vs Pax7 fresh sort]	Skeletal muscle possesses remarkable regenerative potential due to satellite cells, a stem cell population located beneath the muscle basal lamina. By lineage tracing of progenitor cells expressing the Twist2 (Tw2) transcription factor in mice, we discovered a unique myogenic lineage that resides outside the basal lamina of adult muscle and contributes specifically to type IIb/x myofibers during adulthood and muscle regeneration. Tw2+ progenitors are molecularly and anatomically distinct from satellite cells, are highly myogenic in vitro and can fuse with satellite cells. Transplantation of Tw2+ progenitors into adult mice is sufficient to reconstitute new myofibers, and genetic ablation of endogenous Tw2+ progenitors causes wasting of type IIb myofibers. We show that Tw2 expression maintains progenitor cells in an undifferentiated state that is poised to initiate myogenesis in response to appropriate cues that suppress Tw2 expression. Tw2-expressing progenitors represent a previously unrecognized, fiber-type specific progenitor cell involved in muscle growth and regeneration. Overall design: Gene expression profile was generated by comparing freshly sorted Twist2+ and Pax7+ cells from skeletal muscle		GSM2232842: Pax7-pos; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted from freshly sorted tdTO+ cells using Trizol Chloroform purification. RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2500	background strain;;C57BL/6|developmental stage;;adult|genotype;;Pax7-CreERT2/+;R26-tdTO+|source_name;;freshly sorted cells from hind limb skeletal muscle|tissue;;Skeletal Muscle	GEO Accession;;GSM2232842		GSM2232842	Pax7-pos	2507576400	12537882	2017-01-13 15:46:20	1311443450	2507576400	12537882	2	12537882	index:0,count:12537882,average:100,stdev:0|index:1,count:12537882,average:100,stdev:0	GSM2232842_r1				in_mesa	28218909	2.13	2.88	0.19	1618681622	1612467484	1464787119	1469364889	99.62	100.31	10255287	9630278	190.597	568.480	134	81636	80.02	88.66	12098090	8206295	12098090	8206295	83.16	83.53	12098090	8528560	12098090	7730873	151851243	9.38	0.69	0	7.97	0	0.74	0	0.10	0	0.00	0	17.37	0	10255287	0	200	0	196.42	0	1.94	0	0.01	0	1.89	0	0.01	0	224.56	0	1.05	0	87067	0	12537882	0	999887	0	93085	0	12021	0	0	0	2177489	0	1614	0	0	0	29689	0	3679687	0	7985	0	3718975	0	73.82	0	9255400	0	157576	3374758	21.416700512768	12537882.0	10255287.0	87067.0	999887.0	93085.0	12021.0	0.0	2177489.0	9255400.0	81.8	0.7	8.0	0.7	0.1	0.0	17.4	73.8	100	100	100.00	7	1253788200	23.4	26.1	25.7	24.9	0.0	32.4	20.6	bulk
1806478	SRR3901908	SRP078457	SRS1562164	SRX1944721	SRA440331	GEO		A Unique Twist-Dependent Progenitor Cell Contributes to Adult Skeletal Muscle [Tw2 vs Pax7 fresh sort]	Skeletal muscle possesses remarkable regenerative potential due to satellite cells, a stem cell population located beneath the muscle basal lamina. By lineage tracing of progenitor cells expressing the Twist2 (Tw2) transcription factor in mice, we discovered a unique myogenic lineage that resides outside the basal lamina of adult muscle and contributes specifically to type IIb/x myofibers during adulthood and muscle regeneration. Tw2+ progenitors are molecularly and anatomically distinct from satellite cells, are highly myogenic in vitro and can fuse with satellite cells. Transplantation of Tw2+ progenitors into adult mice is sufficient to reconstitute new myofibers, and genetic ablation of endogenous Tw2+ progenitors causes wasting of type IIb myofibers. We show that Tw2 expression maintains progenitor cells in an undifferentiated state that is poised to initiate myogenesis in response to appropriate cues that suppress Tw2 expression. Tw2-expressing progenitors represent a previously unrecognized, fiber-type specific progenitor cell involved in muscle growth and regeneration. Overall design: Gene expression profile was generated by comparing freshly sorted Twist2+ and Pax7+ cells from skeletal muscle		GSM2232842: Pax7-pos; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted from freshly sorted tdTO+ cells using Trizol Chloroform purification. RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2500	background strain;;C57BL/6|developmental stage;;adult|genotype;;Pax7-CreERT2/+;R26-tdTO+|source_name;;freshly sorted cells from hind limb skeletal muscle|tissue;;Skeletal Muscle	GEO Accession;;GSM2232842		GSM2232842	Pax7-pos	2455171200	12275856	2017-01-13 15:46:20	1287461818	2455171200	12275856	2	12275856	index:0,count:12275856,average:100,stdev:0|index:1,count:12275856,average:100,stdev:0	GSM2232842_r2				in_mesa	28218909	2.2	2.89	0.19	1518593400	1512270568	1372473372	1376597797	99.58	100.3	9652943	9072268	189.779	568.029	134	76476	79.91	88.66	11403735	7713780	11403735	7713780	83.19	83.57	11403735	8030237	11403735	7270971	143242927	9.43	0.64	0	7.76	0	0.71	0	0.08	0	0.00	0	20.58	0	9652943	0	200	0	195.53	0	1.93	0	0.01	0	1.86	0	0.01	0	195.54	0	1.37	0	78417	0	12275856	0	952572	0	86632	0	9396	0	0	0	2526885	0	1360	0	0	0	26271	0	3343436	0	7437	0	3378504	0	70.87	0	8700371	0	154201	3081471	19.983469627305	12275856.0	9652943.0	78417.0	952572.0	86632.0	9396.0	0.0	2526885.0	8700371.0	78.6	0.6	7.8	0.7	0.1	0.0	20.6	70.9	100	100	100.00	7	1227585600	23.3	26.1	25.6	24.9	0.0	32.5	20.6	bulk
1806653	SRR3901913	SRP078457	SRS1562167	SRX1944724	SRA440331	GEO		A Unique Twist-Dependent Progenitor Cell Contributes to Adult Skeletal Muscle [Tw2 vs Pax7 fresh sort]	Skeletal muscle possesses remarkable regenerative potential due to satellite cells, a stem cell population located beneath the muscle basal lamina. By lineage tracing of progenitor cells expressing the Twist2 (Tw2) transcription factor in mice, we discovered a unique myogenic lineage that resides outside the basal lamina of adult muscle and contributes specifically to type IIb/x myofibers during adulthood and muscle regeneration. Tw2+ progenitors are molecularly and anatomically distinct from satellite cells, are highly myogenic in vitro and can fuse with satellite cells. Transplantation of Tw2+ progenitors into adult mice is sufficient to reconstitute new myofibers, and genetic ablation of endogenous Tw2+ progenitors causes wasting of type IIb myofibers. We show that Tw2 expression maintains progenitor cells in an undifferentiated state that is poised to initiate myogenesis in response to appropriate cues that suppress Tw2 expression. Tw2-expressing progenitors represent a previously unrecognized, fiber-type specific progenitor cell involved in muscle growth and regeneration. Overall design: Gene expression profile was generated by comparing freshly sorted Twist2+ and Pax7+ cells from skeletal muscle		GSM2232845: Twist2-pos-1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted from freshly sorted tdTO+ cells using Trizol Chloroform purification. RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2500	background strain;;C57BL/6|developmental stage;;adult|genotype;;Tw2-CreERT2/+;R26-tdTO+|source_name;;freshly sorted cells from hind limb skeletal muscle|tissue;;Skeletal Muscle	GEO Accession;;GSM2232845		GSM2232845	Twist2-pos-1	1743584000	8717920	2017-01-13 15:46:20	1309128449	1743584000	8717920	2	8717920	index:0,count:8717920,average:100,stdev:0|index:1,count:8717920,average:100,stdev:0	GSM2232845_r1				in_mesa	28218909	1.5	2.69	0.07	1390976770	1393092555	1331572736	1337249770	100.15	100.43	7943806	6908939	243.093	967.185	163	44144	87.45	91.4	8542003	6946576	8542003	6946576	88.08	88.36	8542003	6996871	8542003	6715531	115237586	8.28	0.54	0	3.94	0	0.29	0	0.08	0	0.00	0	8.51	0	7943806	0	200	0	197.61	0	1.92	0	0.01	0	1.39	0	0.01	0	221.02	0	0.51	0	47196	0	8717920	0	343461	0	25311	0	6923	0	0	0	741880	0	1338	0	0	0	18964	0	4222704	0	4994	0	4248000	0	87.18	0	7600345	0	161183	4024834	24.970586228076	8717920.0	7943806.0	47196.0	343461.0	25311.0	6923.0	0.0	741880.0	7600345.0	91.1	0.5	3.9	0.3	0.1	0.0	8.5	87.2	100	100	100.00	38	871792000	23.9	26.0	25.5	24.6	0.0	33.5	19.6	bulk
1806669	SRR3901914	SRP078457	SRS1562167	SRX1944724	SRA440331	GEO		A Unique Twist-Dependent Progenitor Cell Contributes to Adult Skeletal Muscle [Tw2 vs Pax7 fresh sort]	Skeletal muscle possesses remarkable regenerative potential due to satellite cells, a stem cell population located beneath the muscle basal lamina. By lineage tracing of progenitor cells expressing the Twist2 (Tw2) transcription factor in mice, we discovered a unique myogenic lineage that resides outside the basal lamina of adult muscle and contributes specifically to type IIb/x myofibers during adulthood and muscle regeneration. Tw2+ progenitors are molecularly and anatomically distinct from satellite cells, are highly myogenic in vitro and can fuse with satellite cells. Transplantation of Tw2+ progenitors into adult mice is sufficient to reconstitute new myofibers, and genetic ablation of endogenous Tw2+ progenitors causes wasting of type IIb myofibers. We show that Tw2 expression maintains progenitor cells in an undifferentiated state that is poised to initiate myogenesis in response to appropriate cues that suppress Tw2 expression. Tw2-expressing progenitors represent a previously unrecognized, fiber-type specific progenitor cell involved in muscle growth and regeneration. Overall design: Gene expression profile was generated by comparing freshly sorted Twist2+ and Pax7+ cells from skeletal muscle		GSM2232845: Twist2-pos-1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted from freshly sorted tdTO+ cells using Trizol Chloroform purification. RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2500	background strain;;C57BL/6|developmental stage;;adult|genotype;;Tw2-CreERT2/+;R26-tdTO+|source_name;;freshly sorted cells from hind limb skeletal muscle|tissue;;Skeletal Muscle	GEO Accession;;GSM2232845		GSM2232845	Twist2-pos-1	1711328400	8556642	2017-01-13 15:46:20	1274608193	1711328400	8556642	2	8556642	index:0,count:8556642,average:100,stdev:0|index:1,count:8556642,average:100,stdev:0	GSM2232845_r2				in_mesa	28218909	1.49	2.7	0.07	1370652207	1372591792	1311994702	1317503617	100.14	100.42	7829528	6811874	243.024	966.914	163	44010	87.43	91.39	8420493	6844979	8420493	6844979	88.08	88.36	8420493	6895914	8420493	6618404	113758084	8.30	0.54	0	3.97	0	0.29	0	0.08	0	0.00	0	8.13	0	7829528	0	200	0	197.65	0	1.91	0	0.01	0	1.39	0	0.01	0	265.55	0	0.49	0	46394	0	8556642	0	339382	0	24842	0	6880	0	0	0	695392	0	1186	0	0	0	18951	0	4161608	0	5033	0	4186778	0	87.54	0	7490146	0	161135	3965501	24.609805442641	8556642.0	7829528.0	46394.0	339382.0	24842.0	6880.0	0.0	695392.0	7490146.0	91.5	0.5	4.0	0.3	0.1	0.0	8.1	87.5	100	100	100.00	38	855664200	23.9	26.0	25.5	24.6	0.0	33.7	19.9	bulk
1806685	SRR3901915	SRP078457	SRS1562168	SRX1944725	SRA440331	GEO		A Unique Twist-Dependent Progenitor Cell Contributes to Adult Skeletal Muscle [Tw2 vs Pax7 fresh sort]	Skeletal muscle possesses remarkable regenerative potential due to satellite cells, a stem cell population located beneath the muscle basal lamina. By lineage tracing of progenitor cells expressing the Twist2 (Tw2) transcription factor in mice, we discovered a unique myogenic lineage that resides outside the basal lamina of adult muscle and contributes specifically to type IIb/x myofibers during adulthood and muscle regeneration. Tw2+ progenitors are molecularly and anatomically distinct from satellite cells, are highly myogenic in vitro and can fuse with satellite cells. Transplantation of Tw2+ progenitors into adult mice is sufficient to reconstitute new myofibers, and genetic ablation of endogenous Tw2+ progenitors causes wasting of type IIb myofibers. We show that Tw2 expression maintains progenitor cells in an undifferentiated state that is poised to initiate myogenesis in response to appropriate cues that suppress Tw2 expression. Tw2-expressing progenitors represent a previously unrecognized, fiber-type specific progenitor cell involved in muscle growth and regeneration. Overall design: Gene expression profile was generated by comparing freshly sorted Twist2+ and Pax7+ cells from skeletal muscle		GSM2232846: Twist2-pos-2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted from freshly sorted tdTO+ cells using Trizol Chloroform purification. RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2500	background strain;;C57BL/6|developmental stage;;adult|genotype;;Tw2-CreERT2/+;R26-tdTO+|source_name;;freshly sorted cells from hind limb skeletal muscle|tissue;;Skeletal Muscle	GEO Accession;;GSM2232846		GSM2232846	Twist2-pos-2	2011114600	10055573	2017-01-13 15:46:20	1516773088	2011114600	10055573	2	10055573	index:0,count:10055573,average:100,stdev:0|index:1,count:10055573,average:100,stdev:0	GSM2232846_r1				in_mesa	28218909	1.43	2.73	0.07	1556964649	1559664064	1477736187	1484944207	100.17	100.49	9166761	8200023	225.713	782.127	154	55782	86.72	91.45	9997474	7949853	9997474	7949853	87.61	87.99	9997474	8031036	9997474	7648446	121540714	7.81	0.56	0	4.71	0	0.37	0	0.06	0	0.00	0	8.41	0	9166761	0	200	0	197.45	0	1.64	0	0.01	0	1.54	0	0.01	0	222.09	0	0.55	0	56201	0	10055573	0	473900	0	36986	0	6487	0	0	0	845339	0	1456	0	0	0	21671	0	4723977	0	6755	0	4753859	0	86.45	0	8692861	0	162410	4411537	27.162964103196	10055573.0	9166761.0	56201.0	473900.0	36986.0	6487.0	0.0	845339.0	8692861.0	91.2	0.6	4.7	0.4	0.1	0.0	8.4	86.4	100	100	100.00	38	1005557300	23.8	26.1	25.6	24.5	0.0	33.6	19.8	bulk
1806701	SRR3901916	SRP078457	SRS1562168	SRX1944725	SRA440331	GEO		A Unique Twist-Dependent Progenitor Cell Contributes to Adult Skeletal Muscle [Tw2 vs Pax7 fresh sort]	Skeletal muscle possesses remarkable regenerative potential due to satellite cells, a stem cell population located beneath the muscle basal lamina. By lineage tracing of progenitor cells expressing the Twist2 (Tw2) transcription factor in mice, we discovered a unique myogenic lineage that resides outside the basal lamina of adult muscle and contributes specifically to type IIb/x myofibers during adulthood and muscle regeneration. Tw2+ progenitors are molecularly and anatomically distinct from satellite cells, are highly myogenic in vitro and can fuse with satellite cells. Transplantation of Tw2+ progenitors into adult mice is sufficient to reconstitute new myofibers, and genetic ablation of endogenous Tw2+ progenitors causes wasting of type IIb myofibers. We show that Tw2 expression maintains progenitor cells in an undifferentiated state that is poised to initiate myogenesis in response to appropriate cues that suppress Tw2 expression. Tw2-expressing progenitors represent a previously unrecognized, fiber-type specific progenitor cell involved in muscle growth and regeneration. Overall design: Gene expression profile was generated by comparing freshly sorted Twist2+ and Pax7+ cells from skeletal muscle		GSM2232846: Twist2-pos-2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted from freshly sorted tdTO+ cells using Trizol Chloroform purification. RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2500	background strain;;C57BL/6|developmental stage;;adult|genotype;;Tw2-CreERT2/+;R26-tdTO+|source_name;;freshly sorted cells from hind limb skeletal muscle|tissue;;Skeletal Muscle	GEO Accession;;GSM2232846		GSM2232846	Twist2-pos-2	1963641800	9818209	2017-01-13 15:46:20	1468921496	1963641800	9818209	2	9818209	index:0,count:9818209,average:100,stdev:0|index:1,count:9818209,average:100,stdev:0	GSM2232846_r2				in_mesa	28218909	1.43	2.73	0.07	1524873480	1527490598	1447401314	1454414360	100.17	100.48	8981544	8033729	225.532	785.630	154	54592	86.73	91.45	9794562	7789279	9794562	7789279	87.61	87.99	9794562	7869106	9794562	7494564	119146985	7.81	0.56	0	4.72	0	0.37	0	0.07	0	0.00	0	8.09	0	8981544	0	200	0	197.49	0	1.64	0	0.01	0	1.53	0	0.01	0	304.70	0	0.53	0	55133	0	9818209	0	463709	0	36008	0	6628	0	0	0	794029	0	1295	0	0	0	21347	0	4631212	0	6644	0	4660498	0	86.76	0	8517835	0	161627	4318122	26.716588193804	9818209.0	8981544.0	55133.0	463709.0	36008.0	6628.0	0.0	794029.0	8517835.0	91.5	0.6	4.7	0.4	0.1	0.0	8.1	86.8	100	100	100.00	38	981820900	23.8	26.0	25.6	24.5	0.0	33.8	20.0	bulk
1836906	SRR3902076	SRP078458	SRS1562178	SRX1944748	SRA440332	GEO		A Unique Twist-Dependent Progenitor Cell Contributes to Adult Skeletal Muscle [Tw2 vs Pax7]	Skeletal muscle possesses remarkable regenerative potential due to satellite cells, a stem cell population located beneath the muscle basal lamina. By lineage tracing of progenitor cells expressing the Twist2 (Tw2) transcription factor in mice, we discovered a unique myogenic lineage that resides outside the basal lamina of adult muscle and contributes specifically to type IIb/x myofibers during adulthood and muscle regeneration. Tw2+ progenitors are molecularly and anatomically distinct from satellite cells, are highly myogenic in vitro and can fuse with satellite cells. Transplantation of Tw2+ progenitors into adult mice is sufficient to reconstitute new myofibers, and genetic ablation of endogenous Tw2+ progenitors causes wasting of type IIb myofibers. We show that Tw2 expression maintains progenitor cells in an undifferentiated state that is poised to initiate myogenesis in response to appropriate cues that suppress Tw2 expression. Tw2-expressing progenitors represent a previously unrecognized, fiber-type specific progenitor cell involved in muscle growth and regeneration. Overall design: Gene expression profile was generated by comparing sorted Twist2+ and Pax7+ cells from skeletal muscle after brief culture in growth medium		GSM2232833: Pax7-48-1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted from freshly sorted tdTO+ cells using Trizol Chloroform purification. RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2500	background strain;;C57BL/6|developmental stage;;adult|genotype;;Pax7-CreERT2/+;R26-tdTO+|source_name;;Cultured freshly sorted cells from hind limb skeletal muscle|tissue;;Skeletal Muscle	GEO Accession;;GSM2232833		GSM2232833	Pax7-48-1	1786045400	8930227	2017-01-13 15:46:08	936407450	1786045400	8930227	2	8930227	index:0,count:8930227,average:100,stdev:0|index:1,count:8930227,average:100,stdev:0	GSM2232833_r1						3.13	2.65	0.03	1172890700	1186535650	1076493796	1093303176	101.16	101.56	7296929	6641957	203.366	679.305	134	53469	88.44	96.52	8341960	6453044	8341960	6453044	90.95	91.27	8341960	6636378	8341960	6101917	34390700	2.93	0.95	0	6.85	0	0.56	0	0.03	0	0.00	0	17.70	0	7296929	0	200	0	196.10	0	2.06	0	0.00	0	1.72	0	0.00	0	171.00	0	1.07	0	84734	0	8930227	0	611360	0	50073	0	2303	0	0	0	1580922	0	2772	0	0	0	20635	0	3897439	0	5145	0	3925991	0	74.86	0	6685569	0	132904	3561808	26.799855534822	8930227.0	7296929.0	84734.0	611360.0	50073.0	2303.0	0.0	1580922.0	6685569.0	81.7	0.9	6.8	0.6	0.0	0.0	17.7	74.9	100	100	100.00	7	893022700	22.8	26.3	26.2	24.7	0.0	32.4	20.6	bulk
1836922	SRR3902077	SRP078458	SRS1562178	SRX1944748	SRA440332	GEO		A Unique Twist-Dependent Progenitor Cell Contributes to Adult Skeletal Muscle [Tw2 vs Pax7]	Skeletal muscle possesses remarkable regenerative potential due to satellite cells, a stem cell population located beneath the muscle basal lamina. By lineage tracing of progenitor cells expressing the Twist2 (Tw2) transcription factor in mice, we discovered a unique myogenic lineage that resides outside the basal lamina of adult muscle and contributes specifically to type IIb/x myofibers during adulthood and muscle regeneration. Tw2+ progenitors are molecularly and anatomically distinct from satellite cells, are highly myogenic in vitro and can fuse with satellite cells. Transplantation of Tw2+ progenitors into adult mice is sufficient to reconstitute new myofibers, and genetic ablation of endogenous Tw2+ progenitors causes wasting of type IIb myofibers. We show that Tw2 expression maintains progenitor cells in an undifferentiated state that is poised to initiate myogenesis in response to appropriate cues that suppress Tw2 expression. Tw2-expressing progenitors represent a previously unrecognized, fiber-type specific progenitor cell involved in muscle growth and regeneration. Overall design: Gene expression profile was generated by comparing sorted Twist2+ and Pax7+ cells from skeletal muscle after brief culture in growth medium		GSM2232833: Pax7-48-1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted from freshly sorted tdTO+ cells using Trizol Chloroform purification. RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2500	background strain;;C57BL/6|developmental stage;;adult|genotype;;Pax7-CreERT2/+;R26-tdTO+|source_name;;Cultured freshly sorted cells from hind limb skeletal muscle|tissue;;Skeletal Muscle	GEO Accession;;GSM2232833		GSM2232833	Pax7-48-1	1740282400	8701412	2017-01-13 15:46:08	914681875	1740282400	8701412	2	8701412	index:0,count:8701412,average:100,stdev:0|index:1,count:8701412,average:100,stdev:0	GSM2232833_r2						3.25	2.64	0.03	1088374522	1100777136	997234200	1012684815	101.14	101.55	6796820	6192820	202.399	675.739	143	49707	88.28	96.51	7784078	6000240	7784078	6000240	90.96	91.29	7784078	6182532	7784078	5675570	32206665	2.96	0.88	0	6.66	0	0.53	0	0.02	0	0.00	0	21.33	0	6796820	0	200	0	195.13	0	2.04	0	0.00	0	1.67	0	0.00	0	145.70	0	1.39	0	76338	0	8701412	0	579851	0	46510	0	2021	0	0	0	1856061	0	2377	0	0	0	17942	0	3502718	0	4887	0	3527924	0	71.45	0	6216969	0	129659	3215541	24.799983032416	8701412.0	6796820.0	76338.0	579851.0	46510.0	2021.0	0.0	1856061.0	6216969.0	78.1	0.9	6.7	0.5	0.0	0.0	21.3	71.4	100	100	100.00	7	870141200	22.7	26.4	26.2	24.7	0.0	32.4	20.6	bulk
1836938	SRR3902078	SRP078458	SRS1562179	SRX1944749	SRA440332	GEO		A Unique Twist-Dependent Progenitor Cell Contributes to Adult Skeletal Muscle [Tw2 vs Pax7]	Skeletal muscle possesses remarkable regenerative potential due to satellite cells, a stem cell population located beneath the muscle basal lamina. By lineage tracing of progenitor cells expressing the Twist2 (Tw2) transcription factor in mice, we discovered a unique myogenic lineage that resides outside the basal lamina of adult muscle and contributes specifically to type IIb/x myofibers during adulthood and muscle regeneration. Tw2+ progenitors are molecularly and anatomically distinct from satellite cells, are highly myogenic in vitro and can fuse with satellite cells. Transplantation of Tw2+ progenitors into adult mice is sufficient to reconstitute new myofibers, and genetic ablation of endogenous Tw2+ progenitors causes wasting of type IIb myofibers. We show that Tw2 expression maintains progenitor cells in an undifferentiated state that is poised to initiate myogenesis in response to appropriate cues that suppress Tw2 expression. Tw2-expressing progenitors represent a previously unrecognized, fiber-type specific progenitor cell involved in muscle growth and regeneration. Overall design: Gene expression profile was generated by comparing sorted Twist2+ and Pax7+ cells from skeletal muscle after brief culture in growth medium		GSM2232834: Pax7-48-2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted from freshly sorted tdTO+ cells using Trizol Chloroform purification. RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2500	background strain;;C57BL/6|developmental stage;;adult|genotype;;Pax7-CreERT2/+;R26-tdTO+|source_name;;Cultured freshly sorted cells from hind limb skeletal muscle|tissue;;Skeletal Muscle	GEO Accession;;GSM2232834		GSM2232834	Pax7-48-2	2286794800	11433974	2017-01-13 15:46:08	1193160461	2286794800	11433974	2	11433974	index:0,count:11433974,average:100,stdev:0|index:1,count:11433974,average:100,stdev:0	GSM2232834_r1						3.04	2.66	0.03	1556055541	1572806446	1430773971	1451712309	101.08	101.46	9658909	8733206	206.176	721.030	134	66644	88.42	96.33	10998428	8539942	10998428	8539942	90.77	91.11	10998428	8767155	10998428	8076931	47309453	3.04	0.81	0	6.94	0	0.51	0	0.03	0	0.00	0	14.99	0	9658909	0	200	0	196.27	0	2.14	0	0.00	0	1.76	0	0.00	0	196.01	0	0.98	0	92838	0	11433974	0	794024	0	58507	0	3021	0	0	0	1713537	0	3589	0	0	0	28076	0	5205323	0	7110	0	5244098	0	77.53	0	8864885	0	143383	4746889	33.106358494382	11433974.0	9658909.0	92838.0	794024.0	58507.0	3021.0	0.0	1713537.0	8864885.0	84.5	0.8	6.9	0.5	0.0	0.0	15.0	77.5	100	100	100.00	7	1143397400	22.7	26.5	26.1	24.7	0.0	32.7	20.8	bulk
1836954	SRR3902079	SRP078458	SRS1562179	SRX1944749	SRA440332	GEO		A Unique Twist-Dependent Progenitor Cell Contributes to Adult Skeletal Muscle [Tw2 vs Pax7]	Skeletal muscle possesses remarkable regenerative potential due to satellite cells, a stem cell population located beneath the muscle basal lamina. By lineage tracing of progenitor cells expressing the Twist2 (Tw2) transcription factor in mice, we discovered a unique myogenic lineage that resides outside the basal lamina of adult muscle and contributes specifically to type IIb/x myofibers during adulthood and muscle regeneration. Tw2+ progenitors are molecularly and anatomically distinct from satellite cells, are highly myogenic in vitro and can fuse with satellite cells. Transplantation of Tw2+ progenitors into adult mice is sufficient to reconstitute new myofibers, and genetic ablation of endogenous Tw2+ progenitors causes wasting of type IIb myofibers. We show that Tw2 expression maintains progenitor cells in an undifferentiated state that is poised to initiate myogenesis in response to appropriate cues that suppress Tw2 expression. Tw2-expressing progenitors represent a previously unrecognized, fiber-type specific progenitor cell involved in muscle growth and regeneration. Overall design: Gene expression profile was generated by comparing sorted Twist2+ and Pax7+ cells from skeletal muscle after brief culture in growth medium		GSM2232834: Pax7-48-2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted from freshly sorted tdTO+ cells using Trizol Chloroform purification. RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2500	background strain;;C57BL/6|developmental stage;;adult|genotype;;Pax7-CreERT2/+;R26-tdTO+|source_name;;Cultured freshly sorted cells from hind limb skeletal muscle|tissue;;Skeletal Muscle	GEO Accession;;GSM2232834		GSM2232834	Pax7-48-2	2238566200	11192831	2017-01-13 15:46:08	1172242128	2238566200	11192831	2	11192831	index:0,count:11192831,average:100,stdev:0|index:1,count:11192831,average:100,stdev:0	GSM2232834_r2						3.14	2.67	0.03	1457959406	1473246471	1338281518	1357759708	101.05	101.46	9085803	8224115	205.145	717.715	134	62563	88.26	96.33	10364960	8019011	10364960	8019011	90.79	91.14	10364960	8248816	10364960	7586642	44663682	3.06	0.77	0	6.80	0	0.49	0	0.02	0	0.00	0	18.31	0	9085803	0	200	0	195.33	0	2.13	0	0.00	0	1.76	0	0.00	0	158.02	0	1.30	0	85900	0	11192831	0	761574	0	54916	0	2585	0	0	0	2049527	0	3206	0	0	0	24531	0	4728488	0	6363	0	4762588	0	74.37	0	8324229	0	140260	4330537	30.875067731356	11192831.0	9085803.0	85900.0	761574.0	54916.0	2585.0	0.0	2049527.0	8324229.0	81.2	0.8	6.8	0.5	0.0	0.0	18.3	74.4	100	100	100.00	7	1119283100	22.6	26.5	26.1	24.8	0.0	32.7	20.8	bulk
1837067	SRR3902080	SRP078458	SRS1562180	SRX1944750	SRA440332	GEO		A Unique Twist-Dependent Progenitor Cell Contributes to Adult Skeletal Muscle [Tw2 vs Pax7]	Skeletal muscle possesses remarkable regenerative potential due to satellite cells, a stem cell population located beneath the muscle basal lamina. By lineage tracing of progenitor cells expressing the Twist2 (Tw2) transcription factor in mice, we discovered a unique myogenic lineage that resides outside the basal lamina of adult muscle and contributes specifically to type IIb/x myofibers during adulthood and muscle regeneration. Tw2+ progenitors are molecularly and anatomically distinct from satellite cells, are highly myogenic in vitro and can fuse with satellite cells. Transplantation of Tw2+ progenitors into adult mice is sufficient to reconstitute new myofibers, and genetic ablation of endogenous Tw2+ progenitors causes wasting of type IIb myofibers. We show that Tw2 expression maintains progenitor cells in an undifferentiated state that is poised to initiate myogenesis in response to appropriate cues that suppress Tw2 expression. Tw2-expressing progenitors represent a previously unrecognized, fiber-type specific progenitor cell involved in muscle growth and regeneration. Overall design: Gene expression profile was generated by comparing sorted Twist2+ and Pax7+ cells from skeletal muscle after brief culture in growth medium		GSM2232835: Pax7-GM-1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted from freshly sorted tdTO+ cells using Trizol Chloroform purification. RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2500	background strain;;C57BL/6|developmental stage;;adult|genotype;;Pax7-CreERT2/+;R26-tdTO+|source_name;;Cultured freshly sorted cells from hind limb skeletal muscle|tissue;;Skeletal Muscle	GEO Accession;;GSM2232835		GSM2232835	Pax7-GM-1	1488760000	7443800	2017-01-13 15:46:08	780004535	1488760000	7443800	2	7443800	index:0,count:7443800,average:100,stdev:0|index:1,count:7443800,average:100,stdev:0	GSM2232835_r1						1.73	3.2	0.03	1018950108	1030614950	907630281	921808555	101.14	101.56	6217449	5642590	209.603	691.412	143	44013	86.2	97.02	7420377	5359287	7420377	5359287	91.3	92.01	7420377	5676818	7420377	5082325	26204028	2.57	0.53	0	9.32	0	0.53	0	0.03	0	0.00	0	15.92	0	6217449	0	200	0	196.29	0	2.23	0	0.01	0	1.66	0	0.00	0	175.15	0	1.06	0	39136	0	7443800	0	693525	0	39114	0	2008	0	0	0	1185229	0	2177	0	0	0	20498	0	3123523	0	4504	0	3150702	0	74.21	0	5523924	0	129291	2970096	22.972179037984	7443800.0	6217449.0	39136.0	693525.0	39114.0	2008.0	0.0	1185229.0	5523924.0	83.5	0.5	9.3	0.5	0.0	0.0	15.9	74.2	100	100	100.00	7	744380000	22.8	26.5	26.1	24.6	0.0	32.7	20.8	bulk
1837082	SRR3902081	SRP078458	SRS1562180	SRX1944750	SRA440332	GEO		A Unique Twist-Dependent Progenitor Cell Contributes to Adult Skeletal Muscle [Tw2 vs Pax7]	Skeletal muscle possesses remarkable regenerative potential due to satellite cells, a stem cell population located beneath the muscle basal lamina. By lineage tracing of progenitor cells expressing the Twist2 (Tw2) transcription factor in mice, we discovered a unique myogenic lineage that resides outside the basal lamina of adult muscle and contributes specifically to type IIb/x myofibers during adulthood and muscle regeneration. Tw2+ progenitors are molecularly and anatomically distinct from satellite cells, are highly myogenic in vitro and can fuse with satellite cells. Transplantation of Tw2+ progenitors into adult mice is sufficient to reconstitute new myofibers, and genetic ablation of endogenous Tw2+ progenitors causes wasting of type IIb myofibers. We show that Tw2 expression maintains progenitor cells in an undifferentiated state that is poised to initiate myogenesis in response to appropriate cues that suppress Tw2 expression. Tw2-expressing progenitors represent a previously unrecognized, fiber-type specific progenitor cell involved in muscle growth and regeneration. Overall design: Gene expression profile was generated by comparing sorted Twist2+ and Pax7+ cells from skeletal muscle after brief culture in growth medium		GSM2232835: Pax7-GM-1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted from freshly sorted tdTO+ cells using Trizol Chloroform purification. RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2500	background strain;;C57BL/6|developmental stage;;adult|genotype;;Pax7-CreERT2/+;R26-tdTO+|source_name;;Cultured freshly sorted cells from hind limb skeletal muscle|tissue;;Skeletal Muscle	GEO Accession;;GSM2232835		GSM2232835	Pax7-GM-1	1452484800	7262424	2017-01-13 15:46:08	763228219	1452484800	7262424	2	7262424	index:0,count:7262424,average:100,stdev:0|index:1,count:7262424,average:100,stdev:0	GSM2232835_r2						1.79	3.21	0.04	948884451	959520011	843730463	856849826	101.12	101.55	5813730	5281756	208.737	687.596	145	40934	86.06	97.03	6953552	5003010	6953552	5003010	91.32	92.04	6953552	5308956	6953552	4745612	24504148	2.58	0.51	0	9.05	0	0.50	0	0.02	0	0.00	0	19.42	0	5813730	0	200	0	195.31	0	2.17	0	0.01	0	1.68	0	0.00	0	145.25	0	1.38	0	37032	0	7262424	0	657589	0	36435	0	1656	0	0	0	1410603	0	1900	0	0	0	18005	0	2820291	0	4289	0	2844485	0	71.00	0	5156141	0	126277	2690207	21.304014191024	7262424.0	5813730.0	37032.0	657589.0	36435.0	1656.0	0.0	1410603.0	5156141.0	80.1	0.5	9.1	0.5	0.0	0.0	19.4	71.0	100	100	100.00	7	726242400	22.7	26.6	26.1	24.6	0.0	32.7	20.8	bulk
1837098	SRR3902082	SRP078458	SRS1562181	SRX1944751	SRA440332	GEO		A Unique Twist-Dependent Progenitor Cell Contributes to Adult Skeletal Muscle [Tw2 vs Pax7]	Skeletal muscle possesses remarkable regenerative potential due to satellite cells, a stem cell population located beneath the muscle basal lamina. By lineage tracing of progenitor cells expressing the Twist2 (Tw2) transcription factor in mice, we discovered a unique myogenic lineage that resides outside the basal lamina of adult muscle and contributes specifically to type IIb/x myofibers during adulthood and muscle regeneration. Tw2+ progenitors are molecularly and anatomically distinct from satellite cells, are highly myogenic in vitro and can fuse with satellite cells. Transplantation of Tw2+ progenitors into adult mice is sufficient to reconstitute new myofibers, and genetic ablation of endogenous Tw2+ progenitors causes wasting of type IIb myofibers. We show that Tw2 expression maintains progenitor cells in an undifferentiated state that is poised to initiate myogenesis in response to appropriate cues that suppress Tw2 expression. Tw2-expressing progenitors represent a previously unrecognized, fiber-type specific progenitor cell involved in muscle growth and regeneration. Overall design: Gene expression profile was generated by comparing sorted Twist2+ and Pax7+ cells from skeletal muscle after brief culture in growth medium		GSM2232836: Pax7-GM-2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted from freshly sorted tdTO+ cells using Trizol Chloroform purification. RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2500	background strain;;C57BL/6|developmental stage;;adult|genotype;;Pax7-CreERT2/+;R26-tdTO+|source_name;;Cultured freshly sorted cells from hind limb skeletal muscle|tissue;;Skeletal Muscle	GEO Accession;;GSM2232836		GSM2232836	Pax7-GM-2	892663400	4463317	2017-01-13 15:46:08	465348627	892663400	4463317	2	4463317	index:0,count:4463317,average:100,stdev:0|index:1,count:4463317,average:100,stdev:0	GSM2232836_r1						2.43	3.34	0.04	630014693	634953439	565614388	572607155	100.78	101.24	3847659	3488673	207.804	707.741	145	26997	86.55	96.64	4528263	3330243	4528263	3330243	91.56	92.2	4528263	3522811	4528263	3177269	19085980	3.03	0.71	0	9.00	0	0.48	0	0.04	0	0.00	0	13.28	0	3847659	0	200	0	196.69	0	1.87	0	0.00	0	1.55	0	0.00	0	203.39	0	0.94	0	31472	0	4463317	0	401726	0	21481	0	1591	0	0	0	592586	0	1315	0	0	0	12455	0	1918580	0	2860	0	1935210	0	77.21	0	3445933	0	122246	1807786	14.788099406116	4463317.0	3847659.0	31472.0	401726.0	21481.0	1591.0	0.0	592586.0	3445933.0	86.2	0.7	9.0	0.5	0.0	0.0	13.3	77.2	100	100	100.00	7	446331700	23.3	26.0	25.7	25.1	0.0	32.9	21.0	bulk
1837113	SRR3902083	SRP078458	SRS1562181	SRX1944751	SRA440332	GEO		A Unique Twist-Dependent Progenitor Cell Contributes to Adult Skeletal Muscle [Tw2 vs Pax7]	Skeletal muscle possesses remarkable regenerative potential due to satellite cells, a stem cell population located beneath the muscle basal lamina. By lineage tracing of progenitor cells expressing the Twist2 (Tw2) transcription factor in mice, we discovered a unique myogenic lineage that resides outside the basal lamina of adult muscle and contributes specifically to type IIb/x myofibers during adulthood and muscle regeneration. Tw2+ progenitors are molecularly and anatomically distinct from satellite cells, are highly myogenic in vitro and can fuse with satellite cells. Transplantation of Tw2+ progenitors into adult mice is sufficient to reconstitute new myofibers, and genetic ablation of endogenous Tw2+ progenitors causes wasting of type IIb myofibers. We show that Tw2 expression maintains progenitor cells in an undifferentiated state that is poised to initiate myogenesis in response to appropriate cues that suppress Tw2 expression. Tw2-expressing progenitors represent a previously unrecognized, fiber-type specific progenitor cell involved in muscle growth and regeneration. Overall design: Gene expression profile was generated by comparing sorted Twist2+ and Pax7+ cells from skeletal muscle after brief culture in growth medium		GSM2232836: Pax7-GM-2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted from freshly sorted tdTO+ cells using Trizol Chloroform purification. RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2500	background strain;;C57BL/6|developmental stage;;adult|genotype;;Pax7-CreERT2/+;R26-tdTO+|source_name;;Cultured freshly sorted cells from hind limb skeletal muscle|tissue;;Skeletal Muscle	GEO Accession;;GSM2232836		GSM2232836	Pax7-GM-2	868279400	4341397	2017-01-13 15:46:08	454442671	868279400	4341397	2	4341397	index:0,count:4341397,average:100,stdev:0|index:1,count:4341397,average:100,stdev:0	GSM2232836_r2						2.5	3.35	0.04	592556369	597010852	531203257	537693638	100.75	101.22	3633097	3297291	206.910	705.478	143	25580	86.41	96.63	4283145	3139373	4283145	3139373	91.6	92.24	4283145	3327970	4283145	2996662	18107933	3.06	0.67	0	8.85	0	0.46	0	0.03	0	0.00	0	15.82	0	3633097	0	200	0	195.78	0	1.87	0	0.00	0	1.58	0	0.00	0	139.54	0	1.26	0	29203	0	4341397	0	384166	0	20026	0	1378	0	0	0	686896	0	1154	0	0	0	11173	0	1749870	0	2686	0	1764883	0	74.84	0	3248931	0	119509	1653028	13.831828565213	4341397.0	3633097.0	29203.0	384166.0	20026.0	1378.0	0.0	686896.0	3248931.0	83.7	0.7	8.8	0.5	0.0	0.0	15.8	74.8	100	100	100.00	7	434139700	23.2	26.0	25.6	25.1	0.0	33.0	21.0	bulk
1837129	SRR3902084	SRP078458	SRS1562182	SRX1944752	SRA440332	GEO		A Unique Twist-Dependent Progenitor Cell Contributes to Adult Skeletal Muscle [Tw2 vs Pax7]	Skeletal muscle possesses remarkable regenerative potential due to satellite cells, a stem cell population located beneath the muscle basal lamina. By lineage tracing of progenitor cells expressing the Twist2 (Tw2) transcription factor in mice, we discovered a unique myogenic lineage that resides outside the basal lamina of adult muscle and contributes specifically to type IIb/x myofibers during adulthood and muscle regeneration. Tw2+ progenitors are molecularly and anatomically distinct from satellite cells, are highly myogenic in vitro and can fuse with satellite cells. Transplantation of Tw2+ progenitors into adult mice is sufficient to reconstitute new myofibers, and genetic ablation of endogenous Tw2+ progenitors causes wasting of type IIb myofibers. We show that Tw2 expression maintains progenitor cells in an undifferentiated state that is poised to initiate myogenesis in response to appropriate cues that suppress Tw2 expression. Tw2-expressing progenitors represent a previously unrecognized, fiber-type specific progenitor cell involved in muscle growth and regeneration. Overall design: Gene expression profile was generated by comparing sorted Twist2+ and Pax7+ cells from skeletal muscle after brief culture in growth medium		GSM2232837: Tw2-48hr-1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted from freshly sorted tdTO+ cells using Trizol Chloroform purification. RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2500	background strain;;C57BL/6|developmental stage;;adult|genotype;;Tw2-CreERT2/+;R26-tdTO+|source_name;;Cultured freshly sorted cells from hind limb skeletal muscle|tissue;;Skeletal Muscle	GEO Accession;;GSM2232837		GSM2232837	Tw2-48hr-1	2100561000	10502805	2017-01-13 15:46:08	1094361733	2100561000	10502805	2	10502805	index:0,count:10502805,average:100,stdev:0|index:1,count:10502805,average:100,stdev:0	GSM2232837_r1						3.82	2.82	0.03	1502223802	1510086055	1388214489	1402721851	100.52	101.05	9028907	8105649	216.778	790.409	145	58525	87.83	95.2	10169692	7930540	10169692	7930540	90.02	90.42	10169692	8127865	10169692	7531948	60911806	4.05	0.60	0	6.65	0	0.42	0	0.22	0	0.00	0	13.40	0	9028907	0	200	0	196.60	0	2.05	0	0.00	0	1.62	0	0.00	0	174.24	0	0.95	0	62583	0	10502805	0	698549	0	43621	0	22990	0	0	0	1407287	0	2955	0	0	0	25958	0	4618983	0	6792	0	4654688	0	79.32	0	8330358	0	141125	4316156	30.583922054916	10502805.0	9028907.0	62583.0	698549.0	43621.0	22990.0	0.0	1407287.0	8330358.0	86.0	0.6	6.7	0.4	0.2	0.0	13.4	79.3	100	100	100.00	7	1050280500	23.4	25.9	25.3	25.4	0.0	32.9	20.9	bulk
1837145	SRR3902085	SRP078458	SRS1562182	SRX1944752	SRA440332	GEO		A Unique Twist-Dependent Progenitor Cell Contributes to Adult Skeletal Muscle [Tw2 vs Pax7]	Skeletal muscle possesses remarkable regenerative potential due to satellite cells, a stem cell population located beneath the muscle basal lamina. By lineage tracing of progenitor cells expressing the Twist2 (Tw2) transcription factor in mice, we discovered a unique myogenic lineage that resides outside the basal lamina of adult muscle and contributes specifically to type IIb/x myofibers during adulthood and muscle regeneration. Tw2+ progenitors are molecularly and anatomically distinct from satellite cells, are highly myogenic in vitro and can fuse with satellite cells. Transplantation of Tw2+ progenitors into adult mice is sufficient to reconstitute new myofibers, and genetic ablation of endogenous Tw2+ progenitors causes wasting of type IIb myofibers. We show that Tw2 expression maintains progenitor cells in an undifferentiated state that is poised to initiate myogenesis in response to appropriate cues that suppress Tw2 expression. Tw2-expressing progenitors represent a previously unrecognized, fiber-type specific progenitor cell involved in muscle growth and regeneration. Overall design: Gene expression profile was generated by comparing sorted Twist2+ and Pax7+ cells from skeletal muscle after brief culture in growth medium		GSM2232837: Tw2-48hr-1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted from freshly sorted tdTO+ cells using Trizol Chloroform purification. RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2500	background strain;;C57BL/6|developmental stage;;adult|genotype;;Tw2-CreERT2/+;R26-tdTO+|source_name;;Cultured freshly sorted cells from hind limb skeletal muscle|tissue;;Skeletal Muscle	GEO Accession;;GSM2232837		GSM2232837	Tw2-48hr-1	2053711600	10268558	2017-01-13 15:46:08	1073774120	2053711600	10268558	2	10268558	index:0,count:10268558,average:100,stdev:0|index:1,count:10268558,average:100,stdev:0	GSM2232837_r2						3.94	2.84	0.03	1414326973	1421004759	1304809347	1317973525	100.47	101.01	8531777	7664890	216.018	786.217	143	55117	87.64	95.15	9627604	7477402	9627604	7477402	89.99	90.39	9627604	7677887	9627604	7103553	58006583	4.10	0.58	0	6.55	0	0.40	0	0.18	0	0.00	0	16.34	0	8531777	0	200	0	195.68	0	2.04	0	0.00	0	1.63	0	0.00	0	160.03	0	1.27	0	59108	0	10268558	0	673076	0	41021	0	17976	0	0	0	1677784	0	2610	0	0	0	22727	0	4210572	0	6442	0	4242351	0	76.53	0	7858701	0	138568	3948712	28.496564863461	10268558.0	8531777.0	59108.0	673076.0	41021.0	17976.0	0.0	1677784.0	7858701.0	83.1	0.6	6.6	0.4	0.2	0.0	16.3	76.5	100	100	100.00	7	1026855800	23.4	25.9	25.2	25.5	0.0	32.9	20.9	bulk
1837160	SRR3902086	SRP078458	SRS1562183	SRX1944753	SRA440332	GEO		A Unique Twist-Dependent Progenitor Cell Contributes to Adult Skeletal Muscle [Tw2 vs Pax7]	Skeletal muscle possesses remarkable regenerative potential due to satellite cells, a stem cell population located beneath the muscle basal lamina. By lineage tracing of progenitor cells expressing the Twist2 (Tw2) transcription factor in mice, we discovered a unique myogenic lineage that resides outside the basal lamina of adult muscle and contributes specifically to type IIb/x myofibers during adulthood and muscle regeneration. Tw2+ progenitors are molecularly and anatomically distinct from satellite cells, are highly myogenic in vitro and can fuse with satellite cells. Transplantation of Tw2+ progenitors into adult mice is sufficient to reconstitute new myofibers, and genetic ablation of endogenous Tw2+ progenitors causes wasting of type IIb myofibers. We show that Tw2 expression maintains progenitor cells in an undifferentiated state that is poised to initiate myogenesis in response to appropriate cues that suppress Tw2 expression. Tw2-expressing progenitors represent a previously unrecognized, fiber-type specific progenitor cell involved in muscle growth and regeneration. Overall design: Gene expression profile was generated by comparing sorted Twist2+ and Pax7+ cells from skeletal muscle after brief culture in growth medium		GSM2232838: Tw2-48hr-2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted from freshly sorted tdTO+ cells using Trizol Chloroform purification. RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2500	background strain;;C57BL/6|developmental stage;;adult|genotype;;Tw2-CreERT2/+;R26-tdTO+|source_name;;Cultured freshly sorted cells from hind limb skeletal muscle|tissue;;Skeletal Muscle	GEO Accession;;GSM2232838		GSM2232838	Tw2-48hr-2	3531466400	17657332	2017-01-13 15:46:08	1845400293	3531466400	17657332	2	17657332	index:0,count:17657332,average:100,stdev:0|index:1,count:17657332,average:100,stdev:0	GSM2232838_r1						3.81	2.88	0.03	2377108387	2387408909	2200736559	2221607946	100.43	100.95	14513615	13196445	207.056	711.358	148	103767	87.93	95.11	16306262	12762047	16306262	12762047	90.11	90.5	16306262	13078111	16306262	12143136	99972245	4.21	0.64	0	6.21	0	0.41	0	0.22	0	0.00	0	17.18	0	14513615	0	200	0	196.28	0	1.85	0	0.00	0	1.53	0	0.00	0	148.52	0	1.08	0	112996	0	17657332	0	1096112	0	71706	0	38587	0	0	0	3033424	0	4480	0	0	0	40610	0	7241106	0	11283	0	7297479	0	75.99	0	13417503	0	155627	6709019	43.109608229934	17657332.0	14513615.0	112996.0	1096112.0	71706.0	38587.0	0.0	3033424.0	13417503.0	82.2	0.6	6.2	0.4	0.2	0.0	17.2	76.0	100	100	100.00	7	1765733200	23.6	25.7	25.2	25.5	0.0	32.7	20.7	bulk
1837178	SRR3902087	SRP078458	SRS1562183	SRX1944753	SRA440332	GEO		A Unique Twist-Dependent Progenitor Cell Contributes to Adult Skeletal Muscle [Tw2 vs Pax7]	Skeletal muscle possesses remarkable regenerative potential due to satellite cells, a stem cell population located beneath the muscle basal lamina. By lineage tracing of progenitor cells expressing the Twist2 (Tw2) transcription factor in mice, we discovered a unique myogenic lineage that resides outside the basal lamina of adult muscle and contributes specifically to type IIb/x myofibers during adulthood and muscle regeneration. Tw2+ progenitors are molecularly and anatomically distinct from satellite cells, are highly myogenic in vitro and can fuse with satellite cells. Transplantation of Tw2+ progenitors into adult mice is sufficient to reconstitute new myofibers, and genetic ablation of endogenous Tw2+ progenitors causes wasting of type IIb myofibers. We show that Tw2 expression maintains progenitor cells in an undifferentiated state that is poised to initiate myogenesis in response to appropriate cues that suppress Tw2 expression. Tw2-expressing progenitors represent a previously unrecognized, fiber-type specific progenitor cell involved in muscle growth and regeneration. Overall design: Gene expression profile was generated by comparing sorted Twist2+ and Pax7+ cells from skeletal muscle after brief culture in growth medium		GSM2232838: Tw2-48hr-2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted from freshly sorted tdTO+ cells using Trizol Chloroform purification. RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2500	background strain;;C57BL/6|developmental stage;;adult|genotype;;Tw2-CreERT2/+;R26-tdTO+|source_name;;Cultured freshly sorted cells from hind limb skeletal muscle|tissue;;Skeletal Muscle	GEO Accession;;GSM2232838		GSM2232838	Tw2-48hr-2	3462639000	17313195	2017-01-13 15:46:08	1813696470	3462639000	17313195	2	17313195	index:0,count:17313195,average:100,stdev:0|index:1,count:17313195,average:100,stdev:0	GSM2232838_r2						3.94	2.89	0.03	2216493718	2224237126	2048777338	2066911286	100.35	100.89	13590732	12371071	206.112	712.034	143	96783	87.72	95.05	15291828	11922313	15291828	11922313	90.07	90.48	15291828	12240853	15291828	11349015	94191677	4.25	0.61	0	6.05	0	0.38	0	0.17	0	0.00	0	20.95	0	13590732	0	200	0	195.29	0	1.83	0	0.00	0	1.52	0	0.00	0	130.94	0	1.40	0	105241	0	17313195	0	1047037	0	66570	0	29026	0	0	0	3626867	0	3937	0	0	0	35454	0	6521992	0	10249	0	6571632	0	72.45	0	12543695	0	152540	6053511	39.684744984922	17313195.0	13590732.0	105241.0	1047037.0	66570.0	29026.0	0.0	3626867.0	12543695.0	78.5	0.6	6.0	0.4	0.2	0.0	20.9	72.5	100	100	100.00	7	1731319500	23.5	25.7	25.1	25.6	0.0	32.7	20.7	bulk
1837193	SRR3902088	SRP078458	SRS1562184	SRX1944754	SRA440332	GEO		A Unique Twist-Dependent Progenitor Cell Contributes to Adult Skeletal Muscle [Tw2 vs Pax7]	Skeletal muscle possesses remarkable regenerative potential due to satellite cells, a stem cell population located beneath the muscle basal lamina. By lineage tracing of progenitor cells expressing the Twist2 (Tw2) transcription factor in mice, we discovered a unique myogenic lineage that resides outside the basal lamina of adult muscle and contributes specifically to type IIb/x myofibers during adulthood and muscle regeneration. Tw2+ progenitors are molecularly and anatomically distinct from satellite cells, are highly myogenic in vitro and can fuse with satellite cells. Transplantation of Tw2+ progenitors into adult mice is sufficient to reconstitute new myofibers, and genetic ablation of endogenous Tw2+ progenitors causes wasting of type IIb myofibers. We show that Tw2 expression maintains progenitor cells in an undifferentiated state that is poised to initiate myogenesis in response to appropriate cues that suppress Tw2 expression. Tw2-expressing progenitors represent a previously unrecognized, fiber-type specific progenitor cell involved in muscle growth and regeneration. Overall design: Gene expression profile was generated by comparing sorted Twist2+ and Pax7+ cells from skeletal muscle after brief culture in growth medium		GSM2232839: Tw2-GM-1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted from freshly sorted tdTO+ cells using Trizol Chloroform purification. RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2500	background strain;;C57BL/6|developmental stage;;adult|genotype;;Tw2-CreERT2/+;R26-tdTO+|source_name;;Cultured freshly sorted cells from hind limb skeletal muscle|tissue;;Skeletal Muscle	GEO Accession;;GSM2232839		GSM2232839	Tw2-GM-1	2626670000	13133350	2017-01-13 15:46:08	1369319152	2626670000	13133350	2	13133350	index:0,count:13133350,average:100,stdev:0|index:1,count:13133350,average:100,stdev:0	GSM2232839_r1						2.97	3.64	0.06	1851538192	1856639310	1684748928	1698962717	100.28	100.84	11145445	10081814	209.954	757.116	144	76130	86.06	94.77	12871265	9591876	12871265	9591876	90.26	90.89	12871265	10059961	12871265	9199402	90506971	4.89	0.74	0	7.80	0	0.38	0	0.12	0	0.00	0	14.63	0	11145445	0	200	0	196.72	0	1.71	0	0.00	0	1.40	0	0.00	0	163.03	0	0.98	0	97498	0	13133350	0	1023769	0	50250	0	16222	0	0	0	1921433	0	3372	0	0	0	34057	0	5169861	0	8478	0	5215768	0	77.07	0	10121676	0	151023	4901682	32.456526489343	13133350.0	11145445.0	97498.0	1023769.0	50250.0	16222.0	0.0	1921433.0	10121676.0	84.9	0.7	7.8	0.4	0.1	0.0	14.6	77.1	100	100	100.00	7	1313335000	24.3	25.2	24.6	25.9	0.0	32.9	20.9	bulk
1837209	SRR3902089	SRP078458	SRS1562184	SRX1944754	SRA440332	GEO		A Unique Twist-Dependent Progenitor Cell Contributes to Adult Skeletal Muscle [Tw2 vs Pax7]	Skeletal muscle possesses remarkable regenerative potential due to satellite cells, a stem cell population located beneath the muscle basal lamina. By lineage tracing of progenitor cells expressing the Twist2 (Tw2) transcription factor in mice, we discovered a unique myogenic lineage that resides outside the basal lamina of adult muscle and contributes specifically to type IIb/x myofibers during adulthood and muscle regeneration. Tw2+ progenitors are molecularly and anatomically distinct from satellite cells, are highly myogenic in vitro and can fuse with satellite cells. Transplantation of Tw2+ progenitors into adult mice is sufficient to reconstitute new myofibers, and genetic ablation of endogenous Tw2+ progenitors causes wasting of type IIb myofibers. We show that Tw2 expression maintains progenitor cells in an undifferentiated state that is poised to initiate myogenesis in response to appropriate cues that suppress Tw2 expression. Tw2-expressing progenitors represent a previously unrecognized, fiber-type specific progenitor cell involved in muscle growth and regeneration. Overall design: Gene expression profile was generated by comparing sorted Twist2+ and Pax7+ cells from skeletal muscle after brief culture in growth medium		GSM2232839: Tw2-GM-1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted from freshly sorted tdTO+ cells using Trizol Chloroform purification. RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2500	background strain;;C57BL/6|developmental stage;;adult|genotype;;Tw2-CreERT2/+;R26-tdTO+|source_name;;Cultured freshly sorted cells from hind limb skeletal muscle|tissue;;Skeletal Muscle	GEO Accession;;GSM2232839		GSM2232839	Tw2-GM-1	2569017000	12845085	2017-01-13 15:46:08	1343664168	2569017000	12845085	2	12845085	index:0,count:12845085,average:100,stdev:0|index:1,count:12845085,average:100,stdev:0	GSM2232839_r2						3.07	3.64	0.06	1739638121	1743208767	1580283052	1592768343	100.21	100.79	10513988	9520066	209.157	754.986	143	71230	85.87	94.71	12161946	9028041	12161946	9028041	90.23	90.87	12161946	9486647	12161946	8662020	85767063	4.93	0.71	0	7.64	0	0.37	0	0.10	0	0.00	0	17.68	0	10513988	0	200	0	195.78	0	1.72	0	0.00	0	1.39	0	0.00	0	151.12	0	1.30	0	90871	0	12845085	0	981984	0	47381	0	12839	0	0	0	2270877	0	2940	0	0	0	29948	0	4701364	0	8077	0	4742329	0	74.21	0	9532004	0	148306	4467851	30.125895108762	12845085.0	10513988.0	90871.0	981984.0	47381.0	12839.0	0.0	2270877.0	9532004.0	81.9	0.7	7.6	0.4	0.1	0.0	17.7	74.2	100	100	100.00	7	1284508500	24.2	25.3	24.6	25.9	0.0	32.9	20.9	bulk
1837322	SRR3902090	SRP078458	SRS1562185	SRX1944755	SRA440332	GEO		A Unique Twist-Dependent Progenitor Cell Contributes to Adult Skeletal Muscle [Tw2 vs Pax7]	Skeletal muscle possesses remarkable regenerative potential due to satellite cells, a stem cell population located beneath the muscle basal lamina. By lineage tracing of progenitor cells expressing the Twist2 (Tw2) transcription factor in mice, we discovered a unique myogenic lineage that resides outside the basal lamina of adult muscle and contributes specifically to type IIb/x myofibers during adulthood and muscle regeneration. Tw2+ progenitors are molecularly and anatomically distinct from satellite cells, are highly myogenic in vitro and can fuse with satellite cells. Transplantation of Tw2+ progenitors into adult mice is sufficient to reconstitute new myofibers, and genetic ablation of endogenous Tw2+ progenitors causes wasting of type IIb myofibers. We show that Tw2 expression maintains progenitor cells in an undifferentiated state that is poised to initiate myogenesis in response to appropriate cues that suppress Tw2 expression. Tw2-expressing progenitors represent a previously unrecognized, fiber-type specific progenitor cell involved in muscle growth and regeneration. Overall design: Gene expression profile was generated by comparing sorted Twist2+ and Pax7+ cells from skeletal muscle after brief culture in growth medium		GSM2232840: Tw2-GM-2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted from freshly sorted tdTO+ cells using Trizol Chloroform purification. RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2500	background strain;;C57BL/6|developmental stage;;adult|genotype;;Tw2-CreERT2/+;R26-tdTO+|source_name;;Cultured freshly sorted cells from hind limb skeletal muscle|tissue;;Skeletal Muscle	GEO Accession;;GSM2232840		GSM2232840	Tw2-GM-2	2393451600	11967258	2017-01-13 15:46:08	1247689427	2393451600	11967258	2	11967258	index:0,count:11967258,average:100,stdev:0|index:1,count:11967258,average:100,stdev:0	GSM2232840_r1						2.82	3.58	0.05	1683492446	1690666451	1523487234	1538656675	100.43	101.0	10225215	9242540	208.528	755.445	143	70055	86.74	96.07	11914529	8869833	11914529	8869833	91.17	91.97	11914529	9322181	11914529	8491152	59852641	3.56	0.70	0	8.29	0	0.42	0	0.13	0	0.00	0	14.01	0	10225215	0	200	0	196.64	0	1.78	0	0.00	0	1.44	0	0.00	0	157.81	0	0.98	0	84300	0	11967258	0	992510	0	50158	0	15481	0	0	0	1676404	0	3180	0	0	0	31625	0	4822691	0	7877	0	4865373	0	77.15	0	9232705	0	145627	4545461	31.213037417512	11967258.0	10225215.0	84300.0	992510.0	50158.0	15481.0	0.0	1676404.0	9232705.0	85.4	0.7	8.3	0.4	0.1	0.0	14.0	77.1	100	100	100.00	7	1196725800	24.1	25.4	24.8	25.8	0.0	32.9	20.9	bulk
1837338	SRR3902091	SRP078458	SRS1562185	SRX1944755	SRA440332	GEO		A Unique Twist-Dependent Progenitor Cell Contributes to Adult Skeletal Muscle [Tw2 vs Pax7]	Skeletal muscle possesses remarkable regenerative potential due to satellite cells, a stem cell population located beneath the muscle basal lamina. By lineage tracing of progenitor cells expressing the Twist2 (Tw2) transcription factor in mice, we discovered a unique myogenic lineage that resides outside the basal lamina of adult muscle and contributes specifically to type IIb/x myofibers during adulthood and muscle regeneration. Tw2+ progenitors are molecularly and anatomically distinct from satellite cells, are highly myogenic in vitro and can fuse with satellite cells. Transplantation of Tw2+ progenitors into adult mice is sufficient to reconstitute new myofibers, and genetic ablation of endogenous Tw2+ progenitors causes wasting of type IIb myofibers. We show that Tw2 expression maintains progenitor cells in an undifferentiated state that is poised to initiate myogenesis in response to appropriate cues that suppress Tw2 expression. Tw2-expressing progenitors represent a previously unrecognized, fiber-type specific progenitor cell involved in muscle growth and regeneration. Overall design: Gene expression profile was generated by comparing sorted Twist2+ and Pax7+ cells from skeletal muscle after brief culture in growth medium		GSM2232840: Tw2-GM-2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA was extracted from freshly sorted tdTO+ cells using Trizol Chloroform purification. RNA libraries were prepared for sequencing using standard Illumina protocols	Illumina HiSeq 2500	background strain;;C57BL/6|developmental stage;;adult|genotype;;Tw2-CreERT2/+;R26-tdTO+|source_name;;Cultured freshly sorted cells from hind limb skeletal muscle|tissue;;Skeletal Muscle	GEO Accession;;GSM2232840		GSM2232840	Tw2-GM-2	2350120800	11750604	2017-01-13 15:46:08	1229357721	2350120800	11750604	2	11750604	index:0,count:11750604,average:100,stdev:0|index:1,count:11750604,average:100,stdev:0	GSM2232840_r2						2.91	3.59	0.05	1583712083	1589689774	1431329302	1445181582	100.38	100.97	9656206	8736067	207.731	757.532	145	65838	86.59	96.03	11265145	8361302	11265145	8361302	91.13	91.95	11265145	8800109	11265145	8006276	56875066	3.59	0.66	0	8.08	0	0.40	0	0.10	0	0.00	0	17.32	0	9656206	0	200	0	195.71	0	1.77	0	0.00	0	1.43	0	0.00	0	145.37	0	1.30	0	78023	0	11750604	0	948863	0	47157	0	12046	0	0	0	2035195	0	2781	0	0	0	28350	0	4392911	0	7405	0	4431447	0	74.10	0	8707343	0	143161	4155038	29.023532945425	11750604.0	9656206.0	78023.0	948863.0	47157.0	12046.0	0.0	2035195.0	8707343.0	82.2	0.7	8.1	0.4	0.1	0.0	17.3	74.1	100	100	100.00	7	1175060400	24.0	25.4	24.7	25.8	0.0	32.9	20.9	bulk
432719	SRR3954693	SRP079936	SRS1586475	SRX1978955	SRA444699	GEO		Next Generation Sequencing Comparison of Wild Type and Whsc1-/- Activated B-cell Transcriptomes	Whsc1 gene codes for a SET domain-containing H3K36 dimethylase, whose activity has been suggested, in ex vivo cell culture experiments, to control many aspects of DNA and RNA processing (replication, repair, transcription, etc). Its precise function in vivo is still unclear. Here, we use RNA-seq transcriptome analysis to study the changes in gene expression in the absence of Whsc1. Our results show that, in the experimental system used, loss of Whsc1 caused massive changes in genes affecting many fundamental cellular processes, from cell cycle to ribosome synthesis, DNA repair, replication, etc. Overall design: Whsc1-KO mice are embryonic lethal. We therefore took hematopoietic cells from fetal liver of WT and Whsc1-KO embryo littermates and injected them in to lethally irradiated RAG1-KO recipients and allowed the generation of a full Whsc1-KO hematopoietic system. Then, WT and Whsc1-KO B cells were obtained from the spleen and stimulated with LPS to induce proliferation and class switch recombination. Flow cytometry and cell cycle analyses (among others) showed the existence of serious proliferative alterations in Whsc1-KO cells. Then, we performed paired-end RNAseq analyses of 7 independent WT and 6 independent Whsc1-KO biological replicates and we used these data to identify differentially expressed genes and pathways regulated by Whsc1 in B cells.		GSM2252998: WT_rep1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			RNA was extracted following commercial Trizol® Reagent [Cat No 15596-026, Life TecnologiesTM, GibcoBRL] recommendations. It chemical quality was measure by Nanodrop 1000 Spectrophotometer [Thermo ScientificTM] and it integrity was confirmed using the Agilent 2100 Bioanalyzer. The libraries from the mouse total RNA were prepared using the TruSeq®Stranded mRNA LT Sample Prep Kit (Illumina Inc., Rev.E, October 2013) according to manufacturer’s protocol. Briefly, 0.5 µg of total RNA was used for poly-A based mRNA enrichment with oligo-dT magnetic beads. The mRNA was fragmented (resulting RNA fragment size was 80-250nt, with the major peak at 130nt. The second strand cDNA synthesis was performed in the presence of dUTP instead of dTTP, this allowed to achieve the strand specificity. The blunt-ended double stranded cDNA was 3´adenylated and Illumina indexed adapters were ligated. The ligation product was enriched with 15 PCR cycles and the final library was validated on an Agilent 2100 Bioanalyzer with the DNA 7500 assay. The libraries were sequenced on HiSeq2000 (Illumina, Inc) in paired-end mode with a read length of 2x76bp using TruSeq SBS Kit v3-HS. We generated about 50-70 million paired-end reads for each sample in a fraction of a sequencing flowcell lane, following the manufacturer’s protocol. Image analysis, base calling and quality scoring of the run were processed using the manufacturer’s software Real Time Analysis (RTA 1.13.48) and followed by generation of FASTQ sequence files by CASAVA.	Illumina HiSeq 2000	genotipe;;WT|source_name;;LPS-stimulated splenic B cells|strain;;C57BL/6	GEO Accession;;GSM2252998		GSM2252998	WT_rep1	5057395018	25036609	2017-05-23 16:50:08	3325635502	5057395018	25036609	2	25036609	index:0,count:25036609,average:101,stdev:0|index:1,count:25036609,average:101,stdev:0	GSM2252998_r2				in_mesa	28538178	2.8	3.5	0.24	3811855750	3763801210	3447833774	3426503916	98.74	99.38	24026649	22499141	186.683	794.124	136	201175	77.21	85.61	28383983	18551547	28383983	18551547	81.93	82.29	28383983	19683868	28383983	17831424	513241421	13.46	1.09	0	9.41	0	0.59	0	0.17	0	0.00	0	3.27	0	24026649	0	202	0	200.34	0	1.50	0	0.01	0	1.23	0	0.01	0	233.50	0	0.16	0	272675	0	25036609	0	2357068	0	148486	0	43346	0	0	0	818128	0	6754	0	0	0	83025	0	10153197	0	32853	0	10275829	0	86.55	0	21669581	0	178077	9120376	51.215912217749	25036609.0	24026649.0	272675.0	2357068.0	148486.0	43346.0	0.0	818128.0	21669581.0	96.0	1.1	9.4	0.6	0.2	0.0	3.3	86.6	101	101	101.00	38	2528697509	24.4	24.6	24.3	26.7	0.0	36.4	26.9	bulk
432723	SRR3954694	SRP079936	SRS1586476	SRX1978956	SRA444699	GEO		Next Generation Sequencing Comparison of Wild Type and Whsc1-/- Activated B-cell Transcriptomes	Whsc1 gene codes for a SET domain-containing H3K36 dimethylase, whose activity has been suggested, in ex vivo cell culture experiments, to control many aspects of DNA and RNA processing (replication, repair, transcription, etc). Its precise function in vivo is still unclear. Here, we use RNA-seq transcriptome analysis to study the changes in gene expression in the absence of Whsc1. Our results show that, in the experimental system used, loss of Whsc1 caused massive changes in genes affecting many fundamental cellular processes, from cell cycle to ribosome synthesis, DNA repair, replication, etc. Overall design: Whsc1-KO mice are embryonic lethal. We therefore took hematopoietic cells from fetal liver of WT and Whsc1-KO embryo littermates and injected them in to lethally irradiated RAG1-KO recipients and allowed the generation of a full Whsc1-KO hematopoietic system. Then, WT and Whsc1-KO B cells were obtained from the spleen and stimulated with LPS to induce proliferation and class switch recombination. Flow cytometry and cell cycle analyses (among others) showed the existence of serious proliferative alterations in Whsc1-KO cells. Then, we performed paired-end RNAseq analyses of 7 independent WT and 6 independent Whsc1-KO biological replicates and we used these data to identify differentially expressed genes and pathways regulated by Whsc1 in B cells.		GSM2252999: WT_rep2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			RNA was extracted following commercial Trizol® Reagent [Cat No 15596-026, Life TecnologiesTM, GibcoBRL] recommendations. It chemical quality was measure by Nanodrop 1000 Spectrophotometer [Thermo ScientificTM] and it integrity was confirmed using the Agilent 2100 Bioanalyzer. The libraries from the mouse total RNA were prepared using the TruSeq®Stranded mRNA LT Sample Prep Kit (Illumina Inc., Rev.E, October 2013) according to manufacturer’s protocol. Briefly, 0.5 µg of total RNA was used for poly-A based mRNA enrichment with oligo-dT magnetic beads. The mRNA was fragmented (resulting RNA fragment size was 80-250nt, with the major peak at 130nt. The second strand cDNA synthesis was performed in the presence of dUTP instead of dTTP, this allowed to achieve the strand specificity. The blunt-ended double stranded cDNA was 3´adenylated and Illumina indexed adapters were ligated. The ligation product was enriched with 15 PCR cycles and the final library was validated on an Agilent 2100 Bioanalyzer with the DNA 7500 assay. The libraries were sequenced on HiSeq2000 (Illumina, Inc) in paired-end mode with a read length of 2x76bp using TruSeq SBS Kit v3-HS. We generated about 50-70 million paired-end reads for each sample in a fraction of a sequencing flowcell lane, following the manufacturer’s protocol. Image analysis, base calling and quality scoring of the run were processed using the manufacturer’s software Real Time Analysis (RTA 1.13.48) and followed by generation of FASTQ sequence files by CASAVA.	Illumina HiSeq 2000	genotipe;;WT|source_name;;LPS-stimulated splenic B cells|strain;;C57BL/6	GEO Accession;;GSM2252999		GSM2252999	WT_rep2	3593471324	17789462	2017-05-23 16:50:08	2404648885	3593471324	17789462	2	17789462	index:0,count:17789462,average:101,stdev:0|index:1,count:17789462,average:101,stdev:0	GSM2252999_r1				in_mesa	28538178	2.96	3.43	0.6	2676025397	2634488413	2405404482	2388131865	98.45	99.28	16831645	15791557	187.077	777.034	136	140330	73.11	81.61	20154550	12306205	20154550	12306205	78.13	78.49	20154550	13151349	20154550	11835631	461492172	17.25	1.40	0	9.85	0	0.73	0	0.17	0	0.00	0	4.49	0	16831645	0	202	0	200.34	0	1.45	0	0.01	0	1.18	0	0.01	0	244.44	0	0.17	0	248470	0	17789462	0	1752800	0	129922	0	29626	0	0	0	798269	0	4417	0	0	0	54619	0	6764999	0	19458	0	6843493	0	84.76	0	15078845	0	160853	6113135	38.004482353453	17789462.0	16831645.0	248470.0	1752800.0	129922.0	29626.0	0.0	798269.0	15078845.0	94.6	1.4	9.9	0.7	0.2	0.0	4.5	84.8	101	101	101.00	38	1796735662	24.5	24.3	24.6	26.6	0.0	36.0	25.9	bulk
432727	SRR3954695	SRP079936	SRS1586476	SRX1978956	SRA444699	GEO		Next Generation Sequencing Comparison of Wild Type and Whsc1-/- Activated B-cell Transcriptomes	Whsc1 gene codes for a SET domain-containing H3K36 dimethylase, whose activity has been suggested, in ex vivo cell culture experiments, to control many aspects of DNA and RNA processing (replication, repair, transcription, etc). Its precise function in vivo is still unclear. Here, we use RNA-seq transcriptome analysis to study the changes in gene expression in the absence of Whsc1. Our results show that, in the experimental system used, loss of Whsc1 caused massive changes in genes affecting many fundamental cellular processes, from cell cycle to ribosome synthesis, DNA repair, replication, etc. Overall design: Whsc1-KO mice are embryonic lethal. We therefore took hematopoietic cells from fetal liver of WT and Whsc1-KO embryo littermates and injected them in to lethally irradiated RAG1-KO recipients and allowed the generation of a full Whsc1-KO hematopoietic system. Then, WT and Whsc1-KO B cells were obtained from the spleen and stimulated with LPS to induce proliferation and class switch recombination. Flow cytometry and cell cycle analyses (among others) showed the existence of serious proliferative alterations in Whsc1-KO cells. Then, we performed paired-end RNAseq analyses of 7 independent WT and 6 independent Whsc1-KO biological replicates and we used these data to identify differentially expressed genes and pathways regulated by Whsc1 in B cells.		GSM2252999: WT_rep2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			RNA was extracted following commercial Trizol® Reagent [Cat No 15596-026, Life TecnologiesTM, GibcoBRL] recommendations. It chemical quality was measure by Nanodrop 1000 Spectrophotometer [Thermo ScientificTM] and it integrity was confirmed using the Agilent 2100 Bioanalyzer. The libraries from the mouse total RNA were prepared using the TruSeq®Stranded mRNA LT Sample Prep Kit (Illumina Inc., Rev.E, October 2013) according to manufacturer’s protocol. Briefly, 0.5 µg of total RNA was used for poly-A based mRNA enrichment with oligo-dT magnetic beads. The mRNA was fragmented (resulting RNA fragment size was 80-250nt, with the major peak at 130nt. The second strand cDNA synthesis was performed in the presence of dUTP instead of dTTP, this allowed to achieve the strand specificity. The blunt-ended double stranded cDNA was 3´adenylated and Illumina indexed adapters were ligated. The ligation product was enriched with 15 PCR cycles and the final library was validated on an Agilent 2100 Bioanalyzer with the DNA 7500 assay. The libraries were sequenced on HiSeq2000 (Illumina, Inc) in paired-end mode with a read length of 2x76bp using TruSeq SBS Kit v3-HS. We generated about 50-70 million paired-end reads for each sample in a fraction of a sequencing flowcell lane, following the manufacturer’s protocol. Image analysis, base calling and quality scoring of the run were processed using the manufacturer’s software Real Time Analysis (RTA 1.13.48) and followed by generation of FASTQ sequence files by CASAVA.	Illumina HiSeq 2000	genotipe;;WT|source_name;;LPS-stimulated splenic B cells|strain;;C57BL/6	GEO Accession;;GSM2252999		GSM2252999	WT_rep2	10515047784	52054692	2017-05-23 16:50:08	7250580435	10515047784	52054692	2	52054692	index:0,count:52054692,average:101,stdev:0|index:1,count:52054692,average:101,stdev:0	GSM2252999_r2				in_mesa	28538178	2.93	3.41	0.6	7881241110	7759372334	7094927480	7043813965	98.45	99.28	49430834	46380568	187.984	784.749	136	410357	73.18	81.55	59064687	36172053	59064687	36172053	78.09	78.44	59064687	38598243	59064687	34792780	1364930807	17.32	1.42	0	9.75	0	0.73	0	0.17	0	0.00	0	4.14	0	49430834	0	202	0	200.36	0	1.44	0	0.01	0	1.19	0	0.01	0	307.21	0	0.19	0	738953	0	52054692	0	5075017	0	381503	0	86027	0	0	0	2156328	0	13087	0	0	0	158718	0	19784562	0	57540	0	20013907	0	85.21	0	44355817	0	210285	17859830	84.931545283782	52054692.0	49430834.0	738953.0	5075017.0	381503.0	86027.0	0.0	2156328.0	44355817.0	95.0	1.4	9.7	0.7	0.2	0.0	4.1	85.2	101	101	101.00	38	5257523892	24.6	24.3	24.7	26.4	0.0	35.5	25.5	bulk
432731	SRR3954696	SRP079936	SRS1586477	SRX1978957	SRA444699	GEO		Next Generation Sequencing Comparison of Wild Type and Whsc1-/- Activated B-cell Transcriptomes	Whsc1 gene codes for a SET domain-containing H3K36 dimethylase, whose activity has been suggested, in ex vivo cell culture experiments, to control many aspects of DNA and RNA processing (replication, repair, transcription, etc). Its precise function in vivo is still unclear. Here, we use RNA-seq transcriptome analysis to study the changes in gene expression in the absence of Whsc1. Our results show that, in the experimental system used, loss of Whsc1 caused massive changes in genes affecting many fundamental cellular processes, from cell cycle to ribosome synthesis, DNA repair, replication, etc. Overall design: Whsc1-KO mice are embryonic lethal. We therefore took hematopoietic cells from fetal liver of WT and Whsc1-KO embryo littermates and injected them in to lethally irradiated RAG1-KO recipients and allowed the generation of a full Whsc1-KO hematopoietic system. Then, WT and Whsc1-KO B cells were obtained from the spleen and stimulated with LPS to induce proliferation and class switch recombination. Flow cytometry and cell cycle analyses (among others) showed the existence of serious proliferative alterations in Whsc1-KO cells. Then, we performed paired-end RNAseq analyses of 7 independent WT and 6 independent Whsc1-KO biological replicates and we used these data to identify differentially expressed genes and pathways regulated by Whsc1 in B cells.		GSM2253000: WT_rep3; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			RNA was extracted following commercial Trizol® Reagent [Cat No 15596-026, Life TecnologiesTM, GibcoBRL] recommendations. It chemical quality was measure by Nanodrop 1000 Spectrophotometer [Thermo ScientificTM] and it integrity was confirmed using the Agilent 2100 Bioanalyzer. The libraries from the mouse total RNA were prepared using the TruSeq®Stranded mRNA LT Sample Prep Kit (Illumina Inc., Rev.E, October 2013) according to manufacturer’s protocol. Briefly, 0.5 µg of total RNA was used for poly-A based mRNA enrichment with oligo-dT magnetic beads. The mRNA was fragmented (resulting RNA fragment size was 80-250nt, with the major peak at 130nt. The second strand cDNA synthesis was performed in the presence of dUTP instead of dTTP, this allowed to achieve the strand specificity. The blunt-ended double stranded cDNA was 3´adenylated and Illumina indexed adapters were ligated. The ligation product was enriched with 15 PCR cycles and the final library was validated on an Agilent 2100 Bioanalyzer with the DNA 7500 assay. The libraries were sequenced on HiSeq2000 (Illumina, Inc) in paired-end mode with a read length of 2x76bp using TruSeq SBS Kit v3-HS. We generated about 50-70 million paired-end reads for each sample in a fraction of a sequencing flowcell lane, following the manufacturer’s protocol. Image analysis, base calling and quality scoring of the run were processed using the manufacturer’s software Real Time Analysis (RTA 1.13.48) and followed by generation of FASTQ sequence files by CASAVA.	Illumina HiSeq 2000	genotipe;;WT|source_name;;LPS-stimulated splenic B cells|strain;;C57BL/6	GEO Accession;;GSM2253000		GSM2253000	WT_rep3	12533348762	62046281	2017-05-23 16:50:08	8651269244	12533348762	62046281	2	62046281	index:0,count:62046281,average:101,stdev:0|index:1,count:62046281,average:101,stdev:0	GSM2253000_r1				in_mesa	28538178	2.79	3.35	0.62	9646551348	9504091285	8760871374	8702861358	98.52	99.34	59519871	55651355	192.643	752.465	137	475759	73.69	81.36	70128544	43857544	70128544	43857544	77.92	78.28	70128544	46379324	70128544	42198027	1696607848	17.59	1.08	0	9.05	0	0.59	0	0.16	0	0.00	0	3.31	0	59519871	0	202	0	200.48	0	1.48	0	0.01	0	1.18	0	0.01	0	262.78	0	0.20	0	671271	0	62046281	0	5613520	0	368194	0	102074	0	0	0	2056142	0	16815	0	0	0	192615	0	24311261	0	69810	0	24590501	0	86.88	0	53906351	0	225949	22120669	97.901159111127	62046281.0	59519871.0	671271.0	5613520.0	368194.0	102074.0	0.0	2056142.0	53906351.0	95.9	1.1	9.0	0.6	0.2	0.0	3.3	86.9	101	101	101.00	38	6266674381	24.7	24.3	24.6	26.4	0.0	35.5	25.4	bulk
865428	SRR3954692	SRP079936	SRS1586475	SRX1978955	SRA444699	GEO		Next Generation Sequencing Comparison of Wild Type and Whsc1-/- Activated B-cell Transcriptomes	Whsc1 gene codes for a SET domain-containing H3K36 dimethylase, whose activity has been suggested, in ex vivo cell culture experiments, to control many aspects of DNA and RNA processing (replication, repair, transcription, etc). Its precise function in vivo is still unclear. Here, we use RNA-seq transcriptome analysis to study the changes in gene expression in the absence of Whsc1. Our results show that, in the experimental system used, loss of Whsc1 caused massive changes in genes affecting many fundamental cellular processes, from cell cycle to ribosome synthesis, DNA repair, replication, etc. Overall design: Whsc1-KO mice are embryonic lethal. We therefore took hematopoietic cells from fetal liver of WT and Whsc1-KO embryo littermates and injected them in to lethally irradiated RAG1-KO recipients and allowed the generation of a full Whsc1-KO hematopoietic system. Then, WT and Whsc1-KO B cells were obtained from the spleen and stimulated with LPS to induce proliferation and class switch recombination. Flow cytometry and cell cycle analyses (among others) showed the existence of serious proliferative alterations in Whsc1-KO cells. Then, we performed paired-end RNAseq analyses of 7 independent WT and 6 independent Whsc1-KO biological replicates and we used these data to identify differentially expressed genes and pathways regulated by Whsc1 in B cells.		GSM2252998: WT_rep1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			RNA was extracted following commercial Trizol® Reagent [Cat No 15596-026, Life TecnologiesTM, GibcoBRL] recommendations. It chemical quality was measure by Nanodrop 1000 Spectrophotometer [Thermo ScientificTM] and it integrity was confirmed using the Agilent 2100 Bioanalyzer. The libraries from the mouse total RNA were prepared using the TruSeq®Stranded mRNA LT Sample Prep Kit (Illumina Inc., Rev.E, October 2013) according to manufacturer’s protocol. Briefly, 0.5 µg of total RNA was used for poly-A based mRNA enrichment with oligo-dT magnetic beads. The mRNA was fragmented (resulting RNA fragment size was 80-250nt, with the major peak at 130nt. The second strand cDNA synthesis was performed in the presence of dUTP instead of dTTP, this allowed to achieve the strand specificity. The blunt-ended double stranded cDNA was 3´adenylated and Illumina indexed adapters were ligated. The ligation product was enriched with 15 PCR cycles and the final library was validated on an Agilent 2100 Bioanalyzer with the DNA 7500 assay. The libraries were sequenced on HiSeq2000 (Illumina, Inc) in paired-end mode with a read length of 2x76bp using TruSeq SBS Kit v3-HS. We generated about 50-70 million paired-end reads for each sample in a fraction of a sequencing flowcell lane, following the manufacturer’s protocol. Image analysis, base calling and quality scoring of the run were processed using the manufacturer’s software Real Time Analysis (RTA 1.13.48) and followed by generation of FASTQ sequence files by CASAVA.	Illumina HiSeq 2000	genotipe;;WT|source_name;;LPS-stimulated splenic B cells|strain;;C57BL/6	GEO Accession;;GSM2252998		GSM2252998	WT_rep1	9542738358	47241279	2017-05-23 16:50:08	6608011715	9542738358	47241279	2	47241279	index:0,count:47241279,average:101,stdev:0|index:1,count:47241279,average:101,stdev:0	GSM2252998_r1				in_mesa	28538178	2.83	3.49	0.24	7279889155	7187617955	6598852584	6557634946	98.73	99.38	45496314	42622155	188.895	798.144	136	371429	77.22	85.42	53550910	35131589	53550910	35131589	81.81	82.15	53550910	37220026	53550910	33784096	997050195	13.70	1.05	0	9.25	0	0.58	0	0.16	0	0.00	0	2.95	0	45496314	0	202	0	200.33	0	1.47	0	0.01	0	1.23	0	0.01	0	213.39	0	0.21	0	494354	0	47241279	0	4370145	0	273011	0	77927	0	0	0	1394027	0	12557	0	0	0	152477	0	19002477	0	62366	0	19229877	0	87.06	0	41126169	0	209109	17192030	82.215638733866	47241279.0	45496314.0	494354.0	4370145.0	273011.0	77927.0	0.0	1394027.0	41126169.0	96.3	1.0	9.3	0.6	0.2	0.0	3.0	87.1	101	101	101.00	38	4771369179	24.7	24.5	24.4	26.3	0.0	35.4	25.2	bulk
865468	SRR3954697	SRP079936	SRS1586478	SRX1978958	SRA444699	GEO		Next Generation Sequencing Comparison of Wild Type and Whsc1-/- Activated B-cell Transcriptomes	Whsc1 gene codes for a SET domain-containing H3K36 dimethylase, whose activity has been suggested, in ex vivo cell culture experiments, to control many aspects of DNA and RNA processing (replication, repair, transcription, etc). Its precise function in vivo is still unclear. Here, we use RNA-seq transcriptome analysis to study the changes in gene expression in the absence of Whsc1. Our results show that, in the experimental system used, loss of Whsc1 caused massive changes in genes affecting many fundamental cellular processes, from cell cycle to ribosome synthesis, DNA repair, replication, etc. Overall design: Whsc1-KO mice are embryonic lethal. We therefore took hematopoietic cells from fetal liver of WT and Whsc1-KO embryo littermates and injected them in to lethally irradiated RAG1-KO recipients and allowed the generation of a full Whsc1-KO hematopoietic system. Then, WT and Whsc1-KO B cells were obtained from the spleen and stimulated with LPS to induce proliferation and class switch recombination. Flow cytometry and cell cycle analyses (among others) showed the existence of serious proliferative alterations in Whsc1-KO cells. Then, we performed paired-end RNAseq analyses of 7 independent WT and 6 independent Whsc1-KO biological replicates and we used these data to identify differentially expressed genes and pathways regulated by Whsc1 in B cells.		GSM2253001: WT_rep4; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			RNA was extracted following commercial Trizol® Reagent [Cat No 15596-026, Life TecnologiesTM, GibcoBRL] recommendations. It chemical quality was measure by Nanodrop 1000 Spectrophotometer [Thermo ScientificTM] and it integrity was confirmed using the Agilent 2100 Bioanalyzer. The libraries from the mouse total RNA were prepared using the TruSeq®Stranded mRNA LT Sample Prep Kit (Illumina Inc., Rev.E, October 2013) according to manufacturer’s protocol. Briefly, 0.5 µg of total RNA was used for poly-A based mRNA enrichment with oligo-dT magnetic beads. The mRNA was fragmented (resulting RNA fragment size was 80-250nt, with the major peak at 130nt. The second strand cDNA synthesis was performed in the presence of dUTP instead of dTTP, this allowed to achieve the strand specificity. The blunt-ended double stranded cDNA was 3´adenylated and Illumina indexed adapters were ligated. The ligation product was enriched with 15 PCR cycles and the final library was validated on an Agilent 2100 Bioanalyzer with the DNA 7500 assay. The libraries were sequenced on HiSeq2000 (Illumina, Inc) in paired-end mode with a read length of 2x76bp using TruSeq SBS Kit v3-HS. We generated about 50-70 million paired-end reads for each sample in a fraction of a sequencing flowcell lane, following the manufacturer’s protocol. Image analysis, base calling and quality scoring of the run were processed using the manufacturer’s software Real Time Analysis (RTA 1.13.48) and followed by generation of FASTQ sequence files by CASAVA.	Illumina HiSeq 2000	genotipe;;WT|source_name;;LPS-stimulated splenic B cells|strain;;C57BL/6	GEO Accession;;GSM2253001		GSM2253001	WT_rep4	10496518122	51962961	2017-05-23 16:50:08	6889641117	10496518122	51962961	2	51962961	index:0,count:51962961,average:101,stdev:0|index:1,count:51962961,average:101,stdev:0	GSM2253001_r1				in_mesa	28538178	2.73	3.36	0.2	7992511845	7894457951	7299583818	7250808934	98.77	99.33	49487813	46589199	187.027	774.860	148	426772	79.6	87.35	57287753	39393073	57287753	39393073	83.72	83.94	57287753	41430387	57287753	37857081	931796448	11.66	0.93	0	8.44	0	0.45	0	0.19	0	0.00	0	4.13	0	49487813	0	202	0	200.51	0	1.46	0	0.01	0	1.17	0	0.01	0	260.54	0	0.15	0	481192	0	51962961	0	4388046	0	233416	0	96491	0	0	0	2145241	0	14117	0	0	0	165719	0	21102091	0	72554	0	21354481	0	86.79	0	45099767	0	198795	19203597	96.600000000000	51962961.0	49487813.0	481192.0	4388046.0	233416.0	96491.0	0.0	2145241.0	45099767.0	95.2	0.9	8.4	0.4	0.2	0.0	4.1	86.8	101	101	101.00	38	5248259061	24.5	24.6	24.5	26.4	0.0	36.4	27.0	bulk
865476	SRR3954698	SRP079936	SRS1586479	SRX1978959	SRA444699	GEO		Next Generation Sequencing Comparison of Wild Type and Whsc1-/- Activated B-cell Transcriptomes	Whsc1 gene codes for a SET domain-containing H3K36 dimethylase, whose activity has been suggested, in ex vivo cell culture experiments, to control many aspects of DNA and RNA processing (replication, repair, transcription, etc). Its precise function in vivo is still unclear. Here, we use RNA-seq transcriptome analysis to study the changes in gene expression in the absence of Whsc1. Our results show that, in the experimental system used, loss of Whsc1 caused massive changes in genes affecting many fundamental cellular processes, from cell cycle to ribosome synthesis, DNA repair, replication, etc. Overall design: Whsc1-KO mice are embryonic lethal. We therefore took hematopoietic cells from fetal liver of WT and Whsc1-KO embryo littermates and injected them in to lethally irradiated RAG1-KO recipients and allowed the generation of a full Whsc1-KO hematopoietic system. Then, WT and Whsc1-KO B cells were obtained from the spleen and stimulated with LPS to induce proliferation and class switch recombination. Flow cytometry and cell cycle analyses (among others) showed the existence of serious proliferative alterations in Whsc1-KO cells. Then, we performed paired-end RNAseq analyses of 7 independent WT and 6 independent Whsc1-KO biological replicates and we used these data to identify differentially expressed genes and pathways regulated by Whsc1 in B cells.		GSM2253002: WT_rep5; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			RNA was extracted following commercial Trizol® Reagent [Cat No 15596-026, Life TecnologiesTM, GibcoBRL] recommendations. It chemical quality was measure by Nanodrop 1000 Spectrophotometer [Thermo ScientificTM] and it integrity was confirmed using the Agilent 2100 Bioanalyzer. The libraries from the mouse total RNA were prepared using the TruSeq®Stranded mRNA LT Sample Prep Kit (Illumina Inc., Rev.E, October 2013) according to manufacturer’s protocol. Briefly, 0.5 µg of total RNA was used for poly-A based mRNA enrichment with oligo-dT magnetic beads. The mRNA was fragmented (resulting RNA fragment size was 80-250nt, with the major peak at 130nt. The second strand cDNA synthesis was performed in the presence of dUTP instead of dTTP, this allowed to achieve the strand specificity. The blunt-ended double stranded cDNA was 3´adenylated and Illumina indexed adapters were ligated. The ligation product was enriched with 15 PCR cycles and the final library was validated on an Agilent 2100 Bioanalyzer with the DNA 7500 assay. The libraries were sequenced on HiSeq2000 (Illumina, Inc) in paired-end mode with a read length of 2x76bp using TruSeq SBS Kit v3-HS. We generated about 50-70 million paired-end reads for each sample in a fraction of a sequencing flowcell lane, following the manufacturer’s protocol. Image analysis, base calling and quality scoring of the run were processed using the manufacturer’s software Real Time Analysis (RTA 1.13.48) and followed by generation of FASTQ sequence files by CASAVA.	Illumina HiSeq 2000	genotipe;;WT|source_name;;LPS-stimulated splenic B cells|strain;;C57BL/6	GEO Accession;;GSM2253002		GSM2253002	WT_rep5	12712629822	62933811	2017-05-23 16:50:08	8648761284	12712629822	62933811	2	62933811	index:0,count:62933811,average:101,stdev:0|index:1,count:62933811,average:101,stdev:0	GSM2253002_r1				in_mesa	28538178	2.44	3.06	0.59	9850601584	9677309237	9002992927	8917005241	98.24	99.04	60464232	56975584	189.917	796.822	146	507549	74.35	81.54	70525800	44952715	70525800	44952715	77.88	78.38	70525800	47087334	70525800	43209403	1707848516	17.34	0.92	0	8.48	0	0.58	0	0.15	0	0.00	0	3.19	0	60464232	0	202	0	200.55	0	1.49	0	0.01	0	1.22	0	0.01	0	310.36	0	0.18	0	576114	0	62933811	0	5335083	0	366659	0	94985	0	0	0	2007935	0	16623	0	0	0	185655	0	24055207	0	88464	0	24345949	0	87.60	0	55129149	0	215690	21980484	101.907756502388	62933811.0	60464232.0	576114.0	5335083.0	366659.0	94985.0	0.0	2007935.0	55129149.0	96.1	0.9	8.5	0.6	0.2	0.0	3.2	87.6	101	101	101.00	38	6356314911	24.3	24.5	24.8	26.4	0.0	36.0	26.5	bulk
865485	SRR3954699	SRP079936	SRS1586480	SRX1978960	SRA444699	GEO		Next Generation Sequencing Comparison of Wild Type and Whsc1-/- Activated B-cell Transcriptomes	Whsc1 gene codes for a SET domain-containing H3K36 dimethylase, whose activity has been suggested, in ex vivo cell culture experiments, to control many aspects of DNA and RNA processing (replication, repair, transcription, etc). Its precise function in vivo is still unclear. Here, we use RNA-seq transcriptome analysis to study the changes in gene expression in the absence of Whsc1. Our results show that, in the experimental system used, loss of Whsc1 caused massive changes in genes affecting many fundamental cellular processes, from cell cycle to ribosome synthesis, DNA repair, replication, etc. Overall design: Whsc1-KO mice are embryonic lethal. We therefore took hematopoietic cells from fetal liver of WT and Whsc1-KO embryo littermates and injected them in to lethally irradiated RAG1-KO recipients and allowed the generation of a full Whsc1-KO hematopoietic system. Then, WT and Whsc1-KO B cells were obtained from the spleen and stimulated with LPS to induce proliferation and class switch recombination. Flow cytometry and cell cycle analyses (among others) showed the existence of serious proliferative alterations in Whsc1-KO cells. Then, we performed paired-end RNAseq analyses of 7 independent WT and 6 independent Whsc1-KO biological replicates and we used these data to identify differentially expressed genes and pathways regulated by Whsc1 in B cells.		GSM2253003: WT_rep6; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			RNA was extracted following commercial Trizol® Reagent [Cat No 15596-026, Life TecnologiesTM, GibcoBRL] recommendations. It chemical quality was measure by Nanodrop 1000 Spectrophotometer [Thermo ScientificTM] and it integrity was confirmed using the Agilent 2100 Bioanalyzer. The libraries from the mouse total RNA were prepared using the TruSeq®Stranded mRNA LT Sample Prep Kit (Illumina Inc., Rev.E, October 2013) according to manufacturer’s protocol. Briefly, 0.5 µg of total RNA was used for poly-A based mRNA enrichment with oligo-dT magnetic beads. The mRNA was fragmented (resulting RNA fragment size was 80-250nt, with the major peak at 130nt. The second strand cDNA synthesis was performed in the presence of dUTP instead of dTTP, this allowed to achieve the strand specificity. The blunt-ended double stranded cDNA was 3´adenylated and Illumina indexed adapters were ligated. The ligation product was enriched with 15 PCR cycles and the final library was validated on an Agilent 2100 Bioanalyzer with the DNA 7500 assay. The libraries were sequenced on HiSeq2000 (Illumina, Inc) in paired-end mode with a read length of 2x76bp using TruSeq SBS Kit v3-HS. We generated about 50-70 million paired-end reads for each sample in a fraction of a sequencing flowcell lane, following the manufacturer’s protocol. Image analysis, base calling and quality scoring of the run were processed using the manufacturer’s software Real Time Analysis (RTA 1.13.48) and followed by generation of FASTQ sequence files by CASAVA.	Illumina HiSeq 2000	genotipe;;WT|source_name;;LPS-stimulated splenic B cells|strain;;C57BL/6	GEO Accession;;GSM2253003		GSM2253003	WT_rep6	11560181038	57228619	2017-05-23 16:50:08	7875778213	11560181038	57228619	2	57228619	index:0,count:57228619,average:101,stdev:0|index:1,count:57228619,average:101,stdev:0	GSM2253003_r1				in_mesa	28538178	2.98	3.32	0.22	8922390101	8813163667	8082651414	8031252111	98.78	99.36	54985099	51632718	189.738	699.002	148	467078	77.95	86.25	64508672	42858668	64508672	42858668	82.71	82.92	64508672	45480489	64508672	41203865	1139049726	12.77	0.81	0	9.25	0	0.47	0	0.16	0	0.00	0	3.29	0	54985099	0	202	0	200.52	0	1.45	0	0.01	0	1.17	0	0.01	0	256.89	0	0.17	0	462553	0	57228619	0	5292989	0	270119	0	91944	0	0	0	1881457	0	15934	0	0	0	187482	0	23165942	0	61138	0	23430496	0	86.83	0	49692110	0	216376	21291376	98.399896476504	57228619.0	54985099.0	462553.0	5292989.0	270119.0	91944.0	0.0	1881457.0	49692110.0	96.1	0.8	9.2	0.5	0.2	0.0	3.3	86.8	101	101	101.00	38	5780090519	24.6	24.6	24.2	26.7	0.0	36.0	26.3	bulk
866310	SRR3954700	SRP079936	SRS1586481	SRX1978961	SRA444699	GEO		Next Generation Sequencing Comparison of Wild Type and Whsc1-/- Activated B-cell Transcriptomes	Whsc1 gene codes for a SET domain-containing H3K36 dimethylase, whose activity has been suggested, in ex vivo cell culture experiments, to control many aspects of DNA and RNA processing (replication, repair, transcription, etc). Its precise function in vivo is still unclear. Here, we use RNA-seq transcriptome analysis to study the changes in gene expression in the absence of Whsc1. Our results show that, in the experimental system used, loss of Whsc1 caused massive changes in genes affecting many fundamental cellular processes, from cell cycle to ribosome synthesis, DNA repair, replication, etc. Overall design: Whsc1-KO mice are embryonic lethal. We therefore took hematopoietic cells from fetal liver of WT and Whsc1-KO embryo littermates and injected them in to lethally irradiated RAG1-KO recipients and allowed the generation of a full Whsc1-KO hematopoietic system. Then, WT and Whsc1-KO B cells were obtained from the spleen and stimulated with LPS to induce proliferation and class switch recombination. Flow cytometry and cell cycle analyses (among others) showed the existence of serious proliferative alterations in Whsc1-KO cells. Then, we performed paired-end RNAseq analyses of 7 independent WT and 6 independent Whsc1-KO biological replicates and we used these data to identify differentially expressed genes and pathways regulated by Whsc1 in B cells.		GSM2253004: WT_rep7; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			RNA was extracted following commercial Trizol® Reagent [Cat No 15596-026, Life TecnologiesTM, GibcoBRL] recommendations. It chemical quality was measure by Nanodrop 1000 Spectrophotometer [Thermo ScientificTM] and it integrity was confirmed using the Agilent 2100 Bioanalyzer. The libraries from the mouse total RNA were prepared using the TruSeq®Stranded mRNA LT Sample Prep Kit (Illumina Inc., Rev.E, October 2013) according to manufacturer’s protocol. Briefly, 0.5 µg of total RNA was used for poly-A based mRNA enrichment with oligo-dT magnetic beads. The mRNA was fragmented (resulting RNA fragment size was 80-250nt, with the major peak at 130nt. The second strand cDNA synthesis was performed in the presence of dUTP instead of dTTP, this allowed to achieve the strand specificity. The blunt-ended double stranded cDNA was 3´adenylated and Illumina indexed adapters were ligated. The ligation product was enriched with 15 PCR cycles and the final library was validated on an Agilent 2100 Bioanalyzer with the DNA 7500 assay. The libraries were sequenced on HiSeq2000 (Illumina, Inc) in paired-end mode with a read length of 2x76bp using TruSeq SBS Kit v3-HS. We generated about 50-70 million paired-end reads for each sample in a fraction of a sequencing flowcell lane, following the manufacturer’s protocol. Image analysis, base calling and quality scoring of the run were processed using the manufacturer’s software Real Time Analysis (RTA 1.13.48) and followed by generation of FASTQ sequence files by CASAVA.	Illumina HiSeq 2000	genotipe;;WT|source_name;;LPS-stimulated splenic B cells|strain;;C57BL/6	GEO Accession;;GSM2253004		GSM2253004	WT_rep7	13290451630	65794315	2017-05-23 16:50:08	9022132445	13290451630	65794315	2	65794315	index:0,count:65794315,average:101,stdev:0|index:1,count:65794315,average:101,stdev:0	GSM2253004_r1				in_mesa	28538178	2.75	3.18	0.23	10295740351	10173743065	9385588301	9329620230	98.82	99.4	63198565	59185880	192.518	792.535	151	517767	79.18	87.06	73493817	50039460	73493817	50039460	83.39	83.68	73493817	52703821	73493817	48096176	1242107105	12.06	0.93	0	8.69	0	0.48	0	0.16	0	0.00	0	3.31	0	63198565	0	202	0	200.49	0	1.46	0	0.01	0	1.18	0	0.01	0	241.20	0	0.17	0	610740	0	65794315	0	5719217	0	313691	0	104949	0	0	0	2177110	0	18710	0	0	0	211921	0	27041612	0	87122	0	27359365	0	87.36	0	57479348	0	228589	24791925	108.456334294301	65794315.0	63198565.0	610740.0	5719217.0	313691.0	104949.0	0.0	2177110.0	57479348.0	96.1	0.9	8.7	0.5	0.2	0.0	3.3	87.4	101	101	101.00	38	6645225815	24.4	24.6	24.5	26.4	0.0	36.0	26.3	bulk
1742749	SRR4297979	SRP090506	SRS1715082	SRX2192591	SRA480453	GEO		Deciphering Pancreatic Islet ß Cell and a Cell Maturation Pathways and Characteristic Features at the Single-Cell Level	Pancreatic ß and a cells play essential roles in maintaining glucose homeostasis. However, the mechanisms by which these distinct cell populations are generated, expand, and mature during pancreas development remain unclear. In this study, we addressed this critical question by performing a single-cell transcriptomic analysis of mouse ß and a cells sorted from fetal to adult stages. We discovered that ß and a cells use different regulatory strategies for their maturation and that cell proliferation peaks at different developmental times. However, the quiescent and proliferative cells in both the ß lineage and a lineage are synchronous in their maturation states. The heterogeneity of juvenile ß cells reflects distinct cell-cycling phases, origins, and maturation states, whereas adult ß cells are relatively homogeneous at the transcriptomic level. These analyses provide not only a high-resolution roadmap for islet lineage development but also insights into the mechanisms of cellular heterogeneity, cell number expansion, and maturation of both ß and a cells. Overall design: The overall goal of this study was to define the roadmaps for pancreatic ß- and a-cell development. Specifically, we performed single-cell RNA-seq at various developmental stages of E17.5, P0, P3, P9, P15, P18 and P60 of ß- and a- cells (except P3), as well as endocrine progenitor cells at P0, which were fluorescence-activated cell sorting (FACS) sorted from Insulin-RFP, Gcg-Cre; Rosa-RFP or Ngn3-GFP mouse strains, respectively. To develop a workflow to decipher the maturation process through bulk-cell transcriptomic analysis, we performed RNA-seq using 3-5 × 10^4 sorted cells at various developmental time points as we have done in the single-cell study. The background strains of our mouse samples are: Ngn3-GFP mice: mixed background of C57BL/6 and C3H Ins1-RFP mice: mixed background of C57BL/6 and C3H Gcg-Cre, Rosa-RFP mice: mixed background of C57BL/6, CBA/J and C3H.		GSM2329198: E17.5_beta_#1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA from approximately 3-5 × 10^4 sorted β-cells was extracted by the RNeasy Micro Kit (Qiagen, 74004) followed by mRNA purification using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490). Strand-specific libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB #E7420) following manufacturer’s instructions.	Illumina HiSeq 2000	cell type;;beta cells|developmental stage;;E17.5|source_name;;E17.5 Ins1-RFP+|strain;;Ins1-RFP+|tissue;;Pancreas	GEO Accession;;GSM2329198		GSM2329198	E17.5_beta_#1	3902416588	19318894	2017-05-03 16:29:37	2626838469	3902416588	19318894	2	19318894	index:0,count:19318894,average:101,stdev:0|index:1,count:19318894,average:101,stdev:0	GSM2329198_r1				in_mesa	28467935	2.25	3.52	0.07	3434243761	3418197700	3264114009	3263175867	99.53	99.97	18950533	16839765	242.664	922.122	174	115846	85.36	89.88	20592680	16175535	20592680	16175535	86.27	86.51	20592680	16348698	20592680	15569013	313339124	9.12	0.51	0	4.94	0	0.49	0	0.11	0	0.00	0	1.31	0	18950533	0	202	0	200.57	0	2.10	0	0.01	0	1.71	0	0.01	0	265.45	0	0.23	0	98432	0	19318894	0	954391	0	94883	0	20997	0	0	0	252481	0	6010	0	0	0	63018	0	9341491	0	26478	0	9436997	0	93.15	0	17996142	0	193126	9235137	47.819232003977	19318894.0	18950533.0	98432.0	954391.0	94883.0	20997.0	0.0	252481.0	17996142.0	98.1	0.5	4.9	0.5	0.1	0.0	1.3	93.2	101	101	101.00	38	1951208294	24.7	24.9	24.6	25.8	0.0	36.0	22.1	bulk
1742860	SRR4297980	SRP090506	SRS1715083	SRX2192592	SRA480453	GEO		Deciphering Pancreatic Islet ß Cell and a Cell Maturation Pathways and Characteristic Features at the Single-Cell Level	Pancreatic ß and a cells play essential roles in maintaining glucose homeostasis. However, the mechanisms by which these distinct cell populations are generated, expand, and mature during pancreas development remain unclear. In this study, we addressed this critical question by performing a single-cell transcriptomic analysis of mouse ß and a cells sorted from fetal to adult stages. We discovered that ß and a cells use different regulatory strategies for their maturation and that cell proliferation peaks at different developmental times. However, the quiescent and proliferative cells in both the ß lineage and a lineage are synchronous in their maturation states. The heterogeneity of juvenile ß cells reflects distinct cell-cycling phases, origins, and maturation states, whereas adult ß cells are relatively homogeneous at the transcriptomic level. These analyses provide not only a high-resolution roadmap for islet lineage development but also insights into the mechanisms of cellular heterogeneity, cell number expansion, and maturation of both ß and a cells. Overall design: The overall goal of this study was to define the roadmaps for pancreatic ß- and a-cell development. Specifically, we performed single-cell RNA-seq at various developmental stages of E17.5, P0, P3, P9, P15, P18 and P60 of ß- and a- cells (except P3), as well as endocrine progenitor cells at P0, which were fluorescence-activated cell sorting (FACS) sorted from Insulin-RFP, Gcg-Cre; Rosa-RFP or Ngn3-GFP mouse strains, respectively. To develop a workflow to decipher the maturation process through bulk-cell transcriptomic analysis, we performed RNA-seq using 3-5 × 10^4 sorted cells at various developmental time points as we have done in the single-cell study. The background strains of our mouse samples are: Ngn3-GFP mice: mixed background of C57BL/6 and C3H Ins1-RFP mice: mixed background of C57BL/6 and C3H Gcg-Cre, Rosa-RFP mice: mixed background of C57BL/6, CBA/J and C3H.		GSM2329199: E17.5_beta_#2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA from approximately 3-5 × 10^4 sorted β-cells was extracted by the RNeasy Micro Kit (Qiagen, 74004) followed by mRNA purification using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490). Strand-specific libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB #E7420) following manufacturer’s instructions.	Illumina HiSeq 2000	cell type;;beta cells|developmental stage;;E17.5|source_name;;E17.5 Ins1-RFP+|strain;;Ins1-RFP+|tissue;;Pancreas	GEO Accession;;GSM2329199		GSM2329199	E17.5_beta_#2	3224490448	15962824	2017-05-03 16:29:37	2012974349	3224490448	15962824	2	15962824	index:0,count:15962824,average:101,stdev:0|index:1,count:15962824,average:101,stdev:0	GSM2329199_r1				in_mesa	28467935	2.03	3.25	0.06	2771054476	2771210554	2635952937	2647465213	100.01	100.44	15649948	14027777	232.852	876.144	158	97166	85.3	89.76	16926653	13349621	16926653	13349621	85.59	85.88	16926653	13394502	16926653	12771827	257325342	9.29	0.58	0	4.87	0	0.28	0	0.08	0	0.00	0	1.60	0	15649948	0	202	0	200.44	0	2.19	0	0.01	0	1.76	0	0.01	0	262.40	0	0.42	0	92692	0	15962824	0	777607	0	44588	0	12130	0	0	0	256158	0	4758	0	0	0	46717	0	7576511	0	20808	0	7648794	0	93.17	0	14872341	0	195648	7271797	37.167755356559	15962824.0	15649948.0	92692.0	777607.0	44588.0	12130.0	0.0	256158.0	14872341.0	98.0	0.6	4.9	0.3	0.1	0.0	1.6	93.2	101	101	101.00	38	1612245224	24.1	25.1	25.6	25.1	0.2	36.3	22.2	bulk
1742876	SRR4297981	SRP090506	SRS1715084	SRX2192593	SRA480453	GEO		Deciphering Pancreatic Islet ß Cell and a Cell Maturation Pathways and Characteristic Features at the Single-Cell Level	Pancreatic ß and a cells play essential roles in maintaining glucose homeostasis. However, the mechanisms by which these distinct cell populations are generated, expand, and mature during pancreas development remain unclear. In this study, we addressed this critical question by performing a single-cell transcriptomic analysis of mouse ß and a cells sorted from fetal to adult stages. We discovered that ß and a cells use different regulatory strategies for their maturation and that cell proliferation peaks at different developmental times. However, the quiescent and proliferative cells in both the ß lineage and a lineage are synchronous in their maturation states. The heterogeneity of juvenile ß cells reflects distinct cell-cycling phases, origins, and maturation states, whereas adult ß cells are relatively homogeneous at the transcriptomic level. These analyses provide not only a high-resolution roadmap for islet lineage development but also insights into the mechanisms of cellular heterogeneity, cell number expansion, and maturation of both ß and a cells. Overall design: The overall goal of this study was to define the roadmaps for pancreatic ß- and a-cell development. Specifically, we performed single-cell RNA-seq at various developmental stages of E17.5, P0, P3, P9, P15, P18 and P60 of ß- and a- cells (except P3), as well as endocrine progenitor cells at P0, which were fluorescence-activated cell sorting (FACS) sorted from Insulin-RFP, Gcg-Cre; Rosa-RFP or Ngn3-GFP mouse strains, respectively. To develop a workflow to decipher the maturation process through bulk-cell transcriptomic analysis, we performed RNA-seq using 3-5 × 10^4 sorted cells at various developmental time points as we have done in the single-cell study. The background strains of our mouse samples are: Ngn3-GFP mice: mixed background of C57BL/6 and C3H Ins1-RFP mice: mixed background of C57BL/6 and C3H Gcg-Cre, Rosa-RFP mice: mixed background of C57BL/6, CBA/J and C3H.		GSM2329200: P0_beta_#1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA from approximately 3-5 × 10^4 sorted β-cells was extracted by the RNeasy Micro Kit (Qiagen, 74004) followed by mRNA purification using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490). Strand-specific libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB #E7420) following manufacturer’s instructions.	Illumina HiSeq 2000	cell type;;beta cells|developmental stage;;P0|source_name;;P0 Ins1-RFP+|strain;;Ins1-RFP+|tissue;;Pancreas	GEO Accession;;GSM2329200		GSM2329200	P0_beta_#1	5324062490	26356745	2017-05-03 16:29:37	3533884152	5324062490	26356745	2	26356745	index:0,count:26356745,average:101,stdev:0|index:1,count:26356745,average:101,stdev:0	GSM2329200_r1				in_mesa	28467935	2.03	3.06	0.15	4377982082	4356958444	4170974441	4174559145	99.52	100.09	25466722	23706773	212.948	639.483	145	176181	79.12	83.15	27512840	20148938	27512840	20148938	78.44	78.83	27512840	19976254	27512840	19102980	688574227	15.73	0.76	0	4.69	0	0.24	0	0.14	0	0.00	0	2.99	0	25466722	0	202	0	200.33	0	2.47	0	0.02	0	1.89	0	0.02	0	280.72	0	0.26	0	200059	0	26356745	0	1234829	0	62633	0	38196	0	0	0	789194	0	6158	0	0	0	65639	0	9967332	0	26110	0	10065239	0	91.94	0	24231893	0	177883	9349085	52.557495657258	26356745.0	25466722.0	200059.0	1234829.0	62633.0	38196.0	0.0	789194.0	24231893.0	96.6	0.8	4.7	0.2	0.1	0.0	3.0	91.9	101	101	101.00	38	2662031245	24.8	25.1	24.8	25.2	0.0	36.1	22.7	bulk
1742894	SRR4297982	SRP090506	SRS1715085	SRX2192594	SRA480453	GEO		Deciphering Pancreatic Islet ß Cell and a Cell Maturation Pathways and Characteristic Features at the Single-Cell Level	Pancreatic ß and a cells play essential roles in maintaining glucose homeostasis. However, the mechanisms by which these distinct cell populations are generated, expand, and mature during pancreas development remain unclear. In this study, we addressed this critical question by performing a single-cell transcriptomic analysis of mouse ß and a cells sorted from fetal to adult stages. We discovered that ß and a cells use different regulatory strategies for their maturation and that cell proliferation peaks at different developmental times. However, the quiescent and proliferative cells in both the ß lineage and a lineage are synchronous in their maturation states. The heterogeneity of juvenile ß cells reflects distinct cell-cycling phases, origins, and maturation states, whereas adult ß cells are relatively homogeneous at the transcriptomic level. These analyses provide not only a high-resolution roadmap for islet lineage development but also insights into the mechanisms of cellular heterogeneity, cell number expansion, and maturation of both ß and a cells. Overall design: The overall goal of this study was to define the roadmaps for pancreatic ß- and a-cell development. Specifically, we performed single-cell RNA-seq at various developmental stages of E17.5, P0, P3, P9, P15, P18 and P60 of ß- and a- cells (except P3), as well as endocrine progenitor cells at P0, which were fluorescence-activated cell sorting (FACS) sorted from Insulin-RFP, Gcg-Cre; Rosa-RFP or Ngn3-GFP mouse strains, respectively. To develop a workflow to decipher the maturation process through bulk-cell transcriptomic analysis, we performed RNA-seq using 3-5 × 10^4 sorted cells at various developmental time points as we have done in the single-cell study. The background strains of our mouse samples are: Ngn3-GFP mice: mixed background of C57BL/6 and C3H Ins1-RFP mice: mixed background of C57BL/6 and C3H Gcg-Cre, Rosa-RFP mice: mixed background of C57BL/6, CBA/J and C3H.		GSM2329201: P0_beta_#2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA from approximately 3-5 × 10^4 sorted β-cells was extracted by the RNeasy Micro Kit (Qiagen, 74004) followed by mRNA purification using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490). Strand-specific libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB #E7420) following manufacturer’s instructions.	Illumina HiSeq 2000	cell type;;beta cells|developmental stage;;P0|source_name;;P0 Ins1-RFP+|strain;;Ins1-RFP+|tissue;;Pancreas	GEO Accession;;GSM2329201		GSM2329201	P0_beta_#2	2809186730	13906865	2017-05-03 16:29:37	1888252094	2809186730	13906865	2	13906865	index:0,count:13906865,average:101,stdev:0|index:1,count:13906865,average:101,stdev:0	GSM2329201_r1				in_mesa	28467935	2.02	3.0	0.14	2537758147	2510247598	2427544528	2411778495	98.92	99.35	13457319	11860876	272.604	1094.809	185	66586	78.39	81.98	14414276	10548702	14414276	10548702	78.82	78.96	14414276	10607474	14414276	10160131	435925330	17.18	0.97	0	4.24	0	0.26	0	0.16	0	0.00	0	2.81	0	13457319	0	202	0	200.45	0	2.23	0	0.01	0	1.98	0	0.01	0	325.10	0	0.29	0	134601	0	13906865	0	590003	0	36473	0	22097	0	0	0	390976	0	3441	0	0	0	37658	0	5646240	0	17091	0	5704430	0	92.52	0	12867316	0	194489	5655836	29.080492984179	13906865.0	13457319.0	134601.0	590003.0	36473.0	22097.0	0.0	390976.0	12867316.0	96.8	1.0	4.2	0.3	0.2	0.0	2.8	92.5	101	101	101.00	38	1404593365	24.6	25.2	24.8	25.4	0.0	35.9	21.2	bulk
1742910	SRR4297983	SRP090506	SRS1715086	SRX2192595	SRA480453	GEO		Deciphering Pancreatic Islet ß Cell and a Cell Maturation Pathways and Characteristic Features at the Single-Cell Level	Pancreatic ß and a cells play essential roles in maintaining glucose homeostasis. However, the mechanisms by which these distinct cell populations are generated, expand, and mature during pancreas development remain unclear. In this study, we addressed this critical question by performing a single-cell transcriptomic analysis of mouse ß and a cells sorted from fetal to adult stages. We discovered that ß and a cells use different regulatory strategies for their maturation and that cell proliferation peaks at different developmental times. However, the quiescent and proliferative cells in both the ß lineage and a lineage are synchronous in their maturation states. The heterogeneity of juvenile ß cells reflects distinct cell-cycling phases, origins, and maturation states, whereas adult ß cells are relatively homogeneous at the transcriptomic level. These analyses provide not only a high-resolution roadmap for islet lineage development but also insights into the mechanisms of cellular heterogeneity, cell number expansion, and maturation of both ß and a cells. Overall design: The overall goal of this study was to define the roadmaps for pancreatic ß- and a-cell development. Specifically, we performed single-cell RNA-seq at various developmental stages of E17.5, P0, P3, P9, P15, P18 and P60 of ß- and a- cells (except P3), as well as endocrine progenitor cells at P0, which were fluorescence-activated cell sorting (FACS) sorted from Insulin-RFP, Gcg-Cre; Rosa-RFP or Ngn3-GFP mouse strains, respectively. To develop a workflow to decipher the maturation process through bulk-cell transcriptomic analysis, we performed RNA-seq using 3-5 × 10^4 sorted cells at various developmental time points as we have done in the single-cell study. The background strains of our mouse samples are: Ngn3-GFP mice: mixed background of C57BL/6 and C3H Ins1-RFP mice: mixed background of C57BL/6 and C3H Gcg-Cre, Rosa-RFP mice: mixed background of C57BL/6, CBA/J and C3H.		GSM2329202: P3_beta_#1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA from approximately 3-5 × 10^4 sorted β-cells was extracted by the RNeasy Micro Kit (Qiagen, 74004) followed by mRNA purification using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490). Strand-specific libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB #E7420) following manufacturer’s instructions.	Illumina HiSeq 2000	cell type;;beta cells|developmental stage;;P3|source_name;;P3 Ins1-RFP+|strain;;Ins1-RFP+|tissue;;Pancreas	GEO Accession;;GSM2329202		GSM2329202	P3_beta_#1	4394780680	21756340	2017-05-03 16:29:37	3042063302	4394780680	21756340	2	21756340	index:0,count:21756340,average:101,stdev:0|index:1,count:21756340,average:101,stdev:0	GSM2329202_r1				in_mesa	28467935	3.92	2.76	0.05	3713752474	3701143709	3486907311	3492628354	99.66	100.16	21137141	18816254	233.881	908.710	145	129542	86.18	91.92	23382152	18215515	23382152	18215515	87.96	88.25	23382152	18591924	23382152	17489409	245001069	6.60	0.70	0	6.07	0	0.79	0	0.07	0	0.00	0	1.99	0	21137141	0	202	0	200.08	0	2.25	0	0.01	0	1.84	0	0.01	0	237.34	0	0.39	0	153156	0	21756340	0	1319757	0	171994	0	14887	0	0	0	432318	0	5933	0	0	0	59736	0	10896165	0	26822	0	10988656	0	91.09	0	19817384	0	206327	10714545	51.929921920059	21756340.0	21137141.0	153156.0	1319757.0	171994.0	14887.0	0.0	432318.0	19817384.0	97.2	0.7	6.1	0.8	0.1	0.0	2.0	91.1	101	101	101.00	38	2197390340	24.1	25.0	25.7	25.3	0.0	35.4	20.7	bulk
1742924	SRR4297984	SRP090506	SRS1715087	SRX2192596	SRA480453	GEO		Deciphering Pancreatic Islet ß Cell and a Cell Maturation Pathways and Characteristic Features at the Single-Cell Level	Pancreatic ß and a cells play essential roles in maintaining glucose homeostasis. However, the mechanisms by which these distinct cell populations are generated, expand, and mature during pancreas development remain unclear. In this study, we addressed this critical question by performing a single-cell transcriptomic analysis of mouse ß and a cells sorted from fetal to adult stages. We discovered that ß and a cells use different regulatory strategies for their maturation and that cell proliferation peaks at different developmental times. However, the quiescent and proliferative cells in both the ß lineage and a lineage are synchronous in their maturation states. The heterogeneity of juvenile ß cells reflects distinct cell-cycling phases, origins, and maturation states, whereas adult ß cells are relatively homogeneous at the transcriptomic level. These analyses provide not only a high-resolution roadmap for islet lineage development but also insights into the mechanisms of cellular heterogeneity, cell number expansion, and maturation of both ß and a cells. Overall design: The overall goal of this study was to define the roadmaps for pancreatic ß- and a-cell development. Specifically, we performed single-cell RNA-seq at various developmental stages of E17.5, P0, P3, P9, P15, P18 and P60 of ß- and a- cells (except P3), as well as endocrine progenitor cells at P0, which were fluorescence-activated cell sorting (FACS) sorted from Insulin-RFP, Gcg-Cre; Rosa-RFP or Ngn3-GFP mouse strains, respectively. To develop a workflow to decipher the maturation process through bulk-cell transcriptomic analysis, we performed RNA-seq using 3-5 × 10^4 sorted cells at various developmental time points as we have done in the single-cell study. The background strains of our mouse samples are: Ngn3-GFP mice: mixed background of C57BL/6 and C3H Ins1-RFP mice: mixed background of C57BL/6 and C3H Gcg-Cre, Rosa-RFP mice: mixed background of C57BL/6, CBA/J and C3H.		GSM2329203: P3_beta_#2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA from approximately 3-5 × 10^4 sorted β-cells was extracted by the RNeasy Micro Kit (Qiagen, 74004) followed by mRNA purification using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490). Strand-specific libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB #E7420) following manufacturer’s instructions.	Illumina HiSeq 2000	cell type;;beta cells|developmental stage;;P3|source_name;;P3 Ins1-RFP+|strain;;Ins1-RFP+|tissue;;Pancreas	GEO Accession;;GSM2329203		GSM2329203	P3_beta_#2	3554984264	17598932	2017-05-03 16:29:37	2363120757	3554984264	17598932	2	17598932	index:0,count:17598932,average:101,stdev:0|index:1,count:17598932,average:101,stdev:0	GSM2329203_r1				in_mesa	28467935	2.75	2.95	0.13	3144796252	3110461479	3002876941	2981292160	98.91	99.28	17067267	15303578	253.959	918.909	175	103399	78.34	82.09	18370911	13370970	18370911	13370970	79.47	79.41	18370911	13563546	18370911	12933695	541796312	17.23	1.13	0	4.43	0	0.51	0	0.13	0	0.00	0	2.38	0	17067267	0	202	0	200.57	0	2.13	0	0.01	0	1.96	0	0.01	0	346.21	0	0.25	0	199272	0	17598932	0	779478	0	89592	0	22877	0	0	0	419196	0	4123	0	0	0	43493	0	7449459	0	21270	0	7518345	0	92.55	0	16287789	0	191080	7487754	39.186487335148	17598932.0	17067267.0	199272.0	779478.0	89592.0	22877.0	0.0	419196.0	16287789.0	97.0	1.1	4.4	0.5	0.1	0.0	2.4	92.5	101	101	101.00	38	1777492132	24.7	25.1	24.9	25.3	0.0	36.0	21.4	bulk
1742941	SRR4297985	SRP090506	SRS1715088	SRX2192597	SRA480453	GEO		Deciphering Pancreatic Islet ß Cell and a Cell Maturation Pathways and Characteristic Features at the Single-Cell Level	Pancreatic ß and a cells play essential roles in maintaining glucose homeostasis. However, the mechanisms by which these distinct cell populations are generated, expand, and mature during pancreas development remain unclear. In this study, we addressed this critical question by performing a single-cell transcriptomic analysis of mouse ß and a cells sorted from fetal to adult stages. We discovered that ß and a cells use different regulatory strategies for their maturation and that cell proliferation peaks at different developmental times. However, the quiescent and proliferative cells in both the ß lineage and a lineage are synchronous in their maturation states. The heterogeneity of juvenile ß cells reflects distinct cell-cycling phases, origins, and maturation states, whereas adult ß cells are relatively homogeneous at the transcriptomic level. These analyses provide not only a high-resolution roadmap for islet lineage development but also insights into the mechanisms of cellular heterogeneity, cell number expansion, and maturation of both ß and a cells. Overall design: The overall goal of this study was to define the roadmaps for pancreatic ß- and a-cell development. Specifically, we performed single-cell RNA-seq at various developmental stages of E17.5, P0, P3, P9, P15, P18 and P60 of ß- and a- cells (except P3), as well as endocrine progenitor cells at P0, which were fluorescence-activated cell sorting (FACS) sorted from Insulin-RFP, Gcg-Cre; Rosa-RFP or Ngn3-GFP mouse strains, respectively. To develop a workflow to decipher the maturation process through bulk-cell transcriptomic analysis, we performed RNA-seq using 3-5 × 10^4 sorted cells at various developmental time points as we have done in the single-cell study. The background strains of our mouse samples are: Ngn3-GFP mice: mixed background of C57BL/6 and C3H Ins1-RFP mice: mixed background of C57BL/6 and C3H Gcg-Cre, Rosa-RFP mice: mixed background of C57BL/6, CBA/J and C3H.		GSM2329204: P9_beta_#1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA from approximately 3-5 × 10^4 sorted β-cells was extracted by the RNeasy Micro Kit (Qiagen, 74004) followed by mRNA purification using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490). Strand-specific libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB #E7420) following manufacturer’s instructions.	Illumina HiSeq 2000	cell type;;beta cells|developmental stage;;P9|source_name;;P9 Ins1-RFP+|strain;;Ins1-RFP+|tissue;;Pancreas	GEO Accession;;GSM2329204		GSM2329204	P9_beta_#1	5458459554	27022077	2017-05-03 16:29:37	3624602132	5458459554	27022077	2	27022077	index:0,count:27022077,average:101,stdev:0|index:1,count:27022077,average:101,stdev:0	GSM2329204_r1				in_mesa	28467935	2.77	2.78	0.12	4430369331	4398873209	4192381393	4181762020	99.29	99.75	26118353	24101023	212.770	661.709	145	202874	84.78	89.72	28802318	22143977	28802318	22143977	86.2	86.52	28802318	22515060	28802318	21353918	406944600	9.19	0.97	0	5.31	0	0.88	0	0.07	0	0.00	0	2.39	0	26118353	0	202	0	200.36	0	2.16	0	0.01	0	1.86	0	0.01	0	285.28	0	0.23	0	262580	0	27022077	0	1436153	0	237116	0	20196	0	0	0	646412	0	6469	0	0	0	67446	0	12839582	0	27605	0	12941102	0	91.34	0	24682200	0	195783	12380834	63.237533391561	27022077.0	26118353.0	262580.0	1436153.0	237116.0	20196.0	0.0	646412.0	24682200.0	96.7	1.0	5.3	0.9	0.1	0.0	2.4	91.3	101	101	101.00	38	2729229777	24.5	25.3	25.4	24.8	0.0	36.0	22.5	bulk
1742957	SRR4297986	SRP090506	SRS1715089	SRX2192598	SRA480453	GEO		Deciphering Pancreatic Islet ß Cell and a Cell Maturation Pathways and Characteristic Features at the Single-Cell Level	Pancreatic ß and a cells play essential roles in maintaining glucose homeostasis. However, the mechanisms by which these distinct cell populations are generated, expand, and mature during pancreas development remain unclear. In this study, we addressed this critical question by performing a single-cell transcriptomic analysis of mouse ß and a cells sorted from fetal to adult stages. We discovered that ß and a cells use different regulatory strategies for their maturation and that cell proliferation peaks at different developmental times. However, the quiescent and proliferative cells in both the ß lineage and a lineage are synchronous in their maturation states. The heterogeneity of juvenile ß cells reflects distinct cell-cycling phases, origins, and maturation states, whereas adult ß cells are relatively homogeneous at the transcriptomic level. These analyses provide not only a high-resolution roadmap for islet lineage development but also insights into the mechanisms of cellular heterogeneity, cell number expansion, and maturation of both ß and a cells. Overall design: The overall goal of this study was to define the roadmaps for pancreatic ß- and a-cell development. Specifically, we performed single-cell RNA-seq at various developmental stages of E17.5, P0, P3, P9, P15, P18 and P60 of ß- and a- cells (except P3), as well as endocrine progenitor cells at P0, which were fluorescence-activated cell sorting (FACS) sorted from Insulin-RFP, Gcg-Cre; Rosa-RFP or Ngn3-GFP mouse strains, respectively. To develop a workflow to decipher the maturation process through bulk-cell transcriptomic analysis, we performed RNA-seq using 3-5 × 10^4 sorted cells at various developmental time points as we have done in the single-cell study. The background strains of our mouse samples are: Ngn3-GFP mice: mixed background of C57BL/6 and C3H Ins1-RFP mice: mixed background of C57BL/6 and C3H Gcg-Cre, Rosa-RFP mice: mixed background of C57BL/6, CBA/J and C3H.		GSM2329205: P9_beta_#2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA from approximately 3-5 × 10^4 sorted β-cells was extracted by the RNeasy Micro Kit (Qiagen, 74004) followed by mRNA purification using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490). Strand-specific libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB #E7420) following manufacturer’s instructions.	Illumina HiSeq 2000	cell type;;beta cells|developmental stage;;P9|source_name;;P9 Ins1-RFP+|strain;;Ins1-RFP+|tissue;;Pancreas	GEO Accession;;GSM2329205		GSM2329205	P9_beta_#2	3289028034	16282317	2017-05-03 16:29:38	2197052431	3289028034	16282317	2	16282317	index:0,count:16282317,average:101,stdev:0|index:1,count:16282317,average:101,stdev:0	GSM2329205_r1				in_mesa	28467935	3.87	2.6	0.11	2951364046	2924813547	2779344076	2765964210	99.1	99.52	15506872	13594005	273.687	1022.923	203	88009	79.9	84.9	17152393	12389274	17152393	12389274	81.87	81.75	17152393	12695286	17152393	11930081	407803142	13.82	0.75	0	5.61	0	1.32	0	0.09	0	0.00	0	3.35	0	15506872	0	202	0	200.13	0	2.53	0	0.02	0	2.17	0	0.01	0	250.50	0	0.32	0	122472	0	16282317	0	913931	0	214913	0	14927	0	0	0	545605	0	3938	0	0	0	37929	0	7438335	0	19713	0	7499915	0	89.62	0	14592941	0	172885	7839700	45.346328484253	16282317.0	15506872.0	122472.0	913931.0	214913.0	14927.0	0.0	545605.0	14592941.0	95.2	0.8	5.6	1.3	0.1	0.0	3.4	89.6	101	101	101.00	38	1644514017	24.1	25.3	25.4	25.2	0.0	35.9	21.2	bulk
1742973	SRR4297987	SRP090506	SRS1715090	SRX2192599	SRA480453	GEO		Deciphering Pancreatic Islet ß Cell and a Cell Maturation Pathways and Characteristic Features at the Single-Cell Level	Pancreatic ß and a cells play essential roles in maintaining glucose homeostasis. However, the mechanisms by which these distinct cell populations are generated, expand, and mature during pancreas development remain unclear. In this study, we addressed this critical question by performing a single-cell transcriptomic analysis of mouse ß and a cells sorted from fetal to adult stages. We discovered that ß and a cells use different regulatory strategies for their maturation and that cell proliferation peaks at different developmental times. However, the quiescent and proliferative cells in both the ß lineage and a lineage are synchronous in their maturation states. The heterogeneity of juvenile ß cells reflects distinct cell-cycling phases, origins, and maturation states, whereas adult ß cells are relatively homogeneous at the transcriptomic level. These analyses provide not only a high-resolution roadmap for islet lineage development but also insights into the mechanisms of cellular heterogeneity, cell number expansion, and maturation of both ß and a cells. Overall design: The overall goal of this study was to define the roadmaps for pancreatic ß- and a-cell development. Specifically, we performed single-cell RNA-seq at various developmental stages of E17.5, P0, P3, P9, P15, P18 and P60 of ß- and a- cells (except P3), as well as endocrine progenitor cells at P0, which were fluorescence-activated cell sorting (FACS) sorted from Insulin-RFP, Gcg-Cre; Rosa-RFP or Ngn3-GFP mouse strains, respectively. To develop a workflow to decipher the maturation process through bulk-cell transcriptomic analysis, we performed RNA-seq using 3-5 × 10^4 sorted cells at various developmental time points as we have done in the single-cell study. The background strains of our mouse samples are: Ngn3-GFP mice: mixed background of C57BL/6 and C3H Ins1-RFP mice: mixed background of C57BL/6 and C3H Gcg-Cre, Rosa-RFP mice: mixed background of C57BL/6, CBA/J and C3H.		GSM2329206: P15_beta_#1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA from approximately 3-5 × 10^4 sorted β-cells was extracted by the RNeasy Micro Kit (Qiagen, 74004) followed by mRNA purification using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490). Strand-specific libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB #E7420) following manufacturer’s instructions.	Illumina HiSeq 2000	cell type;;beta cells|developmental stage;;P15|source_name;;P15 Ins1-RFP+|strain;;Ins1-RFP+|tissue;;Pancreas	GEO Accession;;GSM2329206		GSM2329206	P15_beta_#1	4298363656	21279028	2017-05-03 16:29:38	2981333373	4298363656	21279028	2	21279028	index:0,count:21279028,average:101,stdev:0|index:1,count:21279028,average:101,stdev:0	GSM2329206_r1				in_mesa	28467935	6.4	2.47	0.06	3577569237	3548601389	3313867226	3309179097	99.19	99.86	20617387	18609964	227.337	816.271	145	139236	84.74	91.64	23096245	17470415	23096245	17470415	87.35	87.76	23096245	18009886	23096245	16729278	218721588	6.11	0.58	0	7.30	0	0.90	0	0.06	0	0.00	0	2.15	0	20617387	0	202	0	199.99	0	2.41	0	0.01	0	1.92	0	0.01	0	301.59	0	0.40	0	124240	0	21279028	0	1553788	0	191483	0	12697	0	0	0	457461	0	5128	0	0	0	52360	0	10346885	0	23494	0	10427867	0	89.59	0	19063599	0	180961	10118355	55.914561701140	21279028.0	20617387.0	124240.0	1553788.0	191483.0	12697.0	0.0	457461.0	19063599.0	96.9	0.6	7.3	0.9	0.1	0.0	2.1	89.6	101	101	101.00	38	2149181828	24.2	24.7	25.8	25.2	0.0	35.3	20.5	bulk
1742991	SRR4297988	SRP090506	SRS1715091	SRX2192600	SRA480453	GEO		Deciphering Pancreatic Islet ß Cell and a Cell Maturation Pathways and Characteristic Features at the Single-Cell Level	Pancreatic ß and a cells play essential roles in maintaining glucose homeostasis. However, the mechanisms by which these distinct cell populations are generated, expand, and mature during pancreas development remain unclear. In this study, we addressed this critical question by performing a single-cell transcriptomic analysis of mouse ß and a cells sorted from fetal to adult stages. We discovered that ß and a cells use different regulatory strategies for their maturation and that cell proliferation peaks at different developmental times. However, the quiescent and proliferative cells in both the ß lineage and a lineage are synchronous in their maturation states. The heterogeneity of juvenile ß cells reflects distinct cell-cycling phases, origins, and maturation states, whereas adult ß cells are relatively homogeneous at the transcriptomic level. These analyses provide not only a high-resolution roadmap for islet lineage development but also insights into the mechanisms of cellular heterogeneity, cell number expansion, and maturation of both ß and a cells. Overall design: The overall goal of this study was to define the roadmaps for pancreatic ß- and a-cell development. Specifically, we performed single-cell RNA-seq at various developmental stages of E17.5, P0, P3, P9, P15, P18 and P60 of ß- and a- cells (except P3), as well as endocrine progenitor cells at P0, which were fluorescence-activated cell sorting (FACS) sorted from Insulin-RFP, Gcg-Cre; Rosa-RFP or Ngn3-GFP mouse strains, respectively. To develop a workflow to decipher the maturation process through bulk-cell transcriptomic analysis, we performed RNA-seq using 3-5 × 10^4 sorted cells at various developmental time points as we have done in the single-cell study. The background strains of our mouse samples are: Ngn3-GFP mice: mixed background of C57BL/6 and C3H Ins1-RFP mice: mixed background of C57BL/6 and C3H Gcg-Cre, Rosa-RFP mice: mixed background of C57BL/6, CBA/J and C3H.		GSM2329207: P15_beta_#2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA from approximately 3-5 × 10^4 sorted β-cells was extracted by the RNeasy Micro Kit (Qiagen, 74004) followed by mRNA purification using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490). Strand-specific libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB #E7420) following manufacturer’s instructions.	Illumina HiSeq 2000	cell type;;beta cells|developmental stage;;P15|source_name;;P15 Ins1-RFP+|strain;;Ins1-RFP+|tissue;;Pancreas	GEO Accession;;GSM2329207		GSM2329207	P15_beta_#2	4502269324	22288462	2017-05-03 16:29:38	3003452363	4502269324	22288462	2	22288462	index:0,count:22288462,average:101,stdev:0|index:1,count:22288462,average:101,stdev:0	GSM2329207_r1				in_mesa	28467935	4.42	2.69	0.06	3907989002	3892068895	3676444304	3680933842	99.59	100.12	21788430	19552486	240.775	870.427	145	133700	85.8	91.31	23857330	18695461	23857330	18695461	87.49	87.77	23857330	19061739	23857330	17969841	288336024	7.38	0.51	0	5.90	0	0.60	0	0.07	0	0.00	0	1.57	0	21788430	0	202	0	200.35	0	2.33	0	0.01	0	1.84	0	0.01	0	239.52	0	0.26	0	114099	0	22288462	0	1314406	0	134636	0	15590	0	0	0	349806	0	5778	0	0	0	58714	0	10945178	0	24335	0	11034005	0	91.86	0	20474024	0	189695	10779847	56.827259548222	22288462.0	21788430.0	114099.0	1314406.0	134636.0	15590.0	0.0	349806.0	20474024.0	97.8	0.5	5.9	0.6	0.1	0.0	1.6	91.9	101	101	101.00	38	2251134662	24.1	25.1	25.7	25.1	0.0	35.9	21.6	bulk
1743006	SRR4297989	SRP090506	SRS1715092	SRX2192601	SRA480453	GEO		Deciphering Pancreatic Islet ß Cell and a Cell Maturation Pathways and Characteristic Features at the Single-Cell Level	Pancreatic ß and a cells play essential roles in maintaining glucose homeostasis. However, the mechanisms by which these distinct cell populations are generated, expand, and mature during pancreas development remain unclear. In this study, we addressed this critical question by performing a single-cell transcriptomic analysis of mouse ß and a cells sorted from fetal to adult stages. We discovered that ß and a cells use different regulatory strategies for their maturation and that cell proliferation peaks at different developmental times. However, the quiescent and proliferative cells in both the ß lineage and a lineage are synchronous in their maturation states. The heterogeneity of juvenile ß cells reflects distinct cell-cycling phases, origins, and maturation states, whereas adult ß cells are relatively homogeneous at the transcriptomic level. These analyses provide not only a high-resolution roadmap for islet lineage development but also insights into the mechanisms of cellular heterogeneity, cell number expansion, and maturation of both ß and a cells. Overall design: The overall goal of this study was to define the roadmaps for pancreatic ß- and a-cell development. Specifically, we performed single-cell RNA-seq at various developmental stages of E17.5, P0, P3, P9, P15, P18 and P60 of ß- and a- cells (except P3), as well as endocrine progenitor cells at P0, which were fluorescence-activated cell sorting (FACS) sorted from Insulin-RFP, Gcg-Cre; Rosa-RFP or Ngn3-GFP mouse strains, respectively. To develop a workflow to decipher the maturation process through bulk-cell transcriptomic analysis, we performed RNA-seq using 3-5 × 10^4 sorted cells at various developmental time points as we have done in the single-cell study. The background strains of our mouse samples are: Ngn3-GFP mice: mixed background of C57BL/6 and C3H Ins1-RFP mice: mixed background of C57BL/6 and C3H Gcg-Cre, Rosa-RFP mice: mixed background of C57BL/6, CBA/J and C3H.		GSM2329208: P18_beta_#1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA from approximately 3-5 × 10^4 sorted β-cells was extracted by the RNeasy Micro Kit (Qiagen, 74004) followed by mRNA purification using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490). Strand-specific libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB #E7420) following manufacturer’s instructions.	Illumina HiSeq 2000	cell type;;beta cells|developmental stage;;P18|source_name;;P18 Ins1-RFP+|strain;;Ins1-RFP+|tissue;;Pancreas	GEO Accession;;GSM2329208		GSM2329208	P18_beta_#1	4430734458	21934329	2017-05-03 16:29:38	3063925687	4430734458	21934329	2	21934329	index:0,count:21934329,average:101,stdev:0|index:1,count:21934329,average:101,stdev:0	GSM2329208_r1				in_mesa	28467935	5.23	2.53	0.07	3681228879	3652155893	3446034145	3437139674	99.21	99.74	21217681	19206924	229.413	816.000	145	148142	85.06	91.01	23527007	18046857	23527007	18046857	87.02	87.36	23527007	18462622	23527007	17321975	256178696	6.96	0.62	0	6.33	0	0.87	0	0.07	0	0.00	0	2.33	0	21217681	0	202	0	199.99	0	2.34	0	0.01	0	2.00	0	0.01	0	228.88	0	0.40	0	136784	0	21934329	0	1388945	0	191388	0	14678	0	0	0	510582	0	5110	0	0	0	53483	0	10666442	0	26322	0	10751357	0	90.40	0	19828736	0	174986	10426481	59.584658201228	21934329.0	21217681.0	136784.0	1388945.0	191388.0	14678.0	0.0	510582.0	19828736.0	96.7	0.6	6.3	0.9	0.1	0.0	2.3	90.4	101	101	101.00	38	2215367229	24.2	25.0	25.9	24.9	0.0	35.3	20.5	bulk
1743117	SRR4297990	SRP090506	SRS1715093	SRX2192602	SRA480453	GEO		Deciphering Pancreatic Islet ß Cell and a Cell Maturation Pathways and Characteristic Features at the Single-Cell Level	Pancreatic ß and a cells play essential roles in maintaining glucose homeostasis. However, the mechanisms by which these distinct cell populations are generated, expand, and mature during pancreas development remain unclear. In this study, we addressed this critical question by performing a single-cell transcriptomic analysis of mouse ß and a cells sorted from fetal to adult stages. We discovered that ß and a cells use different regulatory strategies for their maturation and that cell proliferation peaks at different developmental times. However, the quiescent and proliferative cells in both the ß lineage and a lineage are synchronous in their maturation states. The heterogeneity of juvenile ß cells reflects distinct cell-cycling phases, origins, and maturation states, whereas adult ß cells are relatively homogeneous at the transcriptomic level. These analyses provide not only a high-resolution roadmap for islet lineage development but also insights into the mechanisms of cellular heterogeneity, cell number expansion, and maturation of both ß and a cells. Overall design: The overall goal of this study was to define the roadmaps for pancreatic ß- and a-cell development. Specifically, we performed single-cell RNA-seq at various developmental stages of E17.5, P0, P3, P9, P15, P18 and P60 of ß- and a- cells (except P3), as well as endocrine progenitor cells at P0, which were fluorescence-activated cell sorting (FACS) sorted from Insulin-RFP, Gcg-Cre; Rosa-RFP or Ngn3-GFP mouse strains, respectively. To develop a workflow to decipher the maturation process through bulk-cell transcriptomic analysis, we performed RNA-seq using 3-5 × 10^4 sorted cells at various developmental time points as we have done in the single-cell study. The background strains of our mouse samples are: Ngn3-GFP mice: mixed background of C57BL/6 and C3H Ins1-RFP mice: mixed background of C57BL/6 and C3H Gcg-Cre, Rosa-RFP mice: mixed background of C57BL/6, CBA/J and C3H.		GSM2329209: P18_beta_#2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA from approximately 3-5 × 10^4 sorted β-cells was extracted by the RNeasy Micro Kit (Qiagen, 74004) followed by mRNA purification using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490). Strand-specific libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB #E7420) following manufacturer’s instructions.	Illumina HiSeq 2000	cell type;;beta cells|developmental stage;;P18|source_name;;P18 Ins1-RFP+|strain;;Ins1-RFP+|tissue;;Pancreas	GEO Accession;;GSM2329209		GSM2329209	P18_beta_#2	3452105260	17089630	2017-05-03 16:29:38	2153409046	3452105260	17089630	2	17089630	index:0,count:17089630,average:101,stdev:0|index:1,count:17089630,average:101,stdev:0	GSM2329209_r1				in_mesa	28467935	8.42	2.0	0.04	2899030850	2879585907	2600725889	2600481709	99.33	99.99	15959719	14261787	246.383	856.213	174	99414	81.34	90.86	19105424	12981397	19105424	12981397	86.78	86.54	19105424	13849756	19105424	12363950	184488104	6.36	0.55	0	9.79	0	3.37	0	0.05	0	0.00	0	3.20	0	15959719	0	202	0	200.10	0	2.71	0	0.02	0	2.17	0	0.02	0	142.74	0	0.40	0	94738	0	17089630	0	1673210	0	575363	0	8072	0	0	0	546476	0	3506	0	0	0	34795	0	7849894	0	16749	0	7904944	0	83.60	0	14286509	0	168327	8717217	51.787395961432	17089630.0	15959719.0	94738.0	1673210.0	575363.0	8072.0	0.0	546476.0	14286509.0	93.4	0.6	9.8	3.4	0.0	0.0	3.2	83.6	101	101	101.00	38	1726052630	23.9	24.9	25.9	25.1	0.2	36.1	21.5	bulk
1743135	SRR4297991	SRP090506	SRS1715094	SRX2192603	SRA480453	GEO		Deciphering Pancreatic Islet ß Cell and a Cell Maturation Pathways and Characteristic Features at the Single-Cell Level	Pancreatic ß and a cells play essential roles in maintaining glucose homeostasis. However, the mechanisms by which these distinct cell populations are generated, expand, and mature during pancreas development remain unclear. In this study, we addressed this critical question by performing a single-cell transcriptomic analysis of mouse ß and a cells sorted from fetal to adult stages. We discovered that ß and a cells use different regulatory strategies for their maturation and that cell proliferation peaks at different developmental times. However, the quiescent and proliferative cells in both the ß lineage and a lineage are synchronous in their maturation states. The heterogeneity of juvenile ß cells reflects distinct cell-cycling phases, origins, and maturation states, whereas adult ß cells are relatively homogeneous at the transcriptomic level. These analyses provide not only a high-resolution roadmap for islet lineage development but also insights into the mechanisms of cellular heterogeneity, cell number expansion, and maturation of both ß and a cells. Overall design: The overall goal of this study was to define the roadmaps for pancreatic ß- and a-cell development. Specifically, we performed single-cell RNA-seq at various developmental stages of E17.5, P0, P3, P9, P15, P18 and P60 of ß- and a- cells (except P3), as well as endocrine progenitor cells at P0, which were fluorescence-activated cell sorting (FACS) sorted from Insulin-RFP, Gcg-Cre; Rosa-RFP or Ngn3-GFP mouse strains, respectively. To develop a workflow to decipher the maturation process through bulk-cell transcriptomic analysis, we performed RNA-seq using 3-5 × 10^4 sorted cells at various developmental time points as we have done in the single-cell study. The background strains of our mouse samples are: Ngn3-GFP mice: mixed background of C57BL/6 and C3H Ins1-RFP mice: mixed background of C57BL/6 and C3H Gcg-Cre, Rosa-RFP mice: mixed background of C57BL/6, CBA/J and C3H.		GSM2329210: P60_beta_#1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA from approximately 3-5 × 10^4 sorted β-cells was extracted by the RNeasy Micro Kit (Qiagen, 74004) followed by mRNA purification using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490). Strand-specific libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB #E7420) following manufacturer’s instructions.	Illumina HiSeq 2000	cell type;;beta cells|developmental stage;;P60|source_name;;P60 Ins1-RFP+|strain;;Ins1-RFP+|tissue;;Pancreas	GEO Accession;;GSM2329210		GSM2329210	P60_beta_#1	4344816788	21508994	2017-05-03 16:29:38	2888948998	4344816788	21508994	2	21508994	index:0,count:21508994,average:101,stdev:0|index:1,count:21508994,average:101,stdev:0	GSM2329210_r1				in_mesa	28467935	2.79	2.32	0.06	3469340765	3429890862	3237520564	3215157942	98.86	99.31	20371946	18931235	214.544	624.339	145	153316	84.08	90.31	23630829	17128591	23630829	17128591	87.23	87.41	23630829	17769678	23630829	16578146	280841594	8.09	0.68	0	6.54	0	2.62	0	0.07	0	0.00	0	2.60	0	20371946	0	202	0	200.35	0	2.15	0	0.01	0	1.96	0	0.01	0	169.44	0	0.23	0	145240	0	21508994	0	1406055	0	563143	0	14530	0	0	0	559375	0	4094	0	0	0	47413	0	10303340	0	20731	0	10375578	0	88.18	0	18965891	0	161703	10937514	67.639524313093	21508994.0	20371946.0	145240.0	1406055.0	563143.0	14530.0	0.0	559375.0	18965891.0	94.7	0.7	6.5	2.6	0.1	0.0	2.6	88.2	101	101	101.00	38	2172408394	24.3	25.3	25.8	24.6	0.0	35.9	22.3	bulk
1743151	SRR4297992	SRP090506	SRS1715095	SRX2192604	SRA480453	GEO		Deciphering Pancreatic Islet ß Cell and a Cell Maturation Pathways and Characteristic Features at the Single-Cell Level	Pancreatic ß and a cells play essential roles in maintaining glucose homeostasis. However, the mechanisms by which these distinct cell populations are generated, expand, and mature during pancreas development remain unclear. In this study, we addressed this critical question by performing a single-cell transcriptomic analysis of mouse ß and a cells sorted from fetal to adult stages. We discovered that ß and a cells use different regulatory strategies for their maturation and that cell proliferation peaks at different developmental times. However, the quiescent and proliferative cells in both the ß lineage and a lineage are synchronous in their maturation states. The heterogeneity of juvenile ß cells reflects distinct cell-cycling phases, origins, and maturation states, whereas adult ß cells are relatively homogeneous at the transcriptomic level. These analyses provide not only a high-resolution roadmap for islet lineage development but also insights into the mechanisms of cellular heterogeneity, cell number expansion, and maturation of both ß and a cells. Overall design: The overall goal of this study was to define the roadmaps for pancreatic ß- and a-cell development. Specifically, we performed single-cell RNA-seq at various developmental stages of E17.5, P0, P3, P9, P15, P18 and P60 of ß- and a- cells (except P3), as well as endocrine progenitor cells at P0, which were fluorescence-activated cell sorting (FACS) sorted from Insulin-RFP, Gcg-Cre; Rosa-RFP or Ngn3-GFP mouse strains, respectively. To develop a workflow to decipher the maturation process through bulk-cell transcriptomic analysis, we performed RNA-seq using 3-5 × 10^4 sorted cells at various developmental time points as we have done in the single-cell study. The background strains of our mouse samples are: Ngn3-GFP mice: mixed background of C57BL/6 and C3H Ins1-RFP mice: mixed background of C57BL/6 and C3H Gcg-Cre, Rosa-RFP mice: mixed background of C57BL/6, CBA/J and C3H.		GSM2329211: P60_beta_#2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA from approximately 3-5 × 10^4 sorted β-cells was extracted by the RNeasy Micro Kit (Qiagen, 74004) followed by mRNA purification using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490). Strand-specific libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB #E7420) following manufacturer’s instructions.	Illumina HiSeq 2000	cell type;;beta cells|developmental stage;;P60|source_name;;P60 Ins1-RFP+|strain;;Ins1-RFP+|tissue;;Pancreas	GEO Accession;;GSM2329211		GSM2329211	P60_beta_#2	4587922374	22712487	2017-05-03 16:29:38	3098847696	4587922374	22712487	2	22712487	index:0,count:22712487,average:101,stdev:0|index:1,count:22712487,average:101,stdev:0	GSM2329211_r1				in_mesa	28467935	5.05	2.61	0.05	3914916704	3888813741	3668700575	3659453635	99.33	99.75	21985278	19820115	242.176	857.108	145	151955	87.26	93.22	24502763	19185019	24502763	19185019	90.34	90.49	24502763	19861762	24502763	18621845	216360533	5.53	0.74	0	6.19	0	1.42	0	0.06	0	0.00	0	1.72	0	21985278	0	202	0	200.44	0	2.05	0	0.01	0	1.76	0	0.01	0	210.73	0	0.23	0	168886	0	22712487	0	1405753	0	321963	0	13601	0	0	0	391645	0	5397	0	0	0	58729	0	11710269	0	25095	0	11799490	0	90.61	0	20579525	0	175242	11803178	67.353591034113	22712487.0	21985278.0	168886.0	1405753.0	321963.0	13601.0	0.0	391645.0	20579525.0	96.8	0.7	6.2	1.4	0.1	0.0	1.7	90.6	101	101	101.00	38	2293961187	24.6	24.8	25.5	25.1	0.0	35.8	21.7	bulk
2819602	SRR4413830	SRP091381	SRS1738015	SRX2236901	SRA483373	GEO		Systematic identification and comparison of expressed profiles of lncRNAs and circRNAs in male and female germline stem cells	Male and female germline stem cells are critical for passing genetic information from generation to generation. Accumulating evidences indicate that long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) play important roles in self-renewal and differentiation of germline stem cells. However, the mechanisms remain largely unknown. In this study, we explored the mRNAs, lncRNAs and circRNAs expression profiles of male and female germline stem cells through high-throughput sequencing. Overall design: mRNA, lncRNA and circRNA profiles of the mouse spermatogonial stem cells (SSCs) and  female germline stem cells (FGSCs) by strand- specific RNA- seq		GSM2341383: SSCs rep1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA from the SSCs and FGSCs were isolated using TRIzol reagent (Invitrogen, life Technologies, USA) according to the manufacturer's protocol. Total RNA from each sample was quantified using Agilent 2100, and RNA integrity was assessed using Agilent 2100. After extracting the total RNA from samples, mRNA and non-coding RNAs are enriched by removing rRNA from the total RNA with kit. By using the fragmentation buffer, the mRNAs and non-coding RNAs are fragmented into short fragments (about 200~500nt), then the first-strand cDNA is synthesized by random hexamer-primer using the fragments as templates, and dTTP is substituted by dUTP during the synthesis of the second strand. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters, then the second strand is degraded using UNG(Uracil-N-Glycosylase) finally. After agarose gel electrophoresis, the suitable fragments are selected for the PCR amplification as templates. During the QC steps, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used in quantification and qualification of the sample library. At last, the library could be sequenced using Illumina HiSeqTM 2000 when necessary.	Illumina HiSeq 2000	age;;3–5 days|cell type;;spermatogonial stem cells|source_name;;SSCs|strain;;C57BL/6|tissue;;testis	GEO Accession;;GSM2341383		GSM2341383	SSCs rep1	7641403800	38207019	2017-06-12 15:56:15	3235385180	7641403800	38207019	2	38207019	index:0,count:38207019,average:100,stdev:0|index:1,count:38207019,average:100,stdev:0	GSM2341383_r1				in_mesa	28404936	5.49	2.62	0.18	5472542605	5388698422	4829111926	4764753622	98.47	98.67	33503343	31467094	192.103	666.319	145	259035	66.78	76.06	39840867	22373950	39840867	22373950	69.97	70.74	39840867	23440880	39840867	20809257	1088555000	19.89	1.53	0	10.70	0	0.37	0	0.18	0	0.00	0	11.76	0	33503343	0	200	0	198.23	0	2.59	0	0.02	0	1.94	0	0.01	0	138.10	0	0.43	0	582802	0	38207019	0	4086539	0	140776	0	70386	0	0	0	4492514	0	8145	0	0	0	284746	0	10787730	0	26213	0	11106834	0	76.99	0	29416804	0	241730	9902288	40.964249369131	38207019.0	33503343.0	582802.0	4086539.0	140776.0	70386.0	0.0	4492514.0	29416804.0	87.7	1.5	10.7	0.4	0.2	0.0	11.8	77.0	100	100	100.00	7	3820701900	22.5	26.5	26.6	24.4	0.0	38.5	27.4	bulk
2819635	SRR4413831	SRP091381	SRS1738014	SRX2236902	SRA483373	GEO		Systematic identification and comparison of expressed profiles of lncRNAs and circRNAs in male and female germline stem cells	Male and female germline stem cells are critical for passing genetic information from generation to generation. Accumulating evidences indicate that long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) play important roles in self-renewal and differentiation of germline stem cells. However, the mechanisms remain largely unknown. In this study, we explored the mRNAs, lncRNAs and circRNAs expression profiles of male and female germline stem cells through high-throughput sequencing. Overall design: mRNA, lncRNA and circRNA profiles of the mouse spermatogonial stem cells (SSCs) and  female germline stem cells (FGSCs) by strand- specific RNA- seq		GSM2341384: SSCs rep2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA from the SSCs and FGSCs were isolated using TRIzol reagent (Invitrogen, life Technologies, USA) according to the manufacturer's protocol. Total RNA from each sample was quantified using Agilent 2100, and RNA integrity was assessed using Agilent 2100. After extracting the total RNA from samples, mRNA and non-coding RNAs are enriched by removing rRNA from the total RNA with kit. By using the fragmentation buffer, the mRNAs and non-coding RNAs are fragmented into short fragments (about 200~500nt), then the first-strand cDNA is synthesized by random hexamer-primer using the fragments as templates, and dTTP is substituted by dUTP during the synthesis of the second strand. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters, then the second strand is degraded using UNG(Uracil-N-Glycosylase) finally. After agarose gel electrophoresis, the suitable fragments are selected for the PCR amplification as templates. During the QC steps, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used in quantification and qualification of the sample library. At last, the library could be sequenced using Illumina HiSeqTM 2000 when necessary.	Illumina HiSeq 2000	age;;3–5 days|cell type;;spermatogonial stem cells|source_name;;SSCs|strain;;C57BL/6|tissue;;testis	GEO Accession;;GSM2341384		GSM2341384	SSCs rep2	8738544200	43692721	2017-06-12 15:56:15	3508243218	8738544200	43692721	2	43692721	index:0,count:43692721,average:100,stdev:0|index:1,count:43692721,average:100,stdev:0	GSM2341384_r1				in_mesa	28404936	5.34	2.62	0.18	6135912545	6031942955	5440165047	5359327144	98.31	98.51	38234581	36073929	185.590	644.477	136	319920	66.16	74.97	45348499	25297475	45348499	25297475	69.25	69.84	45348499	26476702	45348499	23568338	1278424359	20.84	1.81	0	10.28	0	0.41	0	0.20	0	0.00	0	11.88	0	38234581	0	200	0	198.24	0	2.60	0	0.02	0	1.91	0	0.01	0	147.00	0	0.39	0	791297	0	43692721	0	4490052	0	177152	0	88690	0	0	0	5192298	0	9462	0	0	0	311727	0	12211306	0	30400	0	12562895	0	77.23	0	33744529	0	252708	11056010	43.750138499770	43692721.0	38234581.0	791297.0	4490052.0	177152.0	88690.0	0.0	5192298.0	33744529.0	87.5	1.8	10.3	0.4	0.2	0.0	11.9	77.2	100	100	100.00	7	4369272100	22.5	26.5	26.7	24.3	0.0	39.5	30.0	bulk
2819665	SRR4413832	SRP091381	SRS1738017	SRX2236903	SRA483373	GEO		Systematic identification and comparison of expressed profiles of lncRNAs and circRNAs in male and female germline stem cells	Male and female germline stem cells are critical for passing genetic information from generation to generation. Accumulating evidences indicate that long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) play important roles in self-renewal and differentiation of germline stem cells. However, the mechanisms remain largely unknown. In this study, we explored the mRNAs, lncRNAs and circRNAs expression profiles of male and female germline stem cells through high-throughput sequencing. Overall design: mRNA, lncRNA and circRNA profiles of the mouse spermatogonial stem cells (SSCs) and  female germline stem cells (FGSCs) by strand- specific RNA- seq		GSM2341385: SSCs rep3; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA from the SSCs and FGSCs were isolated using TRIzol reagent (Invitrogen, life Technologies, USA) according to the manufacturer's protocol. Total RNA from each sample was quantified using Agilent 2100, and RNA integrity was assessed using Agilent 2100. After extracting the total RNA from samples, mRNA and non-coding RNAs are enriched by removing rRNA from the total RNA with kit. By using the fragmentation buffer, the mRNAs and non-coding RNAs are fragmented into short fragments (about 200~500nt), then the first-strand cDNA is synthesized by random hexamer-primer using the fragments as templates, and dTTP is substituted by dUTP during the synthesis of the second strand. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters, then the second strand is degraded using UNG(Uracil-N-Glycosylase) finally. After agarose gel electrophoresis, the suitable fragments are selected for the PCR amplification as templates. During the QC steps, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used in quantification and qualification of the sample library. At last, the library could be sequenced using Illumina HiSeqTM 2000 when necessary.	Illumina HiSeq 2000	age;;3–5 days|cell type;;spermatogonial stem cells|source_name;;SSCs|strain;;C57BL/6|tissue;;testis	GEO Accession;;GSM2341385		GSM2341385	SSCs rep3	8611273600	43056368	2017-06-12 15:56:16	3384078637	8611273600	43056368	2	43056368	index:0,count:43056368,average:100,stdev:0|index:1,count:43056368,average:100,stdev:0	GSM2341385_r1				in_mesa	28404936	5.39	2.35	0.16	5859150203	5825711223	5129999299	5125981984	99.43	99.92	36776973	34971280	181.916	565.436	137	320004	64.35	73.89	44177004	23667052	44177004	23667052	64.4	65.03	44177004	23684693	44177004	20829752	1164213653	19.87	1.23	0	11.02	0	0.33	0	0.18	0	0.00	0	14.08	0	36776973	0	200	0	197.48	0	2.86	0	0.02	0	3.09	0	0.03	0	139.39	0	0.46	0	528766	0	43056368	0	4746788	0	141640	0	76436	0	0	0	6061319	0	7978	0	0	0	313129	0	10364546	0	36592	0	10722245	0	74.39	0	32030185	0	246743	9390076	38.056098855895	43056368.0	36776973.0	528766.0	4746788.0	141640.0	76436.0	0.0	6061319.0	32030185.0	85.4	1.2	11.0	0.3	0.2	0.0	14.1	74.4	100	100	100.00	7	4305636800	21.9	26.8	27.6	23.7	0.0	39.3	29.6	bulk
2819698	SRR4413833	SRP091381	SRS1738016	SRX2236904	SRA483373	GEO		Systematic identification and comparison of expressed profiles of lncRNAs and circRNAs in male and female germline stem cells	Male and female germline stem cells are critical for passing genetic information from generation to generation. Accumulating evidences indicate that long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) play important roles in self-renewal and differentiation of germline stem cells. However, the mechanisms remain largely unknown. In this study, we explored the mRNAs, lncRNAs and circRNAs expression profiles of male and female germline stem cells through high-throughput sequencing. Overall design: mRNA, lncRNA and circRNA profiles of the mouse spermatogonial stem cells (SSCs) and  female germline stem cells (FGSCs) by strand- specific RNA- seq		GSM2341386: FGSCs rep1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA from the SSCs and FGSCs were isolated using TRIzol reagent (Invitrogen, life Technologies, USA) according to the manufacturer's protocol. Total RNA from each sample was quantified using Agilent 2100, and RNA integrity was assessed using Agilent 2100. After extracting the total RNA from samples, mRNA and non-coding RNAs are enriched by removing rRNA from the total RNA with kit. By using the fragmentation buffer, the mRNAs and non-coding RNAs are fragmented into short fragments (about 200~500nt), then the first-strand cDNA is synthesized by random hexamer-primer using the fragments as templates, and dTTP is substituted by dUTP during the synthesis of the second strand. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters, then the second strand is degraded using UNG(Uracil-N-Glycosylase) finally. After agarose gel electrophoresis, the suitable fragments are selected for the PCR amplification as templates. During the QC steps, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used in quantification and qualification of the sample library. At last, the library could be sequenced using Illumina HiSeqTM 2000 when necessary.	Illumina HiSeq 2000	age;;6 days|cell type;;germline stem cells|source_name;;FGSCs|strain;;C57BL/6|tissue;;ovary	GEO Accession;;GSM2341386		GSM2341386	FGSCs rep1	8719380200	43596901	2017-06-12 15:56:16	3149790788	8719380200	43596901	2	43596901	index:0,count:43596901,average:100,stdev:0|index:1,count:43596901,average:100,stdev:0	GSM2341386_r1				in_mesa	28404936	0.61	4.06	0.07	6457632206	6187853356	5629349748	5419300639	95.82	96.27	39717887	37068667	192.212	677.279	135	297305	62.18	71.7	48272795	24696804	48272795	24696804	65.71	66.74	48272795	26098250	48272795	22988095	1411880757	21.86	1.18	0	12.10	0	0.50	0	0.59	0	0.00	0	7.81	0	39717887	0	200	0	198.32	0	2.26	0	0.02	0	2.12	0	0.01	0	165.73	0	0.31	0	512409	0	43596901	0	5275058	0	218168	0	255509	0	0	0	3405337	0	9315	0	0	0	349203	0	12885708	0	39024	0	13283250	0	79.00	0	34442829	0	265405	11794476	44.439539571598	43596901.0	39717887.0	512409.0	5275058.0	218168.0	255509.0	0.0	3405337.0	34442829.0	91.1	1.2	12.1	0.5	0.6	0.0	7.8	79.0	100	100	100.00	7	4359690100	23.5	26.2	25.1	25.1	0.0	39.9	31.4	bulk
2819729	SRR4413834	SRP091381	SRS1738018	SRX2236905	SRA483373	GEO		Systematic identification and comparison of expressed profiles of lncRNAs and circRNAs in male and female germline stem cells	Male and female germline stem cells are critical for passing genetic information from generation to generation. Accumulating evidences indicate that long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) play important roles in self-renewal and differentiation of germline stem cells. However, the mechanisms remain largely unknown. In this study, we explored the mRNAs, lncRNAs and circRNAs expression profiles of male and female germline stem cells through high-throughput sequencing. Overall design: mRNA, lncRNA and circRNA profiles of the mouse spermatogonial stem cells (SSCs) and  female germline stem cells (FGSCs) by strand- specific RNA- seq		GSM2341387: FGSCs rep2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA from the SSCs and FGSCs were isolated using TRIzol reagent (Invitrogen, life Technologies, USA) according to the manufacturer's protocol. Total RNA from each sample was quantified using Agilent 2100, and RNA integrity was assessed using Agilent 2100. After extracting the total RNA from samples, mRNA and non-coding RNAs are enriched by removing rRNA from the total RNA with kit. By using the fragmentation buffer, the mRNAs and non-coding RNAs are fragmented into short fragments (about 200~500nt), then the first-strand cDNA is synthesized by random hexamer-primer using the fragments as templates, and dTTP is substituted by dUTP during the synthesis of the second strand. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters, then the second strand is degraded using UNG(Uracil-N-Glycosylase) finally. After agarose gel electrophoresis, the suitable fragments are selected for the PCR amplification as templates. During the QC steps, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used in quantification and qualification of the sample library. At last, the library could be sequenced using Illumina HiSeqTM 2000 when necessary.	Illumina HiSeq 2000	age;;6 days|cell type;;germline stem cells|source_name;;FGSCs|strain;;C57BL/6|tissue;;ovary	GEO Accession;;GSM2341387		GSM2341387	FGSCs rep2	8746601400	43733007	2017-06-12 15:56:16	3183166061	8746601400	43733007	2	43733007	index:0,count:43733007,average:100,stdev:0|index:1,count:43733007,average:100,stdev:0	GSM2341387_r1				in_mesa	28404936	0.56	4.2	0.07	6489138204	6213305298	5736505959	5520622691	95.75	96.24	39408090	36662780	195.826	698.040	135	286212	63.59	72.25	47012257	25058893	47012257	25058893	66.73	67.71	47012257	26297750	47012257	23484648	1421542141	21.91	1.69	0	10.80	0	0.44	0	0.61	0	0.00	0	8.84	0	39408090	0	200	0	198.51	0	2.26	0	0.02	0	1.81	0	0.01	0	148.53	0	0.30	0	740042	0	43733007	0	4722470	0	194245	0	264658	0	0	0	3866014	0	10049	0	0	0	343341	0	13345354	0	38179	0	13736923	0	79.31	0	34685620	0	266988	12298671	46.064508517237	43733007.0	39408090.0	740042.0	4722470.0	194245.0	264658.0	0.0	3866014.0	34685620.0	90.1	1.7	10.8	0.4	0.6	0.0	8.8	79.3	100	100	100.00	7	4373300700	23.6	26.1	25.2	25.1	0.0	39.8	31.3	bulk
2819761	SRR4413835	SRP091381	SRS1738019	SRX2236906	SRA483373	GEO		Systematic identification and comparison of expressed profiles of lncRNAs and circRNAs in male and female germline stem cells	Male and female germline stem cells are critical for passing genetic information from generation to generation. Accumulating evidences indicate that long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) play important roles in self-renewal and differentiation of germline stem cells. However, the mechanisms remain largely unknown. In this study, we explored the mRNAs, lncRNAs and circRNAs expression profiles of male and female germline stem cells through high-throughput sequencing. Overall design: mRNA, lncRNA and circRNA profiles of the mouse spermatogonial stem cells (SSCs) and  female germline stem cells (FGSCs) by strand- specific RNA- seq		GSM2341388: FGSCs rep3; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Total RNA from the SSCs and FGSCs were isolated using TRIzol reagent (Invitrogen, life Technologies, USA) according to the manufacturer's protocol. Total RNA from each sample was quantified using Agilent 2100, and RNA integrity was assessed using Agilent 2100. After extracting the total RNA from samples, mRNA and non-coding RNAs are enriched by removing rRNA from the total RNA with kit. By using the fragmentation buffer, the mRNAs and non-coding RNAs are fragmented into short fragments (about 200~500nt), then the first-strand cDNA is synthesized by random hexamer-primer using the fragments as templates, and dTTP is substituted by dUTP during the synthesis of the second strand. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters, then the second strand is degraded using UNG(Uracil-N-Glycosylase) finally. After agarose gel electrophoresis, the suitable fragments are selected for the PCR amplification as templates. During the QC steps, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used in quantification and qualification of the sample library. At last, the library could be sequenced using Illumina HiSeqTM 2000 when necessary.	Illumina HiSeq 2000	age;;6 days|cell type;;germline stem cells|source_name;;FGSCs|strain;;C57BL/6|tissue;;ovary	GEO Accession;;GSM2341388		GSM2341388	FGSCs rep3	8726470000	43632350	2017-06-12 15:56:16	3137001006	8726470000	43632350	2	43632350	index:0,count:43632350,average:100,stdev:0|index:1,count:43632350,average:100,stdev:0	GSM2341388_r1				in_mesa	28404936	0.61	4.34	0.06	6549300396	6267867986	5833274726	5613481563	95.7	96.23	40489392	37640680	191.931	694.419	135	311164	64.34	72.53	47945884	26049530	47945884	26049530	67.43	68.35	47945884	27303817	47945884	24549682	1431997405	21.86	1.29	0	10.48	0	0.46	0	0.60	0	0.00	0	6.14	0	40489392	0	200	0	198.48	0	2.21	0	0.02	0	1.76	0	0.01	0	164.82	0	0.28	0	563137	0	43632350	0	4574277	0	200966	0	263902	0	0	0	2678090	0	10257	0	0	0	316504	0	13930138	0	40158	0	14297057	0	82.31	0	35915115	0	273449	12635157	46.206630852554	43632350.0	40489392.0	563137.0	4574277.0	200966.0	263902.0	0.0	2678090.0	35915115.0	92.8	1.3	10.5	0.5	0.6	0.0	6.1	82.3	100	100	100.00	7	4363235000	24.1	25.8	24.6	25.5	0.0	39.9	31.6	bulk
2753552	SRR5001020	SRP092781	SRS1787383	SRX2333333	SRA491357	GEO		Genome-wide analysis of transcription in in vitro- and in vivo-derived motor neurons	RNA sequencing analysis of Hb9::GFP mouse embryonic fibroblasts, Hb9::GFP+ primary mouse embryonic motor neurons at day E13.5, Hb9::GFP+ mouse embryonic stem cell-derived motor neurons, Hb9::GFP+ mouse induced pluripotent stem cell derived motor neurons, and Hb9::GFP+ mouse induced motor neurons generated using transcription factor overexpression. The goal of this project is to evaluate the ability of directed differentiation and lineage conversion techniques to generate a bona fide neuronal subtype. Overall design: The goal of this study is to determine the level of transcriptional similarity between spinal motor neurons generated from pluripotent stem cells by directed differentation, spinal motor neurons generated from fibroblasts by transcription factor-mediated lineage conversion, and primary spinal motor neuron from embryonic spinal cord. In addition, we tested the effect of culturing ESC-MNs in glia-conditioned media. All neurons were generated using the same Hb9::GFP, C57Bl/6 background, and FACS sorted for Hb9::GFP.		GSM2385557: GFP+ d13.5 m Embryonic MN 12-6-11; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			RNA was extracted using Trizol LS (Life Technologies) according to the manufacturer's instructions Illumina RNA TruSeq RNA seq - RNA-seq libraries were generated from 100-250 ng total RNA using the Illumina TruSeq RNA kit v.2, according to the manufacturers’ directions. Libraries were sequenced at the Broad Institute’s Genomics Platform on a HiSeq 2500. A total of 20–60 million 100 bp, paired end reads were obtained for each sample.	Illumina HiSeq 2500	hb9;;:gfp+: yes|source_name;;mouse embryonic motor neurons	GEO Accession;;GSM2385557		GSM2385557	GFP+ d13.5 m Embryonic MN 12-6-11	3631033224	17975412	2016-11-09 17:57:24	2147594784	3631033224	17975412	2	17975412	index:0,count:17975412,average:101,stdev:0|index:1,count:17975412,average:101,stdev:0	GSM2385557_r1						2.14	3.73	0.07	2756800647	2702519006	2606867122	2567715192	98.03	98.5	17063864	16045578	188.094	644.905	135	177923	79.08	83.73	18638146	13493274	18638146	13493274	79.89	80.13	18638146	13632820	18638146	12914080	388415172	14.09	1.45	0	5.28	0	0.21	0	0.10	0	0.00	0	4.77	0	17063864	0	202	0	199.40	0	1.76	0	0.01	0	1.69	0	0.01	0	239.67	0	0.18	0	260314	0	17975412	0	948370	0	37743	0	17184	0	0	0	856621	0	4972	0	0	0	44980	0	6286927	0	16439	0	6353318	0	89.65	0	16115494	0	191555	5567678	29.065688705594	17975412.0	17063864.0	260314.0	948370.0	37743.0	17184.0	0.0	856621.0	16115494.0	94.9	1.4	5.3	0.2	0.1	0.0	4.8	89.7	101	101	101.00	38	1815516612	25.3	24.8	24.4	25.5	0.0	36.6	20.8	bulk
2753584	SRR5001021	SRP092781	SRS1787384	SRX2333334	SRA491357	GEO		Genome-wide analysis of transcription in in vitro- and in vivo-derived motor neurons	RNA sequencing analysis of Hb9::GFP mouse embryonic fibroblasts, Hb9::GFP+ primary mouse embryonic motor neurons at day E13.5, Hb9::GFP+ mouse embryonic stem cell-derived motor neurons, Hb9::GFP+ mouse induced pluripotent stem cell derived motor neurons, and Hb9::GFP+ mouse induced motor neurons generated using transcription factor overexpression. The goal of this project is to evaluate the ability of directed differentiation and lineage conversion techniques to generate a bona fide neuronal subtype. Overall design: The goal of this study is to determine the level of transcriptional similarity between spinal motor neurons generated from pluripotent stem cells by directed differentation, spinal motor neurons generated from fibroblasts by transcription factor-mediated lineage conversion, and primary spinal motor neuron from embryonic spinal cord. In addition, we tested the effect of culturing ESC-MNs in glia-conditioned media. All neurons were generated using the same Hb9::GFP, C57Bl/6 background, and FACS sorted for Hb9::GFP.		GSM2385558: C57Bl6 Hb9::GFP embryo-MNs E13.5 2, sorted; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			RNA was extracted using Trizol LS (Life Technologies) according to the manufacturer's instructions Illumina RNA TruSeq RNA seq - RNA-seq libraries were generated from 100-250 ng total RNA using the Illumina TruSeq RNA kit v.2, according to the manufacturers’ directions. Libraries were sequenced at the Broad Institute’s Genomics Platform on a HiSeq 2500. A total of 20–60 million 100 bp, paired end reads were obtained for each sample.	Illumina HiSeq 2500	hb9;;:gfp+: yes|source_name;;mouse embryonic motor neurons	GEO Accession;;GSM2385558		GSM2385558	C57Bl6 Hb9::GFP embryo-MNs E13.5 2, sorted	5977649800	29888249	2016-11-09 17:57:24	3864454055	5977649800	29888249	2	29888249	index:0,count:29888249,average:100,stdev:0|index:1,count:29888249,average:100,stdev:0	GSM2385558_r1						4.52	4.05	0.05	4172992484	4032359288	3841819745	3731858716	96.63	97.14	26391316	24723791	190.740	769.565	136	198190	74.53	81.16	29867753	19670589	29867753	19670589	77.91	77.58	29867753	20560564	29867753	18804391	642275771	15.39	1.92	0	7.21	0	0.26	0	0.30	0	0.00	0	11.14	0	26391316	0	200	0	197.07	0	1.66	0	0.01	0	1.36	0	0.01	0	146.19	0	0.21	0	575017	0	29888249	0	2154102	0	77207	0	89441	0	0	0	3330285	0	7502	0	0	0	65721	0	8935725	0	21967	0	9030915	0	81.09	0	24237214	0	203351	7935779	39.025030612094	29888249.0	26391316.0	575017.0	2154102.0	77207.0	89441.0	0.0	3330285.0	24237214.0	88.3	1.9	7.2	0.3	0.3	0.0	11.1	81.1	100	100	100.00	38	2988824900	26.7	23.9	23.5	25.8	0.0	35.9	18.4	bulk
1845275	SRR5061281	SRP094068	SRS1824159	SRX2381806	SRA499628	GEO		RNA-seq analysis of RNA from DBA/2J retinal ganglion cells	RNA-seq analysis from young and pre-glaucomatous DBA/2J retinal ganglion cells and control (age and sex-matched, D2-Gpnmb+) retinal ganglion cells Overall design: Retinal ganglion cell mRNA from 4 month (young) and 9 month (pre-glaucomatous) DBA/2J mice and age and sex-matched D2-Gpnmb+ controls		GSM2409950: D2_4mnths_WaterControl_2017; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Prior to cell collection, all surfaces and volumes were cleaned with 70% ethanol and RNaseZap (ThermoFisher Scientific) solution followed by dH20. Mice were euthanized, eyes enucleated and placed immediately into ice-cold HBSS. Retinas were dissected from the eyes (4 or 9 mo of age, no axon degeneration confirmed by PPD staining) in HBSS on ice and placed directly into 100 μl of a custom HBSS (Gibco), dispase (5 U/ml) (Stemcell Technologies), DNase I (2000 U/ml) (Worthington Biochemical) and SUPERase (1 U/μl) (ThermoFisher Scientific) solution. All retinas were from eyes that had no glaucomatous axon degeneration by PPD staining and analysis. Retinas were incubated for 20 mins at 37 °C and shaken at 350 RPM in an Eppendorf Thermomixer R followed by gentle trituration using a 200 μl pipette. Samples were blocked in 2% BSA, SUPERase (1 U/μl) in HBSS, and stained with conjugated antibodies against Cd11b, Cd11c, Cd34, Cd45.2, GFAP, Thy1.2 as well as DAPI. This cocktail allowed other retina cell types to be accurately removed during FACS. FACS was performed on a FACSAria (BD Biosciences). Thy1.2+ (and negative for all other markers) RGCs were sorted into 300μl buffer RLT + 1% β-ME, vortexed and frozen at -80°C until further processing.	Illumina HiSeq 2500	source_name;;Retinal ganglion cells|strain;;DBA/2J|treatment;;Water Control	GEO Accession;;GSM2409950		GSM2409950	D2_4mnths_WaterControl_2017	8362378800	41811894	2017-03-09 10:01:29	5886581334	8362378800	41811894	2	41811894	index:0,count:41811894,average:100,stdev:0|index:1,count:41811894,average:100,stdev:0	GSM2409950_r1						11.41	2.86	0.14	5079936187	4832985799	4906396568	4700704785	95.14	95.81	33854708	32898338	169.930	866.021	114	255116	50.96	52.9	36093716	17250948	36093716	17250948	49.29	49.5	36093716	16686231	36093716	16141372	2095955451	41.26	5.66	0	2.98	0	0.23	0	0.25	0	0.00	0	18.55	0	33854708	0	200	0	193.35	0	2.24	0	0.02	0	2.54	0	0.02	0	203.96	0	0.55	0	2366155	0	41811894	0	1245385	0	95556	0	104852	0	0	0	7756778	0	3775	0	0	0	32321	0	3911543	0	68781	0	4016420	0	77.99	0	32609323	0	171634	3383392	19.712830791102	41811894.0	33854708.0	2366155.0	1245385.0	95556.0	104852.0	0.0	7756778.0	32609323.0	81.0	5.7	3.0	0.2	0.3	0.0	18.6	78.0	100	100	100.00	38	4181189400	28.4	21.8	22.2	27.5	0.1	34.7	18.4	bulk
1845293	SRR5061282	SRP094068	SRS1824160	SRX2381807	SRA499628	GEO		RNA-seq analysis of RNA from DBA/2J retinal ganglion cells	RNA-seq analysis from young and pre-glaucomatous DBA/2J retinal ganglion cells and control (age and sex-matched, D2-Gpnmb+) retinal ganglion cells Overall design: Retinal ganglion cell mRNA from 4 month (young) and 9 month (pre-glaucomatous) DBA/2J mice and age and sex-matched D2-Gpnmb+ controls		GSM2409951: D2_4mnths_WaterControl_2038; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Prior to cell collection, all surfaces and volumes were cleaned with 70% ethanol and RNaseZap (ThermoFisher Scientific) solution followed by dH20. Mice were euthanized, eyes enucleated and placed immediately into ice-cold HBSS. Retinas were dissected from the eyes (4 or 9 mo of age, no axon degeneration confirmed by PPD staining) in HBSS on ice and placed directly into 100 μl of a custom HBSS (Gibco), dispase (5 U/ml) (Stemcell Technologies), DNase I (2000 U/ml) (Worthington Biochemical) and SUPERase (1 U/μl) (ThermoFisher Scientific) solution. All retinas were from eyes that had no glaucomatous axon degeneration by PPD staining and analysis. Retinas were incubated for 20 mins at 37 °C and shaken at 350 RPM in an Eppendorf Thermomixer R followed by gentle trituration using a 200 μl pipette. Samples were blocked in 2% BSA, SUPERase (1 U/μl) in HBSS, and stained with conjugated antibodies against Cd11b, Cd11c, Cd34, Cd45.2, GFAP, Thy1.2 as well as DAPI. This cocktail allowed other retina cell types to be accurately removed during FACS. FACS was performed on a FACSAria (BD Biosciences). Thy1.2+ (and negative for all other markers) RGCs were sorted into 300μl buffer RLT + 1% β-ME, vortexed and frozen at -80°C until further processing.	Illumina HiSeq 2500	source_name;;Retinal ganglion cells|strain;;DBA/2J|treatment;;Water Control	GEO Accession;;GSM2409951		GSM2409951	D2_4mnths_WaterControl_2038	6945129800	34725649	2017-03-09 10:01:29	4868952821	6945129800	34725649	2	34725649	index:0,count:34725649,average:100,stdev:0|index:1,count:34725649,average:100,stdev:0	GSM2409951_r1						18.33	2.48	0.11	4320482264	4080324174	4161865644	3956557646	94.44	95.07	28472362	27822780	171.620	888.133	124	212269	51.13	53.21	30304436	14558250	30304436	14558250	50.58	50.49	30304436	14402480	30304436	13815004	1754589449	40.61	6.05	0	3.20	0	0.20	0	0.23	0	0.00	0	17.58	0	28472362	0	200	0	193.63	0	2.19	0	0.02	0	2.40	0	0.02	0	202.94	0	0.54	0	2100658	0	34725649	0	1110390	0	70456	0	79123	0	0	0	6103708	0	2686	0	0	0	21332	0	2589801	0	57125	0	2670944	0	78.79	0	27361972	0	145054	2275898	15.690005101548	34725649.0	28472362.0	2100658.0	1110390.0	70456.0	79123.0	0.0	6103708.0	27361972.0	82.0	6.0	3.2	0.2	0.2	0.0	17.6	78.8	100	100	100.00	38	3472564900	28.8	21.3	21.7	28.1	0.1	34.8	18.8	bulk
1845310	SRR5061283	SRP094068	SRS1824161	SRX2381808	SRA499628	GEO		RNA-seq analysis of RNA from DBA/2J retinal ganglion cells	RNA-seq analysis from young and pre-glaucomatous DBA/2J retinal ganglion cells and control (age and sex-matched, D2-Gpnmb+) retinal ganglion cells Overall design: Retinal ganglion cell mRNA from 4 month (young) and 9 month (pre-glaucomatous) DBA/2J mice and age and sex-matched D2-Gpnmb+ controls		GSM2409952: D2_4mnths_WaterControl_2018; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Prior to cell collection, all surfaces and volumes were cleaned with 70% ethanol and RNaseZap (ThermoFisher Scientific) solution followed by dH20. Mice were euthanized, eyes enucleated and placed immediately into ice-cold HBSS. Retinas were dissected from the eyes (4 or 9 mo of age, no axon degeneration confirmed by PPD staining) in HBSS on ice and placed directly into 100 μl of a custom HBSS (Gibco), dispase (5 U/ml) (Stemcell Technologies), DNase I (2000 U/ml) (Worthington Biochemical) and SUPERase (1 U/μl) (ThermoFisher Scientific) solution. All retinas were from eyes that had no glaucomatous axon degeneration by PPD staining and analysis. Retinas were incubated for 20 mins at 37 °C and shaken at 350 RPM in an Eppendorf Thermomixer R followed by gentle trituration using a 200 μl pipette. Samples were blocked in 2% BSA, SUPERase (1 U/μl) in HBSS, and stained with conjugated antibodies against Cd11b, Cd11c, Cd34, Cd45.2, GFAP, Thy1.2 as well as DAPI. This cocktail allowed other retina cell types to be accurately removed during FACS. FACS was performed on a FACSAria (BD Biosciences). Thy1.2+ (and negative for all other markers) RGCs were sorted into 300μl buffer RLT + 1% β-ME, vortexed and frozen at -80°C until further processing.	Illumina HiSeq 2500	source_name;;Retinal ganglion cells|strain;;DBA/2J|treatment;;Water Control	GEO Accession;;GSM2409952		GSM2409952	D2_4mnths_WaterControl_2018	6822437400	34112187	2017-03-09 10:01:29	4782121688	6822437400	34112187	2	34112187	index:0,count:34112187,average:100,stdev:0|index:1,count:34112187,average:100,stdev:0	GSM2409952_r1						9.34	2.76	0.13	4011191770	3799123271	3880778753	3702023384	94.71	95.39	26817658	26082131	170.182	948.660	113	203033	47.42	49.13	28537679	12716321	28537679	12716321	45.64	45.78	28537679	12240523	28537679	11849674	1801124867	44.90	5.37	0	2.75	0	0.22	0	0.24	0	0.00	0	20.92	0	26817658	0	200	0	193.21	0	2.26	0	0.02	0	2.43	0	0.02	0	201.32	0	0.54	0	1830217	0	34112187	0	936521	0	75277	0	82540	0	0	0	7136712	0	2812	0	0	0	24231	0	2900037	0	53541	0	2980621	0	75.87	0	25881137	0	161696	2506018	15.498330199881	34112187.0	26817658.0	1830217.0	936521.0	75277.0	82540.0	0.0	7136712.0	25881137.0	78.6	5.4	2.7	0.2	0.2	0.0	20.9	75.9	100	100	100.00	38	3411218700	28.4	21.9	22.2	27.5	0.1	34.6	18.2	bulk
1845343	SRR5061285	SRP094068	SRS1824163	SRX2381810	SRA499628	GEO		RNA-seq analysis of RNA from DBA/2J retinal ganglion cells	RNA-seq analysis from young and pre-glaucomatous DBA/2J retinal ganglion cells and control (age and sex-matched, D2-Gpnmb+) retinal ganglion cells Overall design: Retinal ganglion cell mRNA from 4 month (young) and 9 month (pre-glaucomatous) DBA/2J mice and age and sex-matched D2-Gpnmb+ controls		GSM2409954: D2_4mnths_WaterControl_2020; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Prior to cell collection, all surfaces and volumes were cleaned with 70% ethanol and RNaseZap (ThermoFisher Scientific) solution followed by dH20. Mice were euthanized, eyes enucleated and placed immediately into ice-cold HBSS. Retinas were dissected from the eyes (4 or 9 mo of age, no axon degeneration confirmed by PPD staining) in HBSS on ice and placed directly into 100 μl of a custom HBSS (Gibco), dispase (5 U/ml) (Stemcell Technologies), DNase I (2000 U/ml) (Worthington Biochemical) and SUPERase (1 U/μl) (ThermoFisher Scientific) solution. All retinas were from eyes that had no glaucomatous axon degeneration by PPD staining and analysis. Retinas were incubated for 20 mins at 37 °C and shaken at 350 RPM in an Eppendorf Thermomixer R followed by gentle trituration using a 200 μl pipette. Samples were blocked in 2% BSA, SUPERase (1 U/μl) in HBSS, and stained with conjugated antibodies against Cd11b, Cd11c, Cd34, Cd45.2, GFAP, Thy1.2 as well as DAPI. This cocktail allowed other retina cell types to be accurately removed during FACS. FACS was performed on a FACSAria (BD Biosciences). Thy1.2+ (and negative for all other markers) RGCs were sorted into 300μl buffer RLT + 1% β-ME, vortexed and frozen at -80°C until further processing.	Illumina HiSeq 2500	source_name;;Retinal ganglion cells|strain;;DBA/2J|treatment;;Water Control	GEO Accession;;GSM2409954		GSM2409954	D2_4mnths_WaterControl_2020	7167056400	35835282	2017-03-09 10:01:29	5036605881	7167056400	35835282	2	35835282	index:0,count:35835282,average:100,stdev:0|index:1,count:35835282,average:100,stdev:0	GSM2409954_r1						9.27	2.81	0.11	4231520034	4019524913	4087495823	3910114058	94.99	95.66	28457348	27566570	169.051	937.190	110	217489	51.94	53.91	30314241	14779756	30314241	14779756	50.25	50.46	30314241	14299804	30314241	13833722	1703527109	40.26	5.20	0	2.90	0	0.23	0	0.22	0	0.00	0	20.14	0	28457348	0	200	0	193.13	0	2.23	0	0.02	0	2.46	0	0.02	0	274.48	0	0.54	0	1862208	0	35835282	0	1039445	0	82130	0	78731	0	0	0	7217073	0	3264	0	0	0	29948	0	3641025	0	57088	0	3731325	0	76.51	0	27417903	0	167213	3124920	18.688259884100	35835282.0	28457348.0	1862208.0	1039445.0	82130.0	78731.0	0.0	7217073.0	27417903.0	79.4	5.2	2.9	0.2	0.2	0.0	20.1	76.5	100	100	100.00	38	3583528200	28.3	22.0	22.3	27.4	0.1	34.7	18.6	bulk
1845356	SRR5061286	SRP094068	SRS1824164	SRX2381811	SRA499628	GEO		RNA-seq analysis of RNA from DBA/2J retinal ganglion cells	RNA-seq analysis from young and pre-glaucomatous DBA/2J retinal ganglion cells and control (age and sex-matched, D2-Gpnmb+) retinal ganglion cells Overall design: Retinal ganglion cell mRNA from 4 month (young) and 9 month (pre-glaucomatous) DBA/2J mice and age and sex-matched D2-Gpnmb+ controls		GSM2409955: D2_4mnths_WaterControl_2021; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Prior to cell collection, all surfaces and volumes were cleaned with 70% ethanol and RNaseZap (ThermoFisher Scientific) solution followed by dH20. Mice were euthanized, eyes enucleated and placed immediately into ice-cold HBSS. Retinas were dissected from the eyes (4 or 9 mo of age, no axon degeneration confirmed by PPD staining) in HBSS on ice and placed directly into 100 μl of a custom HBSS (Gibco), dispase (5 U/ml) (Stemcell Technologies), DNase I (2000 U/ml) (Worthington Biochemical) and SUPERase (1 U/μl) (ThermoFisher Scientific) solution. All retinas were from eyes that had no glaucomatous axon degeneration by PPD staining and analysis. Retinas were incubated for 20 mins at 37 °C and shaken at 350 RPM in an Eppendorf Thermomixer R followed by gentle trituration using a 200 μl pipette. Samples were blocked in 2% BSA, SUPERase (1 U/μl) in HBSS, and stained with conjugated antibodies against Cd11b, Cd11c, Cd34, Cd45.2, GFAP, Thy1.2 as well as DAPI. This cocktail allowed other retina cell types to be accurately removed during FACS. FACS was performed on a FACSAria (BD Biosciences). Thy1.2+ (and negative for all other markers) RGCs were sorted into 300μl buffer RLT + 1% β-ME, vortexed and frozen at -80°C until further processing.	Illumina HiSeq 2500	source_name;;Retinal ganglion cells|strain;;DBA/2J|treatment;;Water Control	GEO Accession;;GSM2409955		GSM2409955	D2_4mnths_WaterControl_2021	5933878800	29669394	2017-03-09 10:01:29	4166561406	5933878800	29669394	2	29669394	index:0,count:29669394,average:100,stdev:0|index:1,count:29669394,average:100,stdev:0	GSM2409955_r1						9.94	2.75	0.1	3908528758	3688535406	3783881204	3595243756	94.37	95.01	24993457	24237124	180.548	913.805	129	171494	50.02	51.78	26506906	12502086	26506906	12502086	48.59	48.72	26506906	12144570	26506906	11764127	1649909432	42.21	5.54	0	2.86	0	0.21	0	0.25	0	0.00	0	15.30	0	24993457	0	200	0	194.36	0	2.24	0	0.02	0	2.43	0	0.02	0	221.14	0	0.55	0	1643273	0	29669394	0	849527	0	63785	0	73998	0	0	0	4538154	0	2844	0	0	0	25215	0	3017912	0	47953	0	3093924	0	81.38	0	24143930	0	159201	2691819	16.908304596077	29669394.0	24993457.0	1643273.0	849527.0	63785.0	73998.0	0.0	4538154.0	24143930.0	84.2	5.5	2.9	0.2	0.2	0.0	15.3	81.4	100	100	100.00	38	2966939400	28.4	21.7	22.1	27.7	0.1	34.7	18.5	bulk
1845371	SRR5061287	SRP094068	SRS1824165	SRX2381812	SRA499628	GEO		RNA-seq analysis of RNA from DBA/2J retinal ganglion cells	RNA-seq analysis from young and pre-glaucomatous DBA/2J retinal ganglion cells and control (age and sex-matched, D2-Gpnmb+) retinal ganglion cells Overall design: Retinal ganglion cell mRNA from 4 month (young) and 9 month (pre-glaucomatous) DBA/2J mice and age and sex-matched D2-Gpnmb+ controls		GSM2409956: D2_4mnths_WaterControl_2026; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Prior to cell collection, all surfaces and volumes were cleaned with 70% ethanol and RNaseZap (ThermoFisher Scientific) solution followed by dH20. Mice were euthanized, eyes enucleated and placed immediately into ice-cold HBSS. Retinas were dissected from the eyes (4 or 9 mo of age, no axon degeneration confirmed by PPD staining) in HBSS on ice and placed directly into 100 μl of a custom HBSS (Gibco), dispase (5 U/ml) (Stemcell Technologies), DNase I (2000 U/ml) (Worthington Biochemical) and SUPERase (1 U/μl) (ThermoFisher Scientific) solution. All retinas were from eyes that had no glaucomatous axon degeneration by PPD staining and analysis. Retinas were incubated for 20 mins at 37 °C and shaken at 350 RPM in an Eppendorf Thermomixer R followed by gentle trituration using a 200 μl pipette. Samples were blocked in 2% BSA, SUPERase (1 U/μl) in HBSS, and stained with conjugated antibodies against Cd11b, Cd11c, Cd34, Cd45.2, GFAP, Thy1.2 as well as DAPI. This cocktail allowed other retina cell types to be accurately removed during FACS. FACS was performed on a FACSAria (BD Biosciences). Thy1.2+ (and negative for all other markers) RGCs were sorted into 300μl buffer RLT + 1% β-ME, vortexed and frozen at -80°C until further processing.	Illumina HiSeq 2500	source_name;;Retinal ganglion cells|strain;;DBA/2J|treatment;;Water Control	GEO Accession;;GSM2409956		GSM2409956	D2_4mnths_WaterControl_2026	6720845200	33604226	2017-03-09 10:01:29	4731549374	6720845200	33604226	2	33604226	index:0,count:33604226,average:100,stdev:0|index:1,count:33604226,average:100,stdev:0	GSM2409956_r1						12.37	2.71	0.17	3965337048	3759531766	3825022919	3652699406	94.81	95.49	26744870	26007906	167.942	963.735	107	209256	50.35	52.33	28539198	13465446	28539198	13465446	48.88	49.0	28539198	13072051	28539198	12607594	1645078336	41.49	5.75	0	3.02	0	0.22	0	0.23	0	0.00	0	19.96	0	26744870	0	200	0	192.92	0	2.22	0	0.02	0	2.46	0	0.02	0	217.97	0	0.55	0	1930855	0	33604226	0	1013655	0	74293	0	78911	0	0	0	6706152	0	2757	0	0	0	23921	0	2915051	0	56445	0	2998174	0	76.57	0	25731215	0	156729	2510900	16.020647104237	33604226.0	26744870.0	1930855.0	1013655.0	74293.0	78911.0	0.0	6706152.0	25731215.0	79.6	5.7	3.0	0.2	0.2	0.0	20.0	76.6	100	100	100.00	38	3360422600	28.6	21.7	22.2	27.5	0.1	34.7	18.7	bulk
1845389	SRR5061288	SRP094068	SRS1824166	SRX2381813	SRA499628	GEO		RNA-seq analysis of RNA from DBA/2J retinal ganglion cells	RNA-seq analysis from young and pre-glaucomatous DBA/2J retinal ganglion cells and control (age and sex-matched, D2-Gpnmb+) retinal ganglion cells Overall design: Retinal ganglion cell mRNA from 4 month (young) and 9 month (pre-glaucomatous) DBA/2J mice and age and sex-matched D2-Gpnmb+ controls		GSM2409957: D2_4mnths_WaterControl_2027; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Prior to cell collection, all surfaces and volumes were cleaned with 70% ethanol and RNaseZap (ThermoFisher Scientific) solution followed by dH20. Mice were euthanized, eyes enucleated and placed immediately into ice-cold HBSS. Retinas were dissected from the eyes (4 or 9 mo of age, no axon degeneration confirmed by PPD staining) in HBSS on ice and placed directly into 100 μl of a custom HBSS (Gibco), dispase (5 U/ml) (Stemcell Technologies), DNase I (2000 U/ml) (Worthington Biochemical) and SUPERase (1 U/μl) (ThermoFisher Scientific) solution. All retinas were from eyes that had no glaucomatous axon degeneration by PPD staining and analysis. Retinas were incubated for 20 mins at 37 °C and shaken at 350 RPM in an Eppendorf Thermomixer R followed by gentle trituration using a 200 μl pipette. Samples were blocked in 2% BSA, SUPERase (1 U/μl) in HBSS, and stained with conjugated antibodies against Cd11b, Cd11c, Cd34, Cd45.2, GFAP, Thy1.2 as well as DAPI. This cocktail allowed other retina cell types to be accurately removed during FACS. FACS was performed on a FACSAria (BD Biosciences). Thy1.2+ (and negative for all other markers) RGCs were sorted into 300μl buffer RLT + 1% β-ME, vortexed and frozen at -80°C until further processing.	Illumina HiSeq 2500	source_name;;Retinal ganglion cells|strain;;DBA/2J|treatment;;Water Control	GEO Accession;;GSM2409957		GSM2409957	D2_4mnths_WaterControl_2027	7780804200	38904021	2017-03-09 10:01:29	5473018870	7780804200	38904021	2	38904021	index:0,count:38904021,average:100,stdev:0|index:1,count:38904021,average:100,stdev:0	GSM2409957_r1						16.12	2.58	0.18	4814262843	4560324014	4641970413	4426438079	94.73	95.36	31821798	31039514	171.581	902.394	114	237548	51.34	53.37	33862155	16337356	33862155	16337356	50.33	50.29	33862155	16015247	33862155	15397008	1953329652	40.57	6.01	0	3.11	0	0.21	0	0.24	0	0.00	0	17.76	0	31821798	0	200	0	193.57	0	2.22	0	0.02	0	2.39	0	0.02	0	208.10	0	0.53	0	2339122	0	38904021	0	1208147	0	81321	0	92178	0	0	0	6908724	0	2838	0	0	0	25719	0	3090504	0	66505	0	3185566	0	78.69	0	30613651	0	161638	2709982	16.765748153281	38904021.0	31821798.0	2339122.0	1208147.0	81321.0	92178.0	0.0	6908724.0	30613651.0	81.8	6.0	3.1	0.2	0.2	0.0	17.8	78.7	100	100	100.00	38	3890402100	28.6	21.4	21.9	27.9	0.1	34.8	18.8	bulk
1845405	SRR5061289	SRP094068	SRS1824167	SRX2381814	SRA499628	GEO		RNA-seq analysis of RNA from DBA/2J retinal ganglion cells	RNA-seq analysis from young and pre-glaucomatous DBA/2J retinal ganglion cells and control (age and sex-matched, D2-Gpnmb+) retinal ganglion cells Overall design: Retinal ganglion cell mRNA from 4 month (young) and 9 month (pre-glaucomatous) DBA/2J mice and age and sex-matched D2-Gpnmb+ controls		GSM2409958: D2_4mnths_WaterControl_2030; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Prior to cell collection, all surfaces and volumes were cleaned with 70% ethanol and RNaseZap (ThermoFisher Scientific) solution followed by dH20. Mice were euthanized, eyes enucleated and placed immediately into ice-cold HBSS. Retinas were dissected from the eyes (4 or 9 mo of age, no axon degeneration confirmed by PPD staining) in HBSS on ice and placed directly into 100 μl of a custom HBSS (Gibco), dispase (5 U/ml) (Stemcell Technologies), DNase I (2000 U/ml) (Worthington Biochemical) and SUPERase (1 U/μl) (ThermoFisher Scientific) solution. All retinas were from eyes that had no glaucomatous axon degeneration by PPD staining and analysis. Retinas were incubated for 20 mins at 37 °C and shaken at 350 RPM in an Eppendorf Thermomixer R followed by gentle trituration using a 200 μl pipette. Samples were blocked in 2% BSA, SUPERase (1 U/μl) in HBSS, and stained with conjugated antibodies against Cd11b, Cd11c, Cd34, Cd45.2, GFAP, Thy1.2 as well as DAPI. This cocktail allowed other retina cell types to be accurately removed during FACS. FACS was performed on a FACSAria (BD Biosciences). Thy1.2+ (and negative for all other markers) RGCs were sorted into 300μl buffer RLT + 1% β-ME, vortexed and frozen at -80°C until further processing.	Illumina HiSeq 2500	source_name;;Retinal ganglion cells|strain;;DBA/2J|treatment;;Water Control	GEO Accession;;GSM2409958		GSM2409958	D2_4mnths_WaterControl_2030	6751184200	33755921	2017-03-09 10:01:29	4748815393	6751184200	33755921	2	33755921	index:0,count:33755921,average:100,stdev:0|index:1,count:33755921,average:100,stdev:0	GSM2409958_r1						8.37	2.63	0.17	4074295298	3808996755	3958322242	3727887948	93.49	94.18	27133375	26659627	169.153	950.727	113	207621	33.73	34.78	28689402	9153152	28689402	9153152	32.74	32.64	28689402	8884411	28689402	8589571	2396318382	58.82	5.82	0	2.42	0	0.21	0	0.33	0	0.00	0	19.08	0	27133375	0	200	0	193.40	0	2.19	0	0.03	0	2.25	0	0.02	0	199.54	0	0.56	0	1965495	0	33755921	0	817684	0	71817	0	110899	0	0	0	6439830	0	1786	0	0	0	15834	0	1709334	0	61437	0	1788391	0	77.96	0	26315691	0	144486	1499744	10.379856871946	33755921.0	27133375.0	1965495.0	817684.0	71817.0	110899.0	0.0	6439830.0	26315691.0	80.4	5.8	2.4	0.2	0.3	0.0	19.1	78.0	100	100	100.00	38	3375592100	28.9	21.3	21.8	28.0	0.1	34.8	18.8	bulk
1845516	SRR5061290	SRP094068	SRS1824168	SRX2381815	SRA499628	GEO		RNA-seq analysis of RNA from DBA/2J retinal ganglion cells	RNA-seq analysis from young and pre-glaucomatous DBA/2J retinal ganglion cells and control (age and sex-matched, D2-Gpnmb+) retinal ganglion cells Overall design: Retinal ganglion cell mRNA from 4 month (young) and 9 month (pre-glaucomatous) DBA/2J mice and age and sex-matched D2-Gpnmb+ controls		GSM2409959: D2_4mnths_WaterControl_2034; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Prior to cell collection, all surfaces and volumes were cleaned with 70% ethanol and RNaseZap (ThermoFisher Scientific) solution followed by dH20. Mice were euthanized, eyes enucleated and placed immediately into ice-cold HBSS. Retinas were dissected from the eyes (4 or 9 mo of age, no axon degeneration confirmed by PPD staining) in HBSS on ice and placed directly into 100 μl of a custom HBSS (Gibco), dispase (5 U/ml) (Stemcell Technologies), DNase I (2000 U/ml) (Worthington Biochemical) and SUPERase (1 U/μl) (ThermoFisher Scientific) solution. All retinas were from eyes that had no glaucomatous axon degeneration by PPD staining and analysis. Retinas were incubated for 20 mins at 37 °C and shaken at 350 RPM in an Eppendorf Thermomixer R followed by gentle trituration using a 200 μl pipette. Samples were blocked in 2% BSA, SUPERase (1 U/μl) in HBSS, and stained with conjugated antibodies against Cd11b, Cd11c, Cd34, Cd45.2, GFAP, Thy1.2 as well as DAPI. This cocktail allowed other retina cell types to be accurately removed during FACS. FACS was performed on a FACSAria (BD Biosciences). Thy1.2+ (and negative for all other markers) RGCs were sorted into 300μl buffer RLT + 1% β-ME, vortexed and frozen at -80°C until further processing.	Illumina HiSeq 2500	source_name;;Retinal ganglion cells|strain;;DBA/2J|treatment;;Water Control	GEO Accession;;GSM2409959		GSM2409959	D2_4mnths_WaterControl_2034	6529330200	32646651	2017-03-09 10:01:29	4596807613	6529330200	32646651	2	32646651	index:0,count:32646651,average:100,stdev:0|index:1,count:32646651,average:100,stdev:0	GSM2409959_r1						10.52	2.83	0.13	3845080870	3660456816	3711263132	3558463342	95.2	95.88	25853145	25098774	168.955	939.460	113	198747	50.9	52.87	27575366	13158903	27575366	13158903	49.04	49.24	27575366	12679236	27575366	12253842	1581902431	41.14	5.64	0	2.96	0	0.23	0	0.23	0	0.00	0	20.35	0	25853145	0	200	0	192.90	0	2.24	0	0.02	0	2.55	0	0.02	0	268.94	0	0.55	0	1842271	0	32646651	0	965837	0	75839	0	75528	0	0	0	6642139	0	2823	0	0	0	24727	0	3010865	0	54361	0	3092776	0	76.23	0	24887308	0	157519	2594898	16.473555571074	32646651.0	25853145.0	1842271.0	965837.0	75839.0	75528.0	0.0	6642139.0	24887308.0	79.2	5.6	3.0	0.2	0.2	0.0	20.3	76.2	100	100	100.00	38	3264665100	28.3	22.0	22.4	27.3	0.1	34.7	18.6	bulk
1845533	SRR5061291	SRP094068	SRS1824169	SRX2381816	SRA499628	GEO		RNA-seq analysis of RNA from DBA/2J retinal ganglion cells	RNA-seq analysis from young and pre-glaucomatous DBA/2J retinal ganglion cells and control (age and sex-matched, D2-Gpnmb+) retinal ganglion cells Overall design: Retinal ganglion cell mRNA from 4 month (young) and 9 month (pre-glaucomatous) DBA/2J mice and age and sex-matched D2-Gpnmb+ controls		GSM2409960: D2_9mnths_WaterControl_246; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Prior to cell collection, all surfaces and volumes were cleaned with 70% ethanol and RNaseZap (ThermoFisher Scientific) solution followed by dH20. Mice were euthanized, eyes enucleated and placed immediately into ice-cold HBSS. Retinas were dissected from the eyes (4 or 9 mo of age, no axon degeneration confirmed by PPD staining) in HBSS on ice and placed directly into 100 μl of a custom HBSS (Gibco), dispase (5 U/ml) (Stemcell Technologies), DNase I (2000 U/ml) (Worthington Biochemical) and SUPERase (1 U/μl) (ThermoFisher Scientific) solution. All retinas were from eyes that had no glaucomatous axon degeneration by PPD staining and analysis. Retinas were incubated for 20 mins at 37 °C and shaken at 350 RPM in an Eppendorf Thermomixer R followed by gentle trituration using a 200 μl pipette. Samples were blocked in 2% BSA, SUPERase (1 U/μl) in HBSS, and stained with conjugated antibodies against Cd11b, Cd11c, Cd34, Cd45.2, GFAP, Thy1.2 as well as DAPI. This cocktail allowed other retina cell types to be accurately removed during FACS. FACS was performed on a FACSAria (BD Biosciences). Thy1.2+ (and negative for all other markers) RGCs were sorted into 300μl buffer RLT + 1% β-ME, vortexed and frozen at -80°C until further processing.	Illumina HiSeq 2500	source_name;;Retinal ganglion cells|strain;;DBA/2J|treatment;;Water Control	GEO Accession;;GSM2409960		GSM2409960	D2_9mnths_WaterControl_246	6972409400	34862047	2017-03-09 10:01:29	4828173651	6972409400	34862047	2	34862047	index:0,count:34862047,average:100,stdev:0|index:1,count:34862047,average:100,stdev:0	GSM2409960_r1						6.58	2.75	0.07	5244121551	5051456793	5111729486	4950281812	96.33	96.84	32153607	31293156	186.292	661.066	146	265839	46.13	47.38	33681374	14831534	33681374	14831534	44.0	44.1	33681374	14146773	33681374	13805986	2561269302	48.84	6.54	0	2.43	0	0.19	0	0.32	0	0.00	0	7.27	0	32153607	0	200	0	195.82	0	2.33	0	0.03	0	2.37	0	0.02	0	228.60	0	0.47	0	2278572	0	34862047	0	847479	0	65494	0	109830	0	0	0	2533116	0	3709	0	0	0	31344	0	3957283	0	54314	0	4046650	0	89.80	0	31306128	0	180683	3646292	20.180603598568	34862047.0	32153607.0	2278572.0	847479.0	65494.0	109830.0	0.0	2533116.0	31306128.0	92.2	6.5	2.4	0.2	0.3	0.0	7.3	89.8	100	100	100.00	38	3486204700	27.9	22.2	22.2	27.7	0.0	35.2	18.9	bulk
1845550	SRR5061292	SRP094068	SRS1824170	SRX2381817	SRA499628	GEO		RNA-seq analysis of RNA from DBA/2J retinal ganglion cells	RNA-seq analysis from young and pre-glaucomatous DBA/2J retinal ganglion cells and control (age and sex-matched, D2-Gpnmb+) retinal ganglion cells Overall design: Retinal ganglion cell mRNA from 4 month (young) and 9 month (pre-glaucomatous) DBA/2J mice and age and sex-matched D2-Gpnmb+ controls		GSM2409961: D2_9mnths_WaterControl_250; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Prior to cell collection, all surfaces and volumes were cleaned with 70% ethanol and RNaseZap (ThermoFisher Scientific) solution followed by dH20. Mice were euthanized, eyes enucleated and placed immediately into ice-cold HBSS. Retinas were dissected from the eyes (4 or 9 mo of age, no axon degeneration confirmed by PPD staining) in HBSS on ice and placed directly into 100 μl of a custom HBSS (Gibco), dispase (5 U/ml) (Stemcell Technologies), DNase I (2000 U/ml) (Worthington Biochemical) and SUPERase (1 U/μl) (ThermoFisher Scientific) solution. All retinas were from eyes that had no glaucomatous axon degeneration by PPD staining and analysis. Retinas were incubated for 20 mins at 37 °C and shaken at 350 RPM in an Eppendorf Thermomixer R followed by gentle trituration using a 200 μl pipette. Samples were blocked in 2% BSA, SUPERase (1 U/μl) in HBSS, and stained with conjugated antibodies against Cd11b, Cd11c, Cd34, Cd45.2, GFAP, Thy1.2 as well as DAPI. This cocktail allowed other retina cell types to be accurately removed during FACS. FACS was performed on a FACSAria (BD Biosciences). Thy1.2+ (and negative for all other markers) RGCs were sorted into 300μl buffer RLT + 1% β-ME, vortexed and frozen at -80°C until further processing.	Illumina HiSeq 2500	source_name;;Retinal ganglion cells|strain;;DBA/2J|treatment;;Water Control	GEO Accession;;GSM2409961		GSM2409961	D2_9mnths_WaterControl_250	6118032600	30590163	2017-03-09 10:01:30	4225332731	6118032600	30590163	2	30590163	index:0,count:30590163,average:100,stdev:0|index:1,count:30590163,average:100,stdev:0	GSM2409961_r1						7.66	2.6	0.09	4512065641	4328206945	4403047124	4247554499	95.93	96.47	27895817	27341177	182.565	655.757	143	236553	42.18	43.28	29171912	11767616	29171912	11767616	40.37	40.47	29171912	11261244	29171912	11003855	2393112843	53.04	6.80	0	2.30	0	0.17	0	0.33	0	0.00	0	8.31	0	27895817	0	200	0	195.40	0	2.41	0	0.03	0	2.28	0	0.02	0	236.32	0	0.49	0	2079797	0	30590163	0	703824	0	52139	0	100239	0	0	0	2541968	0	2398	0	0	0	20572	0	2567816	0	56148	0	2646934	0	88.89	0	27191993	0	160011	2367194	14.793945416253	30590163.0	27895817.0	2079797.0	703824.0	52139.0	100239.0	0.0	2541968.0	27191993.0	91.2	6.8	2.3	0.2	0.3	0.0	8.3	88.9	100	100	100.00	38	3059016300	27.9	22.1	22.2	27.8	0.0	35.2	18.6	bulk
1845564	SRR5061293	SRP094068	SRS1824171	SRX2381818	SRA499628	GEO		RNA-seq analysis of RNA from DBA/2J retinal ganglion cells	RNA-seq analysis from young and pre-glaucomatous DBA/2J retinal ganglion cells and control (age and sex-matched, D2-Gpnmb+) retinal ganglion cells Overall design: Retinal ganglion cell mRNA from 4 month (young) and 9 month (pre-glaucomatous) DBA/2J mice and age and sex-matched D2-Gpnmb+ controls		GSM2409962: D2_9mnths_WaterControl_1070; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Prior to cell collection, all surfaces and volumes were cleaned with 70% ethanol and RNaseZap (ThermoFisher Scientific) solution followed by dH20. Mice were euthanized, eyes enucleated and placed immediately into ice-cold HBSS. Retinas were dissected from the eyes (4 or 9 mo of age, no axon degeneration confirmed by PPD staining) in HBSS on ice and placed directly into 100 μl of a custom HBSS (Gibco), dispase (5 U/ml) (Stemcell Technologies), DNase I (2000 U/ml) (Worthington Biochemical) and SUPERase (1 U/μl) (ThermoFisher Scientific) solution. All retinas were from eyes that had no glaucomatous axon degeneration by PPD staining and analysis. Retinas were incubated for 20 mins at 37 °C and shaken at 350 RPM in an Eppendorf Thermomixer R followed by gentle trituration using a 200 μl pipette. Samples were blocked in 2% BSA, SUPERase (1 U/μl) in HBSS, and stained with conjugated antibodies against Cd11b, Cd11c, Cd34, Cd45.2, GFAP, Thy1.2 as well as DAPI. This cocktail allowed other retina cell types to be accurately removed during FACS. FACS was performed on a FACSAria (BD Biosciences). Thy1.2+ (and negative for all other markers) RGCs were sorted into 300μl buffer RLT + 1% β-ME, vortexed and frozen at -80°C until further processing.	Illumina HiSeq 2500	source_name;;Retinal ganglion cells|strain;;DBA/2J|treatment;;Water Control	GEO Accession;;GSM2409962		GSM2409962	D2_9mnths_WaterControl_1070	6221528800	31107644	2017-03-09 10:01:30	4113130280	6221528800	31107644	2	31107644	index:0,count:31107644,average:100,stdev:0|index:1,count:31107644,average:100,stdev:0	GSM2409962_r1						11.73	2.41	0.09	4758704637	4528107131	4597301797	4404065297	95.15	95.8	28880166	28093778	190.822	765.563	143	227503	48.97	50.78	30652507	14143543	30652507	14143543	47.29	47.28	30652507	13658303	30652507	13168417	2072453640	43.55	5.04	0	3.30	0	0.24	0	0.36	0	0.00	0	6.56	0	28880166	0	200	0	196.46	0	2.40	0	0.03	0	2.49	0	0.03	0	279.27	0	0.42	0	1568265	0	31107644	0	1025871	0	74407	0	111372	0	0	0	2041699	0	3270	0	0	0	28115	0	3463641	0	52969	0	3547995	0	89.54	0	27854295	0	171661	3216803	18.739276830497	31107644.0	28880166.0	1568265.0	1025871.0	74407.0	111372.0	0.0	2041699.0	27854295.0	92.8	5.0	3.3	0.2	0.4	0.0	6.6	89.5	100	100	100.00	38	3110764400	27.7	22.2	22.4	27.6	0.0	36.0	20.5	bulk
1845582	SRR5061294	SRP094068	SRS1824172	SRX2381819	SRA499628	GEO		RNA-seq analysis of RNA from DBA/2J retinal ganglion cells	RNA-seq analysis from young and pre-glaucomatous DBA/2J retinal ganglion cells and control (age and sex-matched, D2-Gpnmb+) retinal ganglion cells Overall design: Retinal ganglion cell mRNA from 4 month (young) and 9 month (pre-glaucomatous) DBA/2J mice and age and sex-matched D2-Gpnmb+ controls		GSM2409963: D2_9mnths_WaterControl_2024; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Prior to cell collection, all surfaces and volumes were cleaned with 70% ethanol and RNaseZap (ThermoFisher Scientific) solution followed by dH20. Mice were euthanized, eyes enucleated and placed immediately into ice-cold HBSS. Retinas were dissected from the eyes (4 or 9 mo of age, no axon degeneration confirmed by PPD staining) in HBSS on ice and placed directly into 100 μl of a custom HBSS (Gibco), dispase (5 U/ml) (Stemcell Technologies), DNase I (2000 U/ml) (Worthington Biochemical) and SUPERase (1 U/μl) (ThermoFisher Scientific) solution. All retinas were from eyes that had no glaucomatous axon degeneration by PPD staining and analysis. Retinas were incubated for 20 mins at 37 °C and shaken at 350 RPM in an Eppendorf Thermomixer R followed by gentle trituration using a 200 μl pipette. Samples were blocked in 2% BSA, SUPERase (1 U/μl) in HBSS, and stained with conjugated antibodies against Cd11b, Cd11c, Cd34, Cd45.2, GFAP, Thy1.2 as well as DAPI. This cocktail allowed other retina cell types to be accurately removed during FACS. FACS was performed on a FACSAria (BD Biosciences). Thy1.2+ (and negative for all other markers) RGCs were sorted into 300μl buffer RLT + 1% β-ME, vortexed and frozen at -80°C until further processing.	Illumina HiSeq 2500	source_name;;Retinal ganglion cells|strain;;DBA/2J|treatment;;Water Control	GEO Accession;;GSM2409963		GSM2409963	D2_9mnths_WaterControl_2024	7234979000	36174895	2017-03-09 10:01:30	5102914339	7234979000	36174895	2	36174895	index:0,count:36174895,average:100,stdev:0|index:1,count:36174895,average:100,stdev:0	GSM2409963_r1						11.31	2.91	0.15	4425117675	4162189831	4270298253	4044904489	94.06	94.72	29486268	28697570	170.319	917.897	113	223655	49.22	51.13	31444175	14513264	31444175	14513264	48.18	48.26	31444175	14206613	31444175	13698989	1873761327	42.34	5.87	0	3.05	0	0.23	0	0.26	0	0.00	0	18.00	0	29486268	0	200	0	193.33	0	2.20	0	0.02	0	2.46	0	0.02	0	181.88	0	0.54	0	2124903	0	36174895	0	1101535	0	82497	0	93030	0	0	0	6513100	0	3234	0	0	0	26929	0	3147914	0	63053	0	3241130	0	78.47	0	28384733	0	158798	2730861	17.197074270457	36174895.0	29486268.0	2124903.0	1101535.0	82497.0	93030.0	0.0	6513100.0	28384733.0	81.5	5.9	3.0	0.2	0.3	0.0	18.0	78.5	100	100	100.00	38	3617489500	28.5	21.6	22.0	27.7	0.1	34.7	18.7	bulk
1845595	SRR5061295	SRP094068	SRS1824173	SRX2381820	SRA499628	GEO		RNA-seq analysis of RNA from DBA/2J retinal ganglion cells	RNA-seq analysis from young and pre-glaucomatous DBA/2J retinal ganglion cells and control (age and sex-matched, D2-Gpnmb+) retinal ganglion cells Overall design: Retinal ganglion cell mRNA from 4 month (young) and 9 month (pre-glaucomatous) DBA/2J mice and age and sex-matched D2-Gpnmb+ controls		GSM2409964: D2_9mnths_WaterControl_2036; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Prior to cell collection, all surfaces and volumes were cleaned with 70% ethanol and RNaseZap (ThermoFisher Scientific) solution followed by dH20. Mice were euthanized, eyes enucleated and placed immediately into ice-cold HBSS. Retinas were dissected from the eyes (4 or 9 mo of age, no axon degeneration confirmed by PPD staining) in HBSS on ice and placed directly into 100 μl of a custom HBSS (Gibco), dispase (5 U/ml) (Stemcell Technologies), DNase I (2000 U/ml) (Worthington Biochemical) and SUPERase (1 U/μl) (ThermoFisher Scientific) solution. All retinas were from eyes that had no glaucomatous axon degeneration by PPD staining and analysis. Retinas were incubated for 20 mins at 37 °C and shaken at 350 RPM in an Eppendorf Thermomixer R followed by gentle trituration using a 200 μl pipette. Samples were blocked in 2% BSA, SUPERase (1 U/μl) in HBSS, and stained with conjugated antibodies against Cd11b, Cd11c, Cd34, Cd45.2, GFAP, Thy1.2 as well as DAPI. This cocktail allowed other retina cell types to be accurately removed during FACS. FACS was performed on a FACSAria (BD Biosciences). Thy1.2+ (and negative for all other markers) RGCs were sorted into 300μl buffer RLT + 1% β-ME, vortexed and frozen at -80°C until further processing.	Illumina HiSeq 2500	source_name;;Retinal ganglion cells|strain;;DBA/2J|treatment;;Water Control	GEO Accession;;GSM2409964		GSM2409964	D2_9mnths_WaterControl_2036	6746944600	33734723	2017-03-09 10:01:30	4736459302	6746944600	33734723	2	33734723	index:0,count:33734723,average:100,stdev:0|index:1,count:33734723,average:100,stdev:0	GSM2409964_r1						10.5	2.71	0.15	4278438763	4018728351	4129846051	3907391871	93.93	94.61	27882647	26995209	176.597	962.691	124	198976	51.64	53.63	29721347	14397528	29721347	14397528	50.29	50.49	29721347	14020971	29721347	13554483	1702637238	39.80	5.17	0	3.08	0	0.22	0	0.24	0	0.00	0	16.88	0	27882647	0	200	0	194.05	0	2.24	0	0.02	0	2.57	0	0.03	0	203.09	0	0.53	0	1742788	0	33734723	0	1037839	0	75591	0	81641	0	0	0	5694844	0	3382	0	0	0	29182	0	3564625	0	53895	0	3651084	0	79.58	0	26844808	0	162455	3133626	19.289193930627	33734723.0	27882647.0	1742788.0	1037839.0	75591.0	81641.0	0.0	5694844.0	26844808.0	82.7	5.2	3.1	0.2	0.2	0.0	16.9	79.6	100	100	100.00	38	3373472300	28.2	21.8	22.4	27.5	0.1	34.8	18.8	bulk
1845610	SRR5061296	SRP094068	SRS1824174	SRX2381821	SRA499628	GEO		RNA-seq analysis of RNA from DBA/2J retinal ganglion cells	RNA-seq analysis from young and pre-glaucomatous DBA/2J retinal ganglion cells and control (age and sex-matched, D2-Gpnmb+) retinal ganglion cells Overall design: Retinal ganglion cell mRNA from 4 month (young) and 9 month (pre-glaucomatous) DBA/2J mice and age and sex-matched D2-Gpnmb+ controls		GSM2409965: D2_9mnths_WaterControl_262; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Prior to cell collection, all surfaces and volumes were cleaned with 70% ethanol and RNaseZap (ThermoFisher Scientific) solution followed by dH20. Mice were euthanized, eyes enucleated and placed immediately into ice-cold HBSS. Retinas were dissected from the eyes (4 or 9 mo of age, no axon degeneration confirmed by PPD staining) in HBSS on ice and placed directly into 100 μl of a custom HBSS (Gibco), dispase (5 U/ml) (Stemcell Technologies), DNase I (2000 U/ml) (Worthington Biochemical) and SUPERase (1 U/μl) (ThermoFisher Scientific) solution. All retinas were from eyes that had no glaucomatous axon degeneration by PPD staining and analysis. Retinas were incubated for 20 mins at 37 °C and shaken at 350 RPM in an Eppendorf Thermomixer R followed by gentle trituration using a 200 μl pipette. Samples were blocked in 2% BSA, SUPERase (1 U/μl) in HBSS, and stained with conjugated antibodies against Cd11b, Cd11c, Cd34, Cd45.2, GFAP, Thy1.2 as well as DAPI. This cocktail allowed other retina cell types to be accurately removed during FACS. FACS was performed on a FACSAria (BD Biosciences). Thy1.2+ (and negative for all other markers) RGCs were sorted into 300μl buffer RLT + 1% β-ME, vortexed and frozen at -80°C until further processing.	Illumina HiSeq 2500	source_name;;Retinal ganglion cells|strain;;DBA/2J|treatment;;Water Control	GEO Accession;;GSM2409965		GSM2409965	D2_9mnths_WaterControl_262	7684861600	38424308	2017-03-09 10:01:30	5351290788	7684861600	38424308	2	38424308	index:0,count:38424308,average:100,stdev:0|index:1,count:38424308,average:100,stdev:0	GSM2409965_r1						5.76	2.33	0.07	5706376088	5483574250	5557096419	5371729720	96.1	96.66	35494249	34635733	180.082	687.978	141	312074	45.44	46.73	37246984	16130279	37246984	16130279	42.8	42.95	37246984	15190418	37246984	14826081	2799291954	49.06	5.60	0	2.54	0	0.18	0	0.28	0	0.00	0	7.17	0	35494249	0	200	0	196.00	0	2.51	0	0.03	0	2.37	0	0.02	0	314.38	0	0.49	0	2150809	0	38424308	0	974623	0	69213	0	106270	0	0	0	2754576	0	4129	0	0	0	33403	0	4272898	0	62267	0	4372697	0	89.84	0	34519626	0	185642	3903661	21.027897781752	38424308.0	35494249.0	2150809.0	974623.0	69213.0	106270.0	0.0	2754576.0	34519626.0	92.4	5.6	2.5	0.2	0.3	0.0	7.2	89.8	100	100	100.00	38	3842430800	27.3	22.7	22.9	27.1	0.0	35.0	18.6	bulk
1845626	SRR5061297	SRP094068	SRS1824175	SRX2381822	SRA499628	GEO		RNA-seq analysis of RNA from DBA/2J retinal ganglion cells	RNA-seq analysis from young and pre-glaucomatous DBA/2J retinal ganglion cells and control (age and sex-matched, D2-Gpnmb+) retinal ganglion cells Overall design: Retinal ganglion cell mRNA from 4 month (young) and 9 month (pre-glaucomatous) DBA/2J mice and age and sex-matched D2-Gpnmb+ controls		GSM2409966: Gpnmb_4mnths_WaterControl_2041; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Prior to cell collection, all surfaces and volumes were cleaned with 70% ethanol and RNaseZap (ThermoFisher Scientific) solution followed by dH20. Mice were euthanized, eyes enucleated and placed immediately into ice-cold HBSS. Retinas were dissected from the eyes (4 or 9 mo of age, no axon degeneration confirmed by PPD staining) in HBSS on ice and placed directly into 100 μl of a custom HBSS (Gibco), dispase (5 U/ml) (Stemcell Technologies), DNase I (2000 U/ml) (Worthington Biochemical) and SUPERase (1 U/μl) (ThermoFisher Scientific) solution. All retinas were from eyes that had no glaucomatous axon degeneration by PPD staining and analysis. Retinas were incubated for 20 mins at 37 °C and shaken at 350 RPM in an Eppendorf Thermomixer R followed by gentle trituration using a 200 μl pipette. Samples were blocked in 2% BSA, SUPERase (1 U/μl) in HBSS, and stained with conjugated antibodies against Cd11b, Cd11c, Cd34, Cd45.2, GFAP, Thy1.2 as well as DAPI. This cocktail allowed other retina cell types to be accurately removed during FACS. FACS was performed on a FACSAria (BD Biosciences). Thy1.2+ (and negative for all other markers) RGCs were sorted into 300μl buffer RLT + 1% β-ME, vortexed and frozen at -80°C until further processing.	Illumina HiSeq 2500	source_name;;Retinal ganglion cells|strain;;D2-Gpnmb+|treatment;;Water Control	GEO Accession;;GSM2409966		GSM2409966	Gpnmb_4mnths_WaterControl_2041	7347622800	36738114	2017-03-09 10:01:30	5164523775	7347622800	36738114	2	36738114	index:0,count:36738114,average:100,stdev:0|index:1,count:36738114,average:100,stdev:0	GSM2409966_r1						12.64	2.49	0.15	4286890009	4016709174	4138953924	3906098409	93.7	94.37	28961278	28228865	167.117	966.931	110	226518	46.31	48.09	30881338	13411441	30881338	13411441	45.26	45.28	30881338	13107113	30881338	12628851	1930416055	45.03	6.07	0	2.92	0	0.21	0	0.25	0	0.00	0	20.71	0	28961278	0	200	0	192.70	0	2.19	0	0.02	0	2.51	0	0.02	0	300.58	0	0.55	0	2231128	0	36738114	0	1071451	0	78392	0	91256	0	0	0	7607188	0	2817	0	0	0	23823	0	2884555	0	60087	0	2971282	0	75.92	0	27889827	0	148581	2477125	16.671882676789	36738114.0	28961278.0	2231128.0	1071451.0	78392.0	91256.0	0.0	7607188.0	27889827.0	78.8	6.1	2.9	0.2	0.2	0.0	20.7	75.9	100	100	100.00	38	3673811400	28.5	21.7	22.0	27.7	0.1	34.7	18.7	bulk
1845643	SRR5061298	SRP094068	SRS1824176	SRX2381823	SRA499628	GEO		RNA-seq analysis of RNA from DBA/2J retinal ganglion cells	RNA-seq analysis from young and pre-glaucomatous DBA/2J retinal ganglion cells and control (age and sex-matched, D2-Gpnmb+) retinal ganglion cells Overall design: Retinal ganglion cell mRNA from 4 month (young) and 9 month (pre-glaucomatous) DBA/2J mice and age and sex-matched D2-Gpnmb+ controls		GSM2409967: Gpnmb_4mnths_WaterControl_2058; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Prior to cell collection, all surfaces and volumes were cleaned with 70% ethanol and RNaseZap (ThermoFisher Scientific) solution followed by dH20. Mice were euthanized, eyes enucleated and placed immediately into ice-cold HBSS. Retinas were dissected from the eyes (4 or 9 mo of age, no axon degeneration confirmed by PPD staining) in HBSS on ice and placed directly into 100 μl of a custom HBSS (Gibco), dispase (5 U/ml) (Stemcell Technologies), DNase I (2000 U/ml) (Worthington Biochemical) and SUPERase (1 U/μl) (ThermoFisher Scientific) solution. All retinas were from eyes that had no glaucomatous axon degeneration by PPD staining and analysis. Retinas were incubated for 20 mins at 37 °C and shaken at 350 RPM in an Eppendorf Thermomixer R followed by gentle trituration using a 200 μl pipette. Samples were blocked in 2% BSA, SUPERase (1 U/μl) in HBSS, and stained with conjugated antibodies against Cd11b, Cd11c, Cd34, Cd45.2, GFAP, Thy1.2 as well as DAPI. This cocktail allowed other retina cell types to be accurately removed during FACS. FACS was performed on a FACSAria (BD Biosciences). Thy1.2+ (and negative for all other markers) RGCs were sorted into 300μl buffer RLT + 1% β-ME, vortexed and frozen at -80°C until further processing.	Illumina HiSeq 2500	source_name;;Retinal ganglion cells|strain;;D2-Gpnmb+|treatment;;Water Control	GEO Accession;;GSM2409967		GSM2409967	Gpnmb_4mnths_WaterControl_2058	5564008600	27820043	2017-03-09 10:01:30	3602719682	5564008600	27820043	2	27820043	index:0,count:27820043,average:100,stdev:0|index:1,count:27820043,average:100,stdev:0	GSM2409967_r1						10.25	2.65	0.11	3367735562	3194582777	3252386895	3106474733	94.86	95.51	22150894	21427780	175.607	929.130	113	156998	51.51	53.5	23618078	11410967	23618078	11410967	49.92	50.15	23618078	11056745	23618078	10697111	1369084434	40.65	6.13	0	2.95	0	0.20	0	0.23	0	0.00	0	19.94	0	22150894	0	200	0	193.28	0	2.24	0	0.02	0	2.53	0	0.02	0	290.30	0	0.48	0	1704506	0	27820043	0	820535	0	56155	0	65095	0	0	0	5547899	0	2554	0	0	0	23481	0	2872220	0	43639	0	2941894	0	76.67	0	21330359	0	155731	2514525	16.146592521720	27820043.0	22150894.0	1704506.0	820535.0	56155.0	65095.0	0.0	5547899.0	21330359.0	79.6	6.1	2.9	0.2	0.2	0.0	19.9	76.7	100	100	100.00	38	2782004300	28.2	22.0	22.2	27.4	0.1	35.6	18.7	bulk
1845658	SRR5061299	SRP094068	SRS1824177	SRX2381824	SRA499628	GEO		RNA-seq analysis of RNA from DBA/2J retinal ganglion cells	RNA-seq analysis from young and pre-glaucomatous DBA/2J retinal ganglion cells and control (age and sex-matched, D2-Gpnmb+) retinal ganglion cells Overall design: Retinal ganglion cell mRNA from 4 month (young) and 9 month (pre-glaucomatous) DBA/2J mice and age and sex-matched D2-Gpnmb+ controls		GSM2409968: Gpnmb_4mnths_WaterControl_2042; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Prior to cell collection, all surfaces and volumes were cleaned with 70% ethanol and RNaseZap (ThermoFisher Scientific) solution followed by dH20. Mice were euthanized, eyes enucleated and placed immediately into ice-cold HBSS. Retinas were dissected from the eyes (4 or 9 mo of age, no axon degeneration confirmed by PPD staining) in HBSS on ice and placed directly into 100 μl of a custom HBSS (Gibco), dispase (5 U/ml) (Stemcell Technologies), DNase I (2000 U/ml) (Worthington Biochemical) and SUPERase (1 U/μl) (ThermoFisher Scientific) solution. All retinas were from eyes that had no glaucomatous axon degeneration by PPD staining and analysis. Retinas were incubated for 20 mins at 37 °C and shaken at 350 RPM in an Eppendorf Thermomixer R followed by gentle trituration using a 200 μl pipette. Samples were blocked in 2% BSA, SUPERase (1 U/μl) in HBSS, and stained with conjugated antibodies against Cd11b, Cd11c, Cd34, Cd45.2, GFAP, Thy1.2 as well as DAPI. This cocktail allowed other retina cell types to be accurately removed during FACS. FACS was performed on a FACSAria (BD Biosciences). Thy1.2+ (and negative for all other markers) RGCs were sorted into 300μl buffer RLT + 1% β-ME, vortexed and frozen at -80°C until further processing.	Illumina HiSeq 2500	source_name;;Retinal ganglion cells|strain;;D2-Gpnmb+|treatment;;Water Control	GEO Accession;;GSM2409968		GSM2409968	Gpnmb_4mnths_WaterControl_2042	6903090600	34515453	2017-03-09 10:01:30	4474421955	6903090600	34515453	2	34515453	index:0,count:34515453,average:100,stdev:0|index:1,count:34515453,average:100,stdev:0	GSM2409968_r1						16.84	2.57	0.11	4330687261	4052947520	4182076130	3939665955	93.59	94.2	28446600	27862190	173.159	892.024	121	210553	46.26	48.0	30186166	13159346	30186166	13159346	46.01	45.82	30186166	13088960	30186166	12561552	1973130146	45.56	6.70	0	2.99	0	0.20	0	0.29	0	0.00	0	17.10	0	28446600	0	200	0	193.56	0	2.15	0	0.02	0	2.28	0	0.02	0	215.72	0	0.47	0	2311676	0	34515453	0	1032103	0	68186	0	98762	0	0	0	5901905	0	2426	0	0	0	19515	0	2219397	0	60503	0	2301841	0	79.43	0	27414497	0	146432	1957264	13.366368006993	34515453.0	28446600.0	2311676.0	1032103.0	68186.0	98762.0	0.0	5901905.0	27414497.0	82.4	6.7	3.0	0.2	0.3	0.0	17.1	79.4	100	100	100.00	38	3451545300	29.1	21.0	21.4	28.4	0.1	35.9	19.6	bulk
1847308	SRR5061300	SRP094068	SRS1824178	SRX2381825	SRA499628	GEO		RNA-seq analysis of RNA from DBA/2J retinal ganglion cells	RNA-seq analysis from young and pre-glaucomatous DBA/2J retinal ganglion cells and control (age and sex-matched, D2-Gpnmb+) retinal ganglion cells Overall design: Retinal ganglion cell mRNA from 4 month (young) and 9 month (pre-glaucomatous) DBA/2J mice and age and sex-matched D2-Gpnmb+ controls		GSM2409969: Gpnmb_4mnths_WaterControl_2047; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Prior to cell collection, all surfaces and volumes were cleaned with 70% ethanol and RNaseZap (ThermoFisher Scientific) solution followed by dH20. Mice were euthanized, eyes enucleated and placed immediately into ice-cold HBSS. Retinas were dissected from the eyes (4 or 9 mo of age, no axon degeneration confirmed by PPD staining) in HBSS on ice and placed directly into 100 μl of a custom HBSS (Gibco), dispase (5 U/ml) (Stemcell Technologies), DNase I (2000 U/ml) (Worthington Biochemical) and SUPERase (1 U/μl) (ThermoFisher Scientific) solution. All retinas were from eyes that had no glaucomatous axon degeneration by PPD staining and analysis. Retinas were incubated for 20 mins at 37 °C and shaken at 350 RPM in an Eppendorf Thermomixer R followed by gentle trituration using a 200 μl pipette. Samples were blocked in 2% BSA, SUPERase (1 U/μl) in HBSS, and stained with conjugated antibodies against Cd11b, Cd11c, Cd34, Cd45.2, GFAP, Thy1.2 as well as DAPI. This cocktail allowed other retina cell types to be accurately removed during FACS. FACS was performed on a FACSAria (BD Biosciences). Thy1.2+ (and negative for all other markers) RGCs were sorted into 300μl buffer RLT + 1% β-ME, vortexed and frozen at -80°C until further processing.	Illumina HiSeq 2500	source_name;;Retinal ganglion cells|strain;;D2-Gpnmb+|treatment;;Water Control	GEO Accession;;GSM2409969		GSM2409969	Gpnmb_4mnths_WaterControl_2047	6964798200	34823991	2017-03-09 10:01:30	4522744508	6964798200	34823991	2	34823991	index:0,count:34823991,average:100,stdev:0|index:1,count:34823991,average:100,stdev:0	GSM2409969_r1						13.08	2.59	0.17	4420351986	4140852530	4287464872	4043577353	93.68	94.31	28731519	28219029	176.007	878.976	123	203249	38.23	39.49	30363833	10983308	30363833	10983308	37.65	37.46	30363833	10817836	30363833	10418432	2403017059	54.36	6.57	0	2.63	0	0.19	0	0.32	0	0.00	0	16.98	0	28731519	0	200	0	193.71	0	2.19	0	0.02	0	2.24	0	0.02	0	299.20	0	0.48	0	2289145	0	34823991	0	916151	0	67888	0	111562	0	0	0	5913022	0	1997	0	0	0	17494	0	1844508	0	63606	0	1927605	0	79.87	0	27815368	0	151125	1648679	10.909373035567	34823991.0	28731519.0	2289145.0	916151.0	67888.0	111562.0	0.0	5913022.0	27815368.0	82.5	6.6	2.6	0.2	0.3	0.0	17.0	79.9	100	100	100.00	38	3482399100	29.0	21.0	21.5	28.4	0.1	35.9	19.6	bulk
1847325	SRR5061301	SRP094068	SRS1824179	SRX2381826	SRA499628	GEO		RNA-seq analysis of RNA from DBA/2J retinal ganglion cells	RNA-seq analysis from young and pre-glaucomatous DBA/2J retinal ganglion cells and control (age and sex-matched, D2-Gpnmb+) retinal ganglion cells Overall design: Retinal ganglion cell mRNA from 4 month (young) and 9 month (pre-glaucomatous) DBA/2J mice and age and sex-matched D2-Gpnmb+ controls		GSM2409970: Gpnmb_4mnths_WaterControl_2049; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Prior to cell collection, all surfaces and volumes were cleaned with 70% ethanol and RNaseZap (ThermoFisher Scientific) solution followed by dH20. Mice were euthanized, eyes enucleated and placed immediately into ice-cold HBSS. Retinas were dissected from the eyes (4 or 9 mo of age, no axon degeneration confirmed by PPD staining) in HBSS on ice and placed directly into 100 μl of a custom HBSS (Gibco), dispase (5 U/ml) (Stemcell Technologies), DNase I (2000 U/ml) (Worthington Biochemical) and SUPERase (1 U/μl) (ThermoFisher Scientific) solution. All retinas were from eyes that had no glaucomatous axon degeneration by PPD staining and analysis. Retinas were incubated for 20 mins at 37 °C and shaken at 350 RPM in an Eppendorf Thermomixer R followed by gentle trituration using a 200 μl pipette. Samples were blocked in 2% BSA, SUPERase (1 U/μl) in HBSS, and stained with conjugated antibodies against Cd11b, Cd11c, Cd34, Cd45.2, GFAP, Thy1.2 as well as DAPI. This cocktail allowed other retina cell types to be accurately removed during FACS. FACS was performed on a FACSAria (BD Biosciences). Thy1.2+ (and negative for all other markers) RGCs were sorted into 300μl buffer RLT + 1% β-ME, vortexed and frozen at -80°C until further processing.	Illumina HiSeq 2500	source_name;;Retinal ganglion cells|strain;;D2-Gpnmb+|treatment;;Water Control	GEO Accession;;GSM2409970		GSM2409970	Gpnmb_4mnths_WaterControl_2049	6766955200	33834776	2017-03-09 10:01:30	4383044507	6766955200	33834776	2	33834776	index:0,count:33834776,average:100,stdev:0|index:1,count:33834776,average:100,stdev:0	GSM2409970_r1						21.7	2.7	0.14	4149506667	3949480578	4001937149	3831190914	95.18	95.73	27435864	27006359	170.490	746.367	119	206741	45.33	47.1	29082386	12436511	29082386	12436511	45.59	45.14	29082386	12509381	29082386	11919337	1986841655	47.88	7.36	0	3.04	0	0.18	0	0.28	0	0.00	0	18.45	0	27435864	0	200	0	193.03	0	2.18	0	0.02	0	2.18	0	0.02	0	172.77	0	0.48	0	2488817	0	33834776	0	1029738	0	61354	0	93395	0	0	0	6244163	0	1883	0	0	0	14335	0	1577711	0	59862	0	1653791	0	78.04	0	26406126	0	136232	1396418	10.250293616771	33834776.0	27435864.0	2488817.0	1029738.0	61354.0	93395.0	0.0	6244163.0	26406126.0	81.1	7.4	3.0	0.2	0.3	0.0	18.5	78.0	100	100	100.00	38	3383477600	29.4	20.7	21.1	28.7	0.1	35.9	19.4	bulk
1847341	SRR5061302	SRP094068	SRS1824180	SRX2381827	SRA499628	GEO		RNA-seq analysis of RNA from DBA/2J retinal ganglion cells	RNA-seq analysis from young and pre-glaucomatous DBA/2J retinal ganglion cells and control (age and sex-matched, D2-Gpnmb+) retinal ganglion cells Overall design: Retinal ganglion cell mRNA from 4 month (young) and 9 month (pre-glaucomatous) DBA/2J mice and age and sex-matched D2-Gpnmb+ controls		GSM2409971: Gpnmb_4mnths_WaterControl_2050; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Prior to cell collection, all surfaces and volumes were cleaned with 70% ethanol and RNaseZap (ThermoFisher Scientific) solution followed by dH20. Mice were euthanized, eyes enucleated and placed immediately into ice-cold HBSS. Retinas were dissected from the eyes (4 or 9 mo of age, no axon degeneration confirmed by PPD staining) in HBSS on ice and placed directly into 100 μl of a custom HBSS (Gibco), dispase (5 U/ml) (Stemcell Technologies), DNase I (2000 U/ml) (Worthington Biochemical) and SUPERase (1 U/μl) (ThermoFisher Scientific) solution. All retinas were from eyes that had no glaucomatous axon degeneration by PPD staining and analysis. Retinas were incubated for 20 mins at 37 °C and shaken at 350 RPM in an Eppendorf Thermomixer R followed by gentle trituration using a 200 μl pipette. Samples were blocked in 2% BSA, SUPERase (1 U/μl) in HBSS, and stained with conjugated antibodies against Cd11b, Cd11c, Cd34, Cd45.2, GFAP, Thy1.2 as well as DAPI. This cocktail allowed other retina cell types to be accurately removed during FACS. FACS was performed on a FACSAria (BD Biosciences). Thy1.2+ (and negative for all other markers) RGCs were sorted into 300μl buffer RLT + 1% β-ME, vortexed and frozen at -80°C until further processing.	Illumina HiSeq 2500	source_name;;Retinal ganglion cells|strain;;D2-Gpnmb+|treatment;;Water Control	GEO Accession;;GSM2409971		GSM2409971	Gpnmb_4mnths_WaterControl_2050	5846898000	29234490	2017-03-09 10:01:30	3788839011	5846898000	29234490	2	29234490	index:0,count:29234490,average:100,stdev:0|index:1,count:29234490,average:100,stdev:0	GSM2409971_r1						19.4	2.75	0.15	3505287770	3298679731	3387337125	3207740598	94.11	94.7	23345987	22999710	168.759	835.832	119	179467	41.26	42.77	24722223	9633313	24722223	9633313	41.88	41.45	24722223	9777247	24722223	9335827	1810644534	51.65	7.63	0	2.82	0	0.18	0	0.30	0	0.00	0	19.66	0	23345987	0	200	0	192.66	0	2.15	0	0.02	0	2.04	0	0.02	0	115.65	0	0.48	0	2231757	0	29234490	0	823097	0	53706	0	87263	0	0	0	5747534	0	1476	0	0	0	11696	0	1185459	0	54377	0	1253008	0	77.04	0	22522890	0	127812	1045536	8.180264763872	29234490.0	23345987.0	2231757.0	823097.0	53706.0	87263.0	0.0	5747534.0	22522890.0	79.9	7.6	2.8	0.2	0.3	0.0	19.7	77.0	100	100	100.00	38	2923449000	29.6	20.5	21.0	28.8	0.1	35.8	19.2	bulk
1847355	SRR5061303	SRP094068	SRS1824181	SRX2381828	SRA499628	GEO		RNA-seq analysis of RNA from DBA/2J retinal ganglion cells	RNA-seq analysis from young and pre-glaucomatous DBA/2J retinal ganglion cells and control (age and sex-matched, D2-Gpnmb+) retinal ganglion cells Overall design: Retinal ganglion cell mRNA from 4 month (young) and 9 month (pre-glaucomatous) DBA/2J mice and age and sex-matched D2-Gpnmb+ controls		GSM2409972: Gpnmb_4mnths_WaterControl_2051; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Prior to cell collection, all surfaces and volumes were cleaned with 70% ethanol and RNaseZap (ThermoFisher Scientific) solution followed by dH20. Mice were euthanized, eyes enucleated and placed immediately into ice-cold HBSS. Retinas were dissected from the eyes (4 or 9 mo of age, no axon degeneration confirmed by PPD staining) in HBSS on ice and placed directly into 100 μl of a custom HBSS (Gibco), dispase (5 U/ml) (Stemcell Technologies), DNase I (2000 U/ml) (Worthington Biochemical) and SUPERase (1 U/μl) (ThermoFisher Scientific) solution. All retinas were from eyes that had no glaucomatous axon degeneration by PPD staining and analysis. Retinas were incubated for 20 mins at 37 °C and shaken at 350 RPM in an Eppendorf Thermomixer R followed by gentle trituration using a 200 μl pipette. Samples were blocked in 2% BSA, SUPERase (1 U/μl) in HBSS, and stained with conjugated antibodies against Cd11b, Cd11c, Cd34, Cd45.2, GFAP, Thy1.2 as well as DAPI. This cocktail allowed other retina cell types to be accurately removed during FACS. FACS was performed on a FACSAria (BD Biosciences). Thy1.2+ (and negative for all other markers) RGCs were sorted into 300μl buffer RLT + 1% β-ME, vortexed and frozen at -80°C until further processing.	Illumina HiSeq 2500	source_name;;Retinal ganglion cells|strain;;D2-Gpnmb+|treatment;;Water Control	GEO Accession;;GSM2409972		GSM2409972	Gpnmb_4mnths_WaterControl_2051	6307314000	31536570	2017-03-09 10:01:30	4101725720	6307314000	31536570	2	31536570	index:0,count:31536570,average:100,stdev:0|index:1,count:31536570,average:100,stdev:0	GSM2409972_r1						19.11	2.41	0.17	3764002182	3527064545	3649891144	3443110616	93.71	94.33	25117032	24713165	168.717	878.882	114	192713	42.17	43.57	26556289	10591552	26556289	10591552	41.78	41.68	26556289	10493408	26556289	10132784	1893955451	50.32	7.22	0	2.56	0	0.19	0	0.29	0	0.00	0	19.88	0	25117032	0	200	0	192.75	0	2.17	0	0.02	0	2.26	0	0.02	0	150.77	0	0.49	0	2278388	0	31536570	0	807429	0	59169	0	90834	0	0	0	6269535	0	1643	0	0	0	13514	0	1441829	0	57789	0	1514775	0	77.08	0	24309603	0	131543	1267119	9.632736063493	31536570.0	25117032.0	2278388.0	807429.0	59169.0	90834.0	0.0	6269535.0	24309603.0	79.6	7.2	2.6	0.2	0.3	0.0	19.9	77.1	100	100	100.00	38	3153657000	29.2	20.9	21.3	28.4	0.1	35.8	19.3	bulk
1847369	SRR5061304	SRP094068	SRS1824182	SRX2381829	SRA499628	GEO		RNA-seq analysis of RNA from DBA/2J retinal ganglion cells	RNA-seq analysis from young and pre-glaucomatous DBA/2J retinal ganglion cells and control (age and sex-matched, D2-Gpnmb+) retinal ganglion cells Overall design: Retinal ganglion cell mRNA from 4 month (young) and 9 month (pre-glaucomatous) DBA/2J mice and age and sex-matched D2-Gpnmb+ controls		GSM2409973: Gpnmb_4mnths_WaterControl_2052; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Prior to cell collection, all surfaces and volumes were cleaned with 70% ethanol and RNaseZap (ThermoFisher Scientific) solution followed by dH20. Mice were euthanized, eyes enucleated and placed immediately into ice-cold HBSS. Retinas were dissected from the eyes (4 or 9 mo of age, no axon degeneration confirmed by PPD staining) in HBSS on ice and placed directly into 100 μl of a custom HBSS (Gibco), dispase (5 U/ml) (Stemcell Technologies), DNase I (2000 U/ml) (Worthington Biochemical) and SUPERase (1 U/μl) (ThermoFisher Scientific) solution. All retinas were from eyes that had no glaucomatous axon degeneration by PPD staining and analysis. Retinas were incubated for 20 mins at 37 °C and shaken at 350 RPM in an Eppendorf Thermomixer R followed by gentle trituration using a 200 μl pipette. Samples were blocked in 2% BSA, SUPERase (1 U/μl) in HBSS, and stained with conjugated antibodies against Cd11b, Cd11c, Cd34, Cd45.2, GFAP, Thy1.2 as well as DAPI. This cocktail allowed other retina cell types to be accurately removed during FACS. FACS was performed on a FACSAria (BD Biosciences). Thy1.2+ (and negative for all other markers) RGCs were sorted into 300μl buffer RLT + 1% β-ME, vortexed and frozen at -80°C until further processing.	Illumina HiSeq 2500	source_name;;Retinal ganglion cells|strain;;D2-Gpnmb+|treatment;;Water Control	GEO Accession;;GSM2409973		GSM2409973	Gpnmb_4mnths_WaterControl_2052	6100274200	30501371	2017-03-09 10:01:30	3961785680	6100274200	30501371	2	30501371	index:0,count:30501371,average:100,stdev:0|index:1,count:30501371,average:100,stdev:0	GSM2409973_r1						15.21	2.59	0.13	3589509357	3398845620	3457648182	3296076903	94.69	95.33	24125113	23538576	168.358	922.320	114	185540	50.59	52.66	25724039	12205944	25724039	12205944	49.38	49.34	25724039	11913703	25724039	11437213	1472264005	41.02	6.63	0	3.10	0	0.21	0	0.23	0	0.00	0	20.46	0	24125113	0	200	0	192.62	0	2.21	0	0.02	0	2.43	0	0.02	0	164.63	0	0.49	0	2020790	0	30501371	0	945401	0	64318	0	70546	0	0	0	6241394	0	2396	0	0	0	19339	0	2293230	0	53234	0	2368199	0	76.00	0	23179712	0	148071	1984041	13.399254411735	30501371.0	24125113.0	2020790.0	945401.0	64318.0	70546.0	0.0	6241394.0	23179712.0	79.1	6.6	3.1	0.2	0.2	0.0	20.5	76.0	100	100	100.00	38	3050137100	28.7	21.5	21.9	27.7	0.1	35.8	19.4	bulk
1847386	SRR5061305	SRP094068	SRS1824183	SRX2381830	SRA499628	GEO		RNA-seq analysis of RNA from DBA/2J retinal ganglion cells	RNA-seq analysis from young and pre-glaucomatous DBA/2J retinal ganglion cells and control (age and sex-matched, D2-Gpnmb+) retinal ganglion cells Overall design: Retinal ganglion cell mRNA from 4 month (young) and 9 month (pre-glaucomatous) DBA/2J mice and age and sex-matched D2-Gpnmb+ controls		GSM2409974: Gpnmb_4mnths_WaterControl_2056; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Prior to cell collection, all surfaces and volumes were cleaned with 70% ethanol and RNaseZap (ThermoFisher Scientific) solution followed by dH20. Mice were euthanized, eyes enucleated and placed immediately into ice-cold HBSS. Retinas were dissected from the eyes (4 or 9 mo of age, no axon degeneration confirmed by PPD staining) in HBSS on ice and placed directly into 100 μl of a custom HBSS (Gibco), dispase (5 U/ml) (Stemcell Technologies), DNase I (2000 U/ml) (Worthington Biochemical) and SUPERase (1 U/μl) (ThermoFisher Scientific) solution. All retinas were from eyes that had no glaucomatous axon degeneration by PPD staining and analysis. Retinas were incubated for 20 mins at 37 °C and shaken at 350 RPM in an Eppendorf Thermomixer R followed by gentle trituration using a 200 μl pipette. Samples were blocked in 2% BSA, SUPERase (1 U/μl) in HBSS, and stained with conjugated antibodies against Cd11b, Cd11c, Cd34, Cd45.2, GFAP, Thy1.2 as well as DAPI. This cocktail allowed other retina cell types to be accurately removed during FACS. FACS was performed on a FACSAria (BD Biosciences). Thy1.2+ (and negative for all other markers) RGCs were sorted into 300μl buffer RLT + 1% β-ME, vortexed and frozen at -80°C until further processing.	Illumina HiSeq 2500	source_name;;Retinal ganglion cells|strain;;D2-Gpnmb+|treatment;;Water Control	GEO Accession;;GSM2409974		GSM2409974	Gpnmb_4mnths_WaterControl_2056	7236940000	36184700	2017-03-09 10:01:30	4690061941	7236940000	36184700	2	36184700	index:0,count:36184700,average:100,stdev:0|index:1,count:36184700,average:100,stdev:0	GSM2409974_r1						11.1	2.7	0.12	4319525180	4093563995	4170597188	3980826452	94.77	95.45	29231247	28505823	164.087	891.049	113	234216	48.52	50.38	31148349	14181923	31148349	14181923	46.73	46.83	31148349	13660038	31148349	13183889	1875067000	43.41	5.58	0	2.98	0	0.22	0	0.27	0	0.00	0	18.73	0	29231247	0	200	0	193.40	0	2.24	0	0.02	0	2.54	0	0.03	0	290.12	0	0.47	0	2019840	0	36184700	0	1079746	0	80182	0	96651	0	0	0	6776620	0	3081	0	0	0	25832	0	3117384	0	58092	0	3204389	0	77.80	0	28151501	0	160456	2671558	16.649785611009	36184700.0	29231247.0	2019840.0	1079746.0	80182.0	96651.0	0.0	6776620.0	28151501.0	80.8	5.6	3.0	0.2	0.3	0.0	18.7	77.8	100	100	100.00	38	3618470000	28.3	21.8	22.1	27.6	0.1	35.9	19.9	bulk
1847401	SRR5061306	SRP094068	SRS1824184	SRX2381831	SRA499628	GEO		RNA-seq analysis of RNA from DBA/2J retinal ganglion cells	RNA-seq analysis from young and pre-glaucomatous DBA/2J retinal ganglion cells and control (age and sex-matched, D2-Gpnmb+) retinal ganglion cells Overall design: Retinal ganglion cell mRNA from 4 month (young) and 9 month (pre-glaucomatous) DBA/2J mice and age and sex-matched D2-Gpnmb+ controls		GSM2409975: Gpnmb_4mnths_WaterControl_2057; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Prior to cell collection, all surfaces and volumes were cleaned with 70% ethanol and RNaseZap (ThermoFisher Scientific) solution followed by dH20. Mice were euthanized, eyes enucleated and placed immediately into ice-cold HBSS. Retinas were dissected from the eyes (4 or 9 mo of age, no axon degeneration confirmed by PPD staining) in HBSS on ice and placed directly into 100 μl of a custom HBSS (Gibco), dispase (5 U/ml) (Stemcell Technologies), DNase I (2000 U/ml) (Worthington Biochemical) and SUPERase (1 U/μl) (ThermoFisher Scientific) solution. All retinas were from eyes that had no glaucomatous axon degeneration by PPD staining and analysis. Retinas were incubated for 20 mins at 37 °C and shaken at 350 RPM in an Eppendorf Thermomixer R followed by gentle trituration using a 200 μl pipette. Samples were blocked in 2% BSA, SUPERase (1 U/μl) in HBSS, and stained with conjugated antibodies against Cd11b, Cd11c, Cd34, Cd45.2, GFAP, Thy1.2 as well as DAPI. This cocktail allowed other retina cell types to be accurately removed during FACS. FACS was performed on a FACSAria (BD Biosciences). Thy1.2+ (and negative for all other markers) RGCs were sorted into 300μl buffer RLT + 1% β-ME, vortexed and frozen at -80°C until further processing.	Illumina HiSeq 2500	source_name;;Retinal ganglion cells|strain;;D2-Gpnmb+|treatment;;Water Control	GEO Accession;;GSM2409975		GSM2409975	Gpnmb_4mnths_WaterControl_2057	7203940800	36019704	2017-03-09 10:01:30	4686230219	7203940800	36019704	2	36019704	index:0,count:36019704,average:100,stdev:0|index:1,count:36019704,average:100,stdev:0	GSM2409975_r1						10.84	2.65	0.14	4501670015	4263081489	4340789118	4140414064	94.7	95.38	29454102	28514043	176.193	954.746	124	209745	52.75	54.85	31437123	15536672	31437123	15536672	51.11	51.32	31437123	15054837	31437123	14536489	1750472436	38.88	6.00	0	3.14	0	0.23	0	0.25	0	0.00	0	17.75	0	29454102	0	200	0	193.50	0	2.27	0	0.02	0	2.58	0	0.03	0	281.89	0	0.49	0	2160129	0	36019704	0	1130646	0	81997	0	89916	0	0	0	6393689	0	3776	0	0	0	29816	0	3751242	0	59727	0	3844561	0	78.63	0	28323456	0	164402	3298807	20.065491903991	36019704.0	29454102.0	2160129.0	1130646.0	81997.0	89916.0	0.0	6393689.0	28323456.0	81.8	6.0	3.1	0.2	0.2	0.0	17.8	78.6	100	100	100.00	38	3601970400	28.2	21.9	22.3	27.4	0.1	35.7	19.3	bulk
1847418	SRR5061307	SRP094068	SRS1824185	SRX2381832	SRA499628	GEO		RNA-seq analysis of RNA from DBA/2J retinal ganglion cells	RNA-seq analysis from young and pre-glaucomatous DBA/2J retinal ganglion cells and control (age and sex-matched, D2-Gpnmb+) retinal ganglion cells Overall design: Retinal ganglion cell mRNA from 4 month (young) and 9 month (pre-glaucomatous) DBA/2J mice and age and sex-matched D2-Gpnmb+ controls		GSM2409976: Gpnmb_9mnths_WaterControl_396; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Prior to cell collection, all surfaces and volumes were cleaned with 70% ethanol and RNaseZap (ThermoFisher Scientific) solution followed by dH20. Mice were euthanized, eyes enucleated and placed immediately into ice-cold HBSS. Retinas were dissected from the eyes (4 or 9 mo of age, no axon degeneration confirmed by PPD staining) in HBSS on ice and placed directly into 100 μl of a custom HBSS (Gibco), dispase (5 U/ml) (Stemcell Technologies), DNase I (2000 U/ml) (Worthington Biochemical) and SUPERase (1 U/μl) (ThermoFisher Scientific) solution. All retinas were from eyes that had no glaucomatous axon degeneration by PPD staining and analysis. Retinas were incubated for 20 mins at 37 °C and shaken at 350 RPM in an Eppendorf Thermomixer R followed by gentle trituration using a 200 μl pipette. Samples were blocked in 2% BSA, SUPERase (1 U/μl) in HBSS, and stained with conjugated antibodies against Cd11b, Cd11c, Cd34, Cd45.2, GFAP, Thy1.2 as well as DAPI. This cocktail allowed other retina cell types to be accurately removed during FACS. FACS was performed on a FACSAria (BD Biosciences). Thy1.2+ (and negative for all other markers) RGCs were sorted into 300μl buffer RLT + 1% β-ME, vortexed and frozen at -80°C until further processing.	Illumina HiSeq 2500	source_name;;Retinal ganglion cells|strain;;D2-Gpnmb+|treatment;;Water Control	GEO Accession;;GSM2409976		GSM2409976	Gpnmb_9mnths_WaterControl_396	7081557400	35407787	2017-03-09 10:01:30	4923109053	7081557400	35407787	2	35407787	index:0,count:35407787,average:100,stdev:0|index:1,count:35407787,average:100,stdev:0	GSM2409976_r1						2.47	2.46	0.07	5385380716	5235348869	5261303563	5143477577	97.21	97.76	32939147	32154150	185.821	668.037	144	274559	41.78	42.81	34433902	13760375	34433902	13760375	38.64	38.78	34433902	12726287	34433902	12464388	2901802840	53.88	5.26	0	2.25	0	0.18	0	0.28	0	0.00	0	6.51	0	32939147	0	200	0	196.28	0	2.40	0	0.03	0	2.57	0	0.03	0	248.48	0	0.49	0	1861981	0	35407787	0	795908	0	62816	0	100356	0	0	0	2305468	0	3074	0	0	0	27796	0	3672419	0	59420	0	3762709	0	90.78	0	32143239	0	171796	3404686	19.818191343221	35407787.0	32939147.0	1861981.0	795908.0	62816.0	100356.0	0.0	2305468.0	32143239.0	93.0	5.3	2.2	0.2	0.3	0.0	6.5	90.8	100	100	100.00	38	3540778700	27.3	22.6	22.8	27.2	0.0	35.1	18.8	bulk
1847433	SRR5061308	SRP094068	SRS1824186	SRX2381833	SRA499628	GEO		RNA-seq analysis of RNA from DBA/2J retinal ganglion cells	RNA-seq analysis from young and pre-glaucomatous DBA/2J retinal ganglion cells and control (age and sex-matched, D2-Gpnmb+) retinal ganglion cells Overall design: Retinal ganglion cell mRNA from 4 month (young) and 9 month (pre-glaucomatous) DBA/2J mice and age and sex-matched D2-Gpnmb+ controls		GSM2409977: Gpnmb_9mnths_WaterControl_2045; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Prior to cell collection, all surfaces and volumes were cleaned with 70% ethanol and RNaseZap (ThermoFisher Scientific) solution followed by dH20. Mice were euthanized, eyes enucleated and placed immediately into ice-cold HBSS. Retinas were dissected from the eyes (4 or 9 mo of age, no axon degeneration confirmed by PPD staining) in HBSS on ice and placed directly into 100 μl of a custom HBSS (Gibco), dispase (5 U/ml) (Stemcell Technologies), DNase I (2000 U/ml) (Worthington Biochemical) and SUPERase (1 U/μl) (ThermoFisher Scientific) solution. All retinas were from eyes that had no glaucomatous axon degeneration by PPD staining and analysis. Retinas were incubated for 20 mins at 37 °C and shaken at 350 RPM in an Eppendorf Thermomixer R followed by gentle trituration using a 200 μl pipette. Samples were blocked in 2% BSA, SUPERase (1 U/μl) in HBSS, and stained with conjugated antibodies against Cd11b, Cd11c, Cd34, Cd45.2, GFAP, Thy1.2 as well as DAPI. This cocktail allowed other retina cell types to be accurately removed during FACS. FACS was performed on a FACSAria (BD Biosciences). Thy1.2+ (and negative for all other markers) RGCs were sorted into 300μl buffer RLT + 1% β-ME, vortexed and frozen at -80°C until further processing.	Illumina HiSeq 2500	source_name;;Retinal ganglion cells|strain;;D2-Gpnmb+|treatment;;Water Control	GEO Accession;;GSM2409977		GSM2409977	Gpnmb_9mnths_WaterControl_2045	6205002200	31025011	2017-03-09 10:01:30	4015233048	6205002200	31025011	2	31025011	index:0,count:31025011,average:100,stdev:0|index:1,count:31025011,average:100,stdev:0	GSM2409977_r1						20.84	2.83	0.13	3687466684	3466028874	3549377988	3357343344	93.99	94.59	24730072	24313542	167.663	855.392	112	195010	45.46	47.33	26314800	11243171	26314800	11243171	45.95	45.54	26314800	11364594	26314800	10818529	1716737888	46.56	7.33	0	3.14	0	0.19	0	0.29	0	0.00	0	19.81	0	24730072	0	200	0	192.66	0	2.15	0	0.02	0	2.14	0	0.02	0	244.40	0	0.48	0	2274481	0	31025011	0	973789	0	59449	0	88971	0	0	0	6146519	0	1865	0	0	0	14093	0	1504813	0	56605	0	1577376	0	76.57	0	23756283	0	137990	1313777	9.520813102399	31025011.0	24730072.0	2274481.0	973789.0	59449.0	88971.0	0.0	6146519.0	23756283.0	79.7	7.3	3.1	0.2	0.3	0.0	19.8	76.6	100	100	100.00	38	3102501100	29.4	20.7	21.2	28.7	0.1	35.9	19.5	bulk
1847450	SRR5061309	SRP094068	SRS1824187	SRX2381834	SRA499628	GEO		RNA-seq analysis of RNA from DBA/2J retinal ganglion cells	RNA-seq analysis from young and pre-glaucomatous DBA/2J retinal ganglion cells and control (age and sex-matched, D2-Gpnmb+) retinal ganglion cells Overall design: Retinal ganglion cell mRNA from 4 month (young) and 9 month (pre-glaucomatous) DBA/2J mice and age and sex-matched D2-Gpnmb+ controls		GSM2409978: Gpnmb_9mnths_WaterControl_2053; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Prior to cell collection, all surfaces and volumes were cleaned with 70% ethanol and RNaseZap (ThermoFisher Scientific) solution followed by dH20. Mice were euthanized, eyes enucleated and placed immediately into ice-cold HBSS. Retinas were dissected from the eyes (4 or 9 mo of age, no axon degeneration confirmed by PPD staining) in HBSS on ice and placed directly into 100 μl of a custom HBSS (Gibco), dispase (5 U/ml) (Stemcell Technologies), DNase I (2000 U/ml) (Worthington Biochemical) and SUPERase (1 U/μl) (ThermoFisher Scientific) solution. All retinas were from eyes that had no glaucomatous axon degeneration by PPD staining and analysis. Retinas were incubated for 20 mins at 37 °C and shaken at 350 RPM in an Eppendorf Thermomixer R followed by gentle trituration using a 200 μl pipette. Samples were blocked in 2% BSA, SUPERase (1 U/μl) in HBSS, and stained with conjugated antibodies against Cd11b, Cd11c, Cd34, Cd45.2, GFAP, Thy1.2 as well as DAPI. This cocktail allowed other retina cell types to be accurately removed during FACS. FACS was performed on a FACSAria (BD Biosciences). Thy1.2+ (and negative for all other markers) RGCs were sorted into 300μl buffer RLT + 1% β-ME, vortexed and frozen at -80°C until further processing.	Illumina HiSeq 2500	source_name;;Retinal ganglion cells|strain;;D2-Gpnmb+|treatment;;Water Control	GEO Accession;;GSM2409978		GSM2409978	Gpnmb_9mnths_WaterControl_2053	5503959800	27519799	2017-03-09 10:01:30	3578864623	5503959800	27519799	2	27519799	index:0,count:27519799,average:100,stdev:0|index:1,count:27519799,average:100,stdev:0	GSM2409978_r1						14.94	2.78	0.17	3478911459	3282266764	3358737296	3190007265	94.35	94.98	22533615	21999824	176.971	906.859	132	158038	48.82	50.67	23938672	11000119	23938672	11000119	48.05	48.0	23938672	10827939	23938672	10419562	1504084730	43.23	7.41	0	2.99	0	0.20	0	0.27	0	0.00	0	17.65	0	22533615	0	200	0	193.17	0	2.19	0	0.02	0	2.35	0	0.02	0	153.60	0	0.49	0	2038910	0	27519799	0	824184	0	55978	0	73134	0	0	0	4857072	0	2156	0	0	0	17283	0	2041874	0	52702	0	2114015	0	78.89	0	21709431	0	143873	1820679	12.654764966324	27519799.0	22533615.0	2038910.0	824184.0	55978.0	73134.0	0.0	4857072.0	21709431.0	81.9	7.4	3.0	0.2	0.3	0.0	17.6	78.9	100	100	100.00	38	2751979900	28.8	21.2	21.7	28.2	0.1	35.7	19.1	bulk
1847563	SRR5061310	SRP094068	SRS1824188	SRX2381835	SRA499628	GEO		RNA-seq analysis of RNA from DBA/2J retinal ganglion cells	RNA-seq analysis from young and pre-glaucomatous DBA/2J retinal ganglion cells and control (age and sex-matched, D2-Gpnmb+) retinal ganglion cells Overall design: Retinal ganglion cell mRNA from 4 month (young) and 9 month (pre-glaucomatous) DBA/2J mice and age and sex-matched D2-Gpnmb+ controls		GSM2409979: Gpnmb_9mnths_WaterControl_2055; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Prior to cell collection, all surfaces and volumes were cleaned with 70% ethanol and RNaseZap (ThermoFisher Scientific) solution followed by dH20. Mice were euthanized, eyes enucleated and placed immediately into ice-cold HBSS. Retinas were dissected from the eyes (4 or 9 mo of age, no axon degeneration confirmed by PPD staining) in HBSS on ice and placed directly into 100 μl of a custom HBSS (Gibco), dispase (5 U/ml) (Stemcell Technologies), DNase I (2000 U/ml) (Worthington Biochemical) and SUPERase (1 U/μl) (ThermoFisher Scientific) solution. All retinas were from eyes that had no glaucomatous axon degeneration by PPD staining and analysis. Retinas were incubated for 20 mins at 37 °C and shaken at 350 RPM in an Eppendorf Thermomixer R followed by gentle trituration using a 200 μl pipette. Samples were blocked in 2% BSA, SUPERase (1 U/μl) in HBSS, and stained with conjugated antibodies against Cd11b, Cd11c, Cd34, Cd45.2, GFAP, Thy1.2 as well as DAPI. This cocktail allowed other retina cell types to be accurately removed during FACS. FACS was performed on a FACSAria (BD Biosciences). Thy1.2+ (and negative for all other markers) RGCs were sorted into 300μl buffer RLT + 1% β-ME, vortexed and frozen at -80°C until further processing.	Illumina HiSeq 2500	source_name;;Retinal ganglion cells|strain;;D2-Gpnmb+|treatment;;Water Control	GEO Accession;;GSM2409979		GSM2409979	Gpnmb_9mnths_WaterControl_2055	4937904800	24689524	2017-03-09 10:01:30	3211778036	4937904800	24689524	2	24689524	index:0,count:24689524,average:100,stdev:0|index:1,count:24689524,average:100,stdev:0	GSM2409979_r1						10.5	2.67	0.1	3096615206	2934844526	2988376461	2852477993	94.78	95.45	20246995	19627095	176.653	962.355	124	143892	50.29	52.25	21583333	10182462	21583333	10182462	48.47	48.6	21583333	9813524	21583333	9471337	1285929800	41.53	5.97	0	3.08	0	0.23	0	0.28	0	0.00	0	17.49	0	20246995	0	200	0	193.65	0	2.27	0	0.03	0	2.51	0	0.03	0	287.64	0	0.48	0	1473331	0	24689524	0	759374	0	56213	0	68241	0	0	0	4318075	0	2551	0	0	0	19912	0	2432027	0	38411	0	2492901	0	78.93	0	19487621	0	147159	2140103	14.542793848830	24689524.0	20246995.0	1473331.0	759374.0	56213.0	68241.0	0.0	4318075.0	19487621.0	82.0	6.0	3.1	0.2	0.3	0.0	17.5	78.9	100	100	100.00	38	2468952400	28.2	21.9	22.3	27.4	0.1	35.8	19.7	bulk
1847577	SRR5061311	SRP094068	SRS1824189	SRX2381836	SRA499628	GEO		RNA-seq analysis of RNA from DBA/2J retinal ganglion cells	RNA-seq analysis from young and pre-glaucomatous DBA/2J retinal ganglion cells and control (age and sex-matched, D2-Gpnmb+) retinal ganglion cells Overall design: Retinal ganglion cell mRNA from 4 month (young) and 9 month (pre-glaucomatous) DBA/2J mice and age and sex-matched D2-Gpnmb+ controls		GSM2409980: Gpnmb_9mnths_WaterControl_469; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Prior to cell collection, all surfaces and volumes were cleaned with 70% ethanol and RNaseZap (ThermoFisher Scientific) solution followed by dH20. Mice were euthanized, eyes enucleated and placed immediately into ice-cold HBSS. Retinas were dissected from the eyes (4 or 9 mo of age, no axon degeneration confirmed by PPD staining) in HBSS on ice and placed directly into 100 μl of a custom HBSS (Gibco), dispase (5 U/ml) (Stemcell Technologies), DNase I (2000 U/ml) (Worthington Biochemical) and SUPERase (1 U/μl) (ThermoFisher Scientific) solution. All retinas were from eyes that had no glaucomatous axon degeneration by PPD staining and analysis. Retinas were incubated for 20 mins at 37 °C and shaken at 350 RPM in an Eppendorf Thermomixer R followed by gentle trituration using a 200 μl pipette. Samples were blocked in 2% BSA, SUPERase (1 U/μl) in HBSS, and stained with conjugated antibodies against Cd11b, Cd11c, Cd34, Cd45.2, GFAP, Thy1.2 as well as DAPI. This cocktail allowed other retina cell types to be accurately removed during FACS. FACS was performed on a FACSAria (BD Biosciences). Thy1.2+ (and negative for all other markers) RGCs were sorted into 300μl buffer RLT + 1% β-ME, vortexed and frozen at -80°C until further processing.	Illumina HiSeq 2500	source_name;;Retinal ganglion cells|strain;;D2-Gpnmb+|treatment;;Water Control	GEO Accession;;GSM2409980		GSM2409980	Gpnmb_9mnths_WaterControl_469	6242693000	31213465	2017-03-09 10:01:30	4337904016	6242693000	31213465	2	31213465	index:0,count:31213465,average:100,stdev:0|index:1,count:31213465,average:100,stdev:0	GSM2409980_r1						3.82	2.57	0.08	4660517687	4589247445	4521912781	4480518802	98.47	99.08	28579385	27701982	185.955	677.862	146	236707	53.75	55.5	30147291	15362367	30147291	15362367	49.41	49.76	30147291	14122394	30147291	13773874	1915001779	41.09	5.91	0	2.88	0	0.19	0	0.23	0	0.00	0	8.02	0	28579385	0	200	0	195.61	0	2.57	0	0.03	0	2.54	0	0.03	0	341.55	0	0.51	0	1845472	0	31213465	0	900192	0	59258	0	72298	0	0	0	2502524	0	4064	0	0	0	29741	0	4193441	0	50742	0	4277988	0	88.68	0	27679193	0	152694	3880277	25.412111805310	31213465.0	28579385.0	1845472.0	900192.0	59258.0	72298.0	0.0	2502524.0	27679193.0	91.6	5.9	2.9	0.2	0.2	0.0	8.0	88.7	100	100	100.00	38	3121346500	26.9	23.0	23.2	26.9	0.0	34.9	18.2	bulk
1847592	SRR5061312	SRP094068	SRS1824190	SRX2381837	SRA499628	GEO		RNA-seq analysis of RNA from DBA/2J retinal ganglion cells	RNA-seq analysis from young and pre-glaucomatous DBA/2J retinal ganglion cells and control (age and sex-matched, D2-Gpnmb+) retinal ganglion cells Overall design: Retinal ganglion cell mRNA from 4 month (young) and 9 month (pre-glaucomatous) DBA/2J mice and age and sex-matched D2-Gpnmb+ controls		GSM2409981: Gpnmb_9mnths_WaterControl_478; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Prior to cell collection, all surfaces and volumes were cleaned with 70% ethanol and RNaseZap (ThermoFisher Scientific) solution followed by dH20. Mice were euthanized, eyes enucleated and placed immediately into ice-cold HBSS. Retinas were dissected from the eyes (4 or 9 mo of age, no axon degeneration confirmed by PPD staining) in HBSS on ice and placed directly into 100 μl of a custom HBSS (Gibco), dispase (5 U/ml) (Stemcell Technologies), DNase I (2000 U/ml) (Worthington Biochemical) and SUPERase (1 U/μl) (ThermoFisher Scientific) solution. All retinas were from eyes that had no glaucomatous axon degeneration by PPD staining and analysis. Retinas were incubated for 20 mins at 37 °C and shaken at 350 RPM in an Eppendorf Thermomixer R followed by gentle trituration using a 200 μl pipette. Samples were blocked in 2% BSA, SUPERase (1 U/μl) in HBSS, and stained with conjugated antibodies against Cd11b, Cd11c, Cd34, Cd45.2, GFAP, Thy1.2 as well as DAPI. This cocktail allowed other retina cell types to be accurately removed during FACS. FACS was performed on a FACSAria (BD Biosciences). Thy1.2+ (and negative for all other markers) RGCs were sorted into 300μl buffer RLT + 1% β-ME, vortexed and frozen at -80°C until further processing.	Illumina HiSeq 2500	source_name;;Retinal ganglion cells|strain;;D2-Gpnmb+|treatment;;Water Control	GEO Accession;;GSM2409981		GSM2409981	Gpnmb_9mnths_WaterControl_478	7639506200	38197531	2017-03-09 10:01:30	5298918751	7639506200	38197531	2	38197531	index:0,count:38197531,average:100,stdev:0|index:1,count:38197531,average:100,stdev:0	GSM2409981_r1						2.16	2.36	0.09	5674248751	5460307883	5543354732	5366815142	96.23	96.82	34290924	33523925	195.621	815.326	143	204818	35.33	36.21	35875030	12113551	35875030	12113551	32.87	32.98	35875030	11271315	35875030	11033914	3422713744	60.32	6.71	0	2.18	0	0.18	0	0.30	0	0.00	0	9.76	0	34290924	0	200	0	194.77	0	2.46	0	0.03	0	2.28	0	0.02	0	217.24	0	0.54	0	2563886	0	38197531	0	832960	0	67338	0	112972	0	0	0	3726297	0	2931	0	0	0	23837	0	2907690	0	91465	0	3025923	0	87.59	0	33457964	0	167351	2734828	16.341868288806	38197531.0	34290924.0	2563886.0	832960.0	67338.0	112972.0	0.0	3726297.0	33457964.0	89.8	6.7	2.2	0.2	0.3	0.0	9.8	87.6	100	100	100.00	38	3819753100	27.4	22.4	23.0	27.3	0.0	35.2	18.8	bulk
1847609	SRR5061313	SRP094068	SRS1824191	SRX2381838	SRA499628	GEO		RNA-seq analysis of RNA from DBA/2J retinal ganglion cells	RNA-seq analysis from young and pre-glaucomatous DBA/2J retinal ganglion cells and control (age and sex-matched, D2-Gpnmb+) retinal ganglion cells Overall design: Retinal ganglion cell mRNA from 4 month (young) and 9 month (pre-glaucomatous) DBA/2J mice and age and sex-matched D2-Gpnmb+ controls		GSM2409982: Gpnmb_9mnths_WaterControl_481; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Prior to cell collection, all surfaces and volumes were cleaned with 70% ethanol and RNaseZap (ThermoFisher Scientific) solution followed by dH20. Mice were euthanized, eyes enucleated and placed immediately into ice-cold HBSS. Retinas were dissected from the eyes (4 or 9 mo of age, no axon degeneration confirmed by PPD staining) in HBSS on ice and placed directly into 100 μl of a custom HBSS (Gibco), dispase (5 U/ml) (Stemcell Technologies), DNase I (2000 U/ml) (Worthington Biochemical) and SUPERase (1 U/μl) (ThermoFisher Scientific) solution. All retinas were from eyes that had no glaucomatous axon degeneration by PPD staining and analysis. Retinas were incubated for 20 mins at 37 °C and shaken at 350 RPM in an Eppendorf Thermomixer R followed by gentle trituration using a 200 μl pipette. Samples were blocked in 2% BSA, SUPERase (1 U/μl) in HBSS, and stained with conjugated antibodies against Cd11b, Cd11c, Cd34, Cd45.2, GFAP, Thy1.2 as well as DAPI. This cocktail allowed other retina cell types to be accurately removed during FACS. FACS was performed on a FACSAria (BD Biosciences). Thy1.2+ (and negative for all other markers) RGCs were sorted into 300μl buffer RLT + 1% β-ME, vortexed and frozen at -80°C until further processing.	Illumina HiSeq 2500	source_name;;Retinal ganglion cells|strain;;D2-Gpnmb+|treatment;;Water Control	GEO Accession;;GSM2409982		GSM2409982	Gpnmb_9mnths_WaterControl_481	8758472200	43792361	2017-03-09 10:01:30	6093187929	8758472200	43792361	2	43792361	index:0,count:43792361,average:100,stdev:0|index:1,count:43792361,average:100,stdev:0	GSM2409982_r1						5.58	2.45	0.07	6629396510	6500446903	6411131542	6326778987	98.05	98.68	39641522	38398937	192.849	717.318	165	295530	53.86	55.81	42019174	21348991	42019174	21348991	49.9	50.27	42019174	19781637	42019174	19231203	2686511875	40.52	6.48	0	3.17	0	0.20	0	0.20	0	0.00	0	9.08	0	39641522	0	200	0	194.61	0	2.71	0	0.03	0	2.55	0	0.03	0	300.29	0	0.56	0	2837159	0	43792361	0	1388581	0	86996	0	89549	0	0	0	3974294	0	5823	0	0	0	42127	0	5819965	0	104630	0	5972545	0	87.35	0	38252941	0	165530	5531269	33.415507762943	43792361.0	39641522.0	2837159.0	1388581.0	86996.0	89549.0	0.0	3974294.0	38252941.0	90.5	6.5	3.2	0.2	0.2	0.0	9.1	87.4	100	100	100.00	38	4379236100	26.4	23.3	23.9	26.4	0.0	34.8	18.2	bulk
1847625	SRR5061314	SRP094068	SRS1824192	SRX2381839	SRA499628	GEO		RNA-seq analysis of RNA from DBA/2J retinal ganglion cells	RNA-seq analysis from young and pre-glaucomatous DBA/2J retinal ganglion cells and control (age and sex-matched, D2-Gpnmb+) retinal ganglion cells Overall design: Retinal ganglion cell mRNA from 4 month (young) and 9 month (pre-glaucomatous) DBA/2J mice and age and sex-matched D2-Gpnmb+ controls		GSM2409983: Gpnmb_9mnths_WaterControl_1383; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Prior to cell collection, all surfaces and volumes were cleaned with 70% ethanol and RNaseZap (ThermoFisher Scientific) solution followed by dH20. Mice were euthanized, eyes enucleated and placed immediately into ice-cold HBSS. Retinas were dissected from the eyes (4 or 9 mo of age, no axon degeneration confirmed by PPD staining) in HBSS on ice and placed directly into 100 μl of a custom HBSS (Gibco), dispase (5 U/ml) (Stemcell Technologies), DNase I (2000 U/ml) (Worthington Biochemical) and SUPERase (1 U/μl) (ThermoFisher Scientific) solution. All retinas were from eyes that had no glaucomatous axon degeneration by PPD staining and analysis. Retinas were incubated for 20 mins at 37 °C and shaken at 350 RPM in an Eppendorf Thermomixer R followed by gentle trituration using a 200 μl pipette. Samples were blocked in 2% BSA, SUPERase (1 U/μl) in HBSS, and stained with conjugated antibodies against Cd11b, Cd11c, Cd34, Cd45.2, GFAP, Thy1.2 as well as DAPI. This cocktail allowed other retina cell types to be accurately removed during FACS. FACS was performed on a FACSAria (BD Biosciences). Thy1.2+ (and negative for all other markers) RGCs were sorted into 300μl buffer RLT + 1% β-ME, vortexed and frozen at -80°C until further processing.	Illumina HiSeq 2500	source_name;;Retinal ganglion cells|strain;;D2-Gpnmb+|treatment;;Water Control	GEO Accession;;GSM2409983		GSM2409983	Gpnmb_9mnths_WaterControl_1383	7849979400	39249897	2017-03-09 10:01:30	5408777302	7849979400	39249897	2	39249897	index:0,count:39249897,average:100,stdev:0|index:1,count:39249897,average:100,stdev:0	GSM2409983_r1						13.6	2.27	0.08	6114485922	5850650163	5911057226	5691475010	95.69	96.29	36616160	35537981	192.452	715.726	149	292838	54.69	56.64	38752101	20024444	38752101	20024444	53.13	53.15	38752101	19454795	38752101	18788133	2328410184	38.08	4.98	0	3.22	0	0.23	0	0.35	0	0.00	0	6.13	0	36616160	0	200	0	196.42	0	2.35	0	0.02	0	2.51	0	0.02	0	275.98	0	0.45	0	1953346	0	39249897	0	1264431	0	90057	0	136847	0	0	0	2406833	0	4168	0	0	0	40253	0	4867110	0	69133	0	4980664	0	90.07	0	35351729	0	172319	4567539	26.506299363390	39249897.0	36616160.0	1953346.0	1264431.0	90057.0	136847.0	0.0	2406833.0	35351729.0	93.3	5.0	3.2	0.2	0.3	0.0	6.1	90.1	100	100	100.00	38	3924989700	28.0	21.9	22.2	27.8	0.0	35.3	19.8	bulk
1847642	SRR5061315	SRP094068	SRS1824193	SRX2381840	SRA499628	GEO		RNA-seq analysis of RNA from DBA/2J retinal ganglion cells	RNA-seq analysis from young and pre-glaucomatous DBA/2J retinal ganglion cells and control (age and sex-matched, D2-Gpnmb+) retinal ganglion cells Overall design: Retinal ganglion cell mRNA from 4 month (young) and 9 month (pre-glaucomatous) DBA/2J mice and age and sex-matched D2-Gpnmb+ controls		GSM2409984: Gpnmb_9mnths_WaterControl_1384; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Prior to cell collection, all surfaces and volumes were cleaned with 70% ethanol and RNaseZap (ThermoFisher Scientific) solution followed by dH20. Mice were euthanized, eyes enucleated and placed immediately into ice-cold HBSS. Retinas were dissected from the eyes (4 or 9 mo of age, no axon degeneration confirmed by PPD staining) in HBSS on ice and placed directly into 100 μl of a custom HBSS (Gibco), dispase (5 U/ml) (Stemcell Technologies), DNase I (2000 U/ml) (Worthington Biochemical) and SUPERase (1 U/μl) (ThermoFisher Scientific) solution. All retinas were from eyes that had no glaucomatous axon degeneration by PPD staining and analysis. Retinas were incubated for 20 mins at 37 °C and shaken at 350 RPM in an Eppendorf Thermomixer R followed by gentle trituration using a 200 μl pipette. Samples were blocked in 2% BSA, SUPERase (1 U/μl) in HBSS, and stained with conjugated antibodies against Cd11b, Cd11c, Cd34, Cd45.2, GFAP, Thy1.2 as well as DAPI. This cocktail allowed other retina cell types to be accurately removed during FACS. FACS was performed on a FACSAria (BD Biosciences). Thy1.2+ (and negative for all other markers) RGCs were sorted into 300μl buffer RLT + 1% β-ME, vortexed and frozen at -80°C until further processing.	Illumina HiSeq 2500	source_name;;Retinal ganglion cells|strain;;D2-Gpnmb+|treatment;;Water Control	GEO Accession;;GSM2409984		GSM2409984	Gpnmb_9mnths_WaterControl_1384	6401848200	32009241	2017-03-09 10:01:30	4417501127	6401848200	32009241	2	32009241	index:0,count:32009241,average:100,stdev:0|index:1,count:32009241,average:100,stdev:0	GSM2409984_r1						10.61	2.63	0.13	5116673514	4937091465	4947032105	4803029139	96.49	97.09	29946443	28963428	200.513	723.800	160	226348	55.06	57.02	31693300	16489110	31693300	16489110	52.88	52.88	31693300	15835442	31693300	15293050	1957647722	38.26	4.90	0	3.21	0	0.24	0	0.33	0	0.00	0	5.87	0	29946443	0	200	0	196.52	0	2.42	0	0.03	0	2.58	0	0.03	0	266.13	0	0.44	0	1568088	0	32009241	0	1028273	0	76192	0	107213	0	0	0	1879393	0	3539	0	0	0	35502	0	4325491	0	57066	0	4421598	0	90.34	0	28918170	0	170199	4133391	24.285636225830	32009241.0	29946443.0	1568088.0	1028273.0	76192.0	107213.0	0.0	1879393.0	28918170.0	93.6	4.9	3.2	0.2	0.3	0.0	5.9	90.3	100	100	100.00	38	3200924100	27.7	22.2	22.5	27.5	0.0	35.3	19.9	bulk
3690640	SRR5061284	SRP094068	SRS1824162	SRX2381809	SRA499628	GEO		RNA-seq analysis of RNA from DBA/2J retinal ganglion cells	RNA-seq analysis from young and pre-glaucomatous DBA/2J retinal ganglion cells and control (age and sex-matched, D2-Gpnmb+) retinal ganglion cells Overall design: Retinal ganglion cell mRNA from 4 month (young) and 9 month (pre-glaucomatous) DBA/2J mice and age and sex-matched D2-Gpnmb+ controls		GSM2409953: D2_4mnths_WaterControl_2019; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Prior to cell collection, all surfaces and volumes were cleaned with 70% ethanol and RNaseZap (ThermoFisher Scientific) solution followed by dH20. Mice were euthanized, eyes enucleated and placed immediately into ice-cold HBSS. Retinas were dissected from the eyes (4 or 9 mo of age, no axon degeneration confirmed by PPD staining) in HBSS on ice and placed directly into 100 μl of a custom HBSS (Gibco), dispase (5 U/ml) (Stemcell Technologies), DNase I (2000 U/ml) (Worthington Biochemical) and SUPERase (1 U/μl) (ThermoFisher Scientific) solution. All retinas were from eyes that had no glaucomatous axon degeneration by PPD staining and analysis. Retinas were incubated for 20 mins at 37 °C and shaken at 350 RPM in an Eppendorf Thermomixer R followed by gentle trituration using a 200 μl pipette. Samples were blocked in 2% BSA, SUPERase (1 U/μl) in HBSS, and stained with conjugated antibodies against Cd11b, Cd11c, Cd34, Cd45.2, GFAP, Thy1.2 as well as DAPI. This cocktail allowed other retina cell types to be accurately removed during FACS. FACS was performed on a FACSAria (BD Biosciences). Thy1.2+ (and negative for all other markers) RGCs were sorted into 300μl buffer RLT + 1% β-ME, vortexed and frozen at -80°C until further processing.	Illumina HiSeq 2500	source_name;;Retinal ganglion cells|strain;;DBA/2J|treatment;;Water Control	GEO Accession;;GSM2409953		GSM2409953	D2_4mnths_WaterControl_2019	7075901200	35379506	2017-03-09 10:01:29	4978457777	7075901200	35379506	2	35379506	index:0,count:35379506,average:100,stdev:0|index:1,count:35379506,average:100,stdev:0	GSM2409953_r1						7.74	2.82	0.15	4131407019	3933794162	4009678688	3844670170	95.22	95.88	28289790	27723300	160.013	849.897	113	238346	39.75	41.03	29955771	11245783	29955771	11245783	37.74	37.71	29955771	10677032	29955771	10336369	2199532069	53.24	5.76	0	2.50	0	0.23	0	0.28	0	0.00	0	19.53	0	28289790	0	200	0	193.04	0	2.24	0	0.03	0	2.34	0	0.02	0	210.52	0	0.55	0	2038423	0	35379506	0	882992	0	80588	0	100569	0	0	0	6908559	0	2244	0	0	0	21206	0	2349446	0	62530	0	2435426	0	77.47	0	27406798	0	159465	2004415	12.569623428339	35379506.0	28289790.0	2038423.0	882992.0	80588.0	100569.0	0.0	6908559.0	27406798.0	80.0	5.8	2.5	0.2	0.3	0.0	19.5	77.5	100	100	100.00	38	3537950600	28.7	21.6	22.0	27.6	0.1	34.8	18.8	bulk
1601934	SRR5242718	SRP099194	SRS1967815	SRX2549492	SRA536929	GEO		Comparison of Wild type and Pofut1-deleted skeletal muscle in young and old mice	Pofut1 is an essential gene that glycosylates proteins containing EGF-like repeats, including Notch Receptors (NotchRs).  Work in mice and in Drosophila has shown that O-fucosylation by Pofut1 is required for NotchR ligands to bind to and activate NotchRs.  As such, Pofut1 deletion in skeletal myofibers allows for an analysis of potential functions and molecular changes of Pofut1 in skeletal muscle that derive from its expression in skeletal myofibers. In this study we compared gene expression profiles between quadriceps muscles in young (2 month) and old (17 month) mice where Protein O-fucosyltransferase 1 (Pofut1) was deleted specifically in skeletal myofibers via use of a human skeletal alpha actin Cre transgene (Scre) and a loxP flanked Pofut1 gene (SCreFF) and mice which bore the only the Scre transgene but did not have floxed Pofut1 alleles (SCre++). Overall design: A total of eighteen samples in three groups were analyzed for this study. The first group is Pofut1flox/flox quadriceps. The second group is Skeletal a actin cre/Pofut1 wild type quadriceps. The third group is skeletal a actin cre/Pofut1flox/flox quadriceps. For each group, three of the samples are replicates from young (2 month) mice, and three of the samples are replicates from old (17 month) mice.		GSM2482651: 32 FF; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Trizol extraction of total RNA was performed according to the manufacturer's protocol followed by purification on a silica-gel-based membrane (Rneasy-Mini; Qiagen, Valecia, CA). Libraries were constructed from first strand cDNA using ScriptSeqTM v2 RNA-Seq library preparation kit. Briefly, 50ng of rRNA-depleted RNA was fragmented and reverse transcribed using random primers containing a 5' tagging sequence, followed by 3'end tagging with a terminal-tagging oligo to yield di-tagged, single-stranded cDNA. Following purification by a magnetic bead-based approach, the di-tagged cDNA was amplified by limit-cycle PCR using primer pairs that anneal to tagging sequences and add adaptor sequences required for sequencing cluster generation. Amplified RNA-seq libraries were purified using AMPure XP System.	Illumina HiSeq 4000	age;;Young (2 months)|genotype/variation;;Pofut1flox/flox control|source_name;;Quadriceps muscle|strain;;C57BL/6|tissue;;Quadriceps muscle	GEO Accession;;GSM2482651		GSM2482651	32 FF	11517904001	43016260	2017-03-27 16:31:04	4565416865	11517904001	43016260	2	43016260	index:0,count:43016260,average:133.79,stdev:28.05|index:1,count:43016260,average:133.97,stdev:28.07	GSM2482651_r1				in_mesa	28265002	5.99	2.1	0.02	7541178771	7533723779	7146809637	7163401502	99.9	100.23	40586155	35978632	233.623	914.590	113	161285	74.92	79.75	44397886	30409037	44397886	30409037	76.81	76.68	44397886	31177695	44397886	29237659	1445099623	19.16	1.61	0	5.72	0	0.31	0	0.23	0	0.00	0	5.10	0	40591132	0	267	0	263.44	0	1.71	0	0.01	0	1.71	0	0.00	0	207.03	0	0.50	0	690454	0	43016260	0	2461372	0	132330	0	98748	0	0	0	2194050	0	7769	0	0	0	110853	0	26282033	0	67164	0	26467819	0	88.64	0	38129760	0	190593	19701323	103.368554983656	43016260.0	40591132.0	690454.0	2461372.0	132330.0	98748.0	0.0	2194050.0	38129760.0	94.4	1.6	5.7	0.3	0.2	0.0	5.1	88.6	35	151	133.79	8	5754987118	27.7	23.3	25.0	24.1	0.0	39.8	29.8	bulk
1601949	SRR5242719	SRP099194	SRS1967816	SRX2549493	SRA536929	GEO		Comparison of Wild type and Pofut1-deleted skeletal muscle in young and old mice	Pofut1 is an essential gene that glycosylates proteins containing EGF-like repeats, including Notch Receptors (NotchRs).  Work in mice and in Drosophila has shown that O-fucosylation by Pofut1 is required for NotchR ligands to bind to and activate NotchRs.  As such, Pofut1 deletion in skeletal myofibers allows for an analysis of potential functions and molecular changes of Pofut1 in skeletal muscle that derive from its expression in skeletal myofibers. In this study we compared gene expression profiles between quadriceps muscles in young (2 month) and old (17 month) mice where Protein O-fucosyltransferase 1 (Pofut1) was deleted specifically in skeletal myofibers via use of a human skeletal alpha actin Cre transgene (Scre) and a loxP flanked Pofut1 gene (SCreFF) and mice which bore the only the Scre transgene but did not have floxed Pofut1 alleles (SCre++). Overall design: A total of eighteen samples in three groups were analyzed for this study. The first group is Pofut1flox/flox quadriceps. The second group is Skeletal a actin cre/Pofut1 wild type quadriceps. The third group is skeletal a actin cre/Pofut1flox/flox quadriceps. For each group, three of the samples are replicates from young (2 month) mice, and three of the samples are replicates from old (17 month) mice.		GSM2482652: 57 FF; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Trizol extraction of total RNA was performed according to the manufacturer's protocol followed by purification on a silica-gel-based membrane (Rneasy-Mini; Qiagen, Valecia, CA). Libraries were constructed from first strand cDNA using ScriptSeqTM v2 RNA-Seq library preparation kit. Briefly, 50ng of rRNA-depleted RNA was fragmented and reverse transcribed using random primers containing a 5' tagging sequence, followed by 3'end tagging with a terminal-tagging oligo to yield di-tagged, single-stranded cDNA. Following purification by a magnetic bead-based approach, the di-tagged cDNA was amplified by limit-cycle PCR using primer pairs that anneal to tagging sequences and add adaptor sequences required for sequencing cluster generation. Amplified RNA-seq libraries were purified using AMPure XP System.	Illumina HiSeq 4000	age;;Young (2 months)|genotype/variation;;Pofut1flox/flox control|source_name;;Quadriceps muscle|strain;;C57BL/6|tissue;;Quadriceps muscle	GEO Accession;;GSM2482652		GSM2482652	57 FF	11866789951	44066449	2017-03-27 16:31:04	4715186779	11866789951	44066449	2	44066449	index:0,count:44066449,average:134.56,stdev:27.23|index:1,count:44066449,average:134.73,stdev:27.25	GSM2482652_r1				in_mesa	28265002	4.52	1.94	0.05	7874947999	7873855897	7506928909	7528485839	99.99	100.29	41859444	37040657	238.152	908.757	113	156691	76.01	80.37	45511355	31821763	45511355	31821763	77.4	77.38	45511355	32402773	45511355	30636454	1473377605	18.71	1.36	0	5.15	0	0.30	0	0.30	0	0.00	0	4.40	0	41862872	0	269	0	265.31	0	1.68	0	0.00	0	1.60	0	0.00	0	299.89	0	0.48	0	599504	0	44066449	0	2269123	0	130174	0	132621	0	0	0	1940782	0	7829	0	0	0	116537	0	28237621	0	66504	0	28428491	0	89.85	0	39593749	0	191112	21268407	111.287658545774	44066449.0	41862872.0	599504.0	2269123.0	130174.0	132621.0	0.0	1940782.0	39593749.0	95.0	1.4	5.1	0.3	0.3	0.0	4.4	89.9	35	151	134.56	8	5929740635	27.6	23.2	25.4	23.8	0.1	39.8	29.5	bulk
1602061	SRR5242720	SRP099194	SRS1967817	SRX2549494	SRA536929	GEO		Comparison of Wild type and Pofut1-deleted skeletal muscle in young and old mice	Pofut1 is an essential gene that glycosylates proteins containing EGF-like repeats, including Notch Receptors (NotchRs).  Work in mice and in Drosophila has shown that O-fucosylation by Pofut1 is required for NotchR ligands to bind to and activate NotchRs.  As such, Pofut1 deletion in skeletal myofibers allows for an analysis of potential functions and molecular changes of Pofut1 in skeletal muscle that derive from its expression in skeletal myofibers. In this study we compared gene expression profiles between quadriceps muscles in young (2 month) and old (17 month) mice where Protein O-fucosyltransferase 1 (Pofut1) was deleted specifically in skeletal myofibers via use of a human skeletal alpha actin Cre transgene (Scre) and a loxP flanked Pofut1 gene (SCreFF) and mice which bore the only the Scre transgene but did not have floxed Pofut1 alleles (SCre++). Overall design: A total of eighteen samples in three groups were analyzed for this study. The first group is Pofut1flox/flox quadriceps. The second group is Skeletal a actin cre/Pofut1 wild type quadriceps. The third group is skeletal a actin cre/Pofut1flox/flox quadriceps. For each group, three of the samples are replicates from young (2 month) mice, and three of the samples are replicates from old (17 month) mice.		GSM2482653: 92 FF; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			Trizol extraction of total RNA was performed according to the manufacturer's protocol followed by purification on a silica-gel-based membrane (Rneasy-Mini; Qiagen, Valecia, CA). Libraries were constructed from first strand cDNA using ScriptSeqTM v2 RNA-Seq library preparation kit. Briefly, 50ng of rRNA-depleted RNA was fragmented and reverse transcribed using random primers containing a 5' tagging sequence, followed by 3'end tagging with a terminal-tagging oligo to yield di-tagged, single-stranded cDNA. Following purification by a magnetic bead-based approach, the di-tagged cDNA was amplified by limit-cycle PCR using primer pairs that anneal to tagging sequences and add adaptor sequences required for sequencing cluster generation. Amplified RNA-seq libraries were purified using AMPure XP System.	Illumina HiSeq 4000	age;;Young (2 months)|genotype/variation;;Pofut1flox/flox control|source_name;;Quadriceps muscle|strain;;C57BL/6|tissue;;Quadriceps muscle	GEO Accession;;GSM2482653		GSM2482653	92 FF	12205503410	45759102	2017-03-27 16:31:04	4783682260	12205503410	45759102	2	45759102	index:0,count:45759102,average:133.29,stdev:27.84|index:1,count:45759102,average:133.45,stdev:27.86	GSM2482653_r1				in_mesa	28265002	4.56	1.93	0.06	7929868381	7933855736	7549945125	7578010695	100.05	100.37	43651102	38888658	225.614	863.933	113	187893	75.93	80.42	47622446	33145491	47622446	33145491	77.34	77.34	47622446	33764010	47622446	31875697	1466297927	18.49	1.36	0	5.33	0	0.32	0	0.20	0	0.00	0	4.08	0	43654265	0	266	0	262.69	0	1.78	0	0.00	0	1.74	0	0.00	0	219.64	0	0.47	0	620510	0	45759102	0	2437791	0	144260	0	91968	0	0	0	1868609	0	8174	0	0	0	125044	0	28987845	0	70612	0	29191675	0	90.07	0	41216474	0	189525	21308467	112.430903574726	45759102.0	43654265.0	620510.0	2437791.0	144260.0	91968.0	0.0	1868609.0	41216474.0	95.4	1.4	5.3	0.3	0.2	0.0	4.1	90.1	35	151	133.29	8	6099024326	27.7	23.3	25.3	23.8	0.0	39.8	30.1	bulk
3827828	SRR5277343	SRP100479	SRS1995332	SRX2581273	SRA539333	GEO		Pancreatic alpha and beta-cellular clocks have distinct molecular properties and impact on islet hormone secretion and gene expression	We performed a parallel analysis of the molecular properties of a- and ß-cell oscillators, using a mouse model expressing three reporter genes: one labeling a-cells, one specific for ß-cells, and a third monitoring circadian gene expression. Diurnal transcriptome analysis in separated a- and ß-cells revealed that a high number of genes with key roles in islet physiology, including regulators of glucose sensing and hormone secretion, are differentially expressed in these cell types. This study represents the first parallel large-scale circadian in vivo transcriptome analysis in separated a- and ß-cells. Overall design: 24 samples in duplicates (time course design)		GSM2497927: ZT8 beta_2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			RNeasy Plus Micro Kit Qiagen Libraries were prepared according to the Illumina TruSeq Stranded Total RNA kit (with  Ribo-Zero TM gold probes) according to manufacturer's specifications. Input material was from 80 to 100 ng.	Illumina HiSeq 2500	cell type;;pancreatic beta cell|source_name;;mouse beta cell|strain;;triple reporter mouse|time;;islet isolation time ZT8 (3PM)	GEO Accession;;GSM2497927		GSM2497927	ZT8 beta_2	2223469400	22234694	2017-02-23 15:30:41	1401269521	2223469400	22234694	2	22234694	index:0,count:22234694,average:50,stdev:0|index:1,count:22234694,average:50,stdev:0	GSM2497927_r1				in_mesa	28275001	2.66	2.19	0.04	1711696629	1696151941	1374868324	1365559552	99.09	99.32	17509810	16227349	167.472	668.519	117	186843	68.28	84.94	22267056	11955475	22267056	11955475	82.28	82.53	22267056	14406753	22267056	11615886	195315174	11.41	0.88	0	15.45	0	0.17	0	0.13	0	0.00	0	20.95	0	17509810	0	100	0	99.13	0	1.47	0	0.00	0	1.17	0	0.00	0	163.69	0	0.19	0	195703	0	22234694	0	3435214	0	37648	0	29412	0	0	0	4657824	0	995	0	0	0	14991	0	2717294	0	5581	0	2738861	0	63.30	0	14074596	0	124449	2760392	22.180909448851	22234694.0	17509810.0	195703.0	3435214.0	37648.0	29412.0	0.0	4657824.0	14074596.0	78.7	0.9	15.4	0.2	0.1	0.0	20.9	63.3	50	50	50.00	38	1111734700	19.7	28.1	30.0	22.2	0.0	37.3	23.3	bulk
3827860	SRR5277344	SRP100479	SRS1995334	SRX2581274	SRA539333	GEO		Pancreatic alpha and beta-cellular clocks have distinct molecular properties and impact on islet hormone secretion and gene expression	We performed a parallel analysis of the molecular properties of a- and ß-cell oscillators, using a mouse model expressing three reporter genes: one labeling a-cells, one specific for ß-cells, and a third monitoring circadian gene expression. Diurnal transcriptome analysis in separated a- and ß-cells revealed that a high number of genes with key roles in islet physiology, including regulators of glucose sensing and hormone secretion, are differentially expressed in these cell types. This study represents the first parallel large-scale circadian in vivo transcriptome analysis in separated a- and ß-cells. Overall design: 24 samples in duplicates (time course design)		GSM2497928: ZT8 beta_1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			RNeasy Plus Micro Kit Qiagen Libraries were prepared according to the Illumina TruSeq Stranded Total RNA kit (with  Ribo-Zero TM gold probes) according to manufacturer's specifications. Input material was from 80 to 100 ng.	Illumina HiSeq 2500	cell type;;pancreatic beta cell|source_name;;mouse beta cell|strain;;triple reporter mouse|time;;islet isolation time ZT8 (3PM)	GEO Accession;;GSM2497928		GSM2497928	ZT8 beta_1	2338162400	23381624	2017-02-23 15:30:41	1469275851	2338162400	23381624	2	23381624	index:0,count:23381624,average:50,stdev:0|index:1,count:23381624,average:50,stdev:0	GSM2497928_r1				in_mesa	28275001	3.5	2.19	0.03	1785602973	1768087209	1426097731	1415635107	99.02	99.27	18251477	16815334	171.794	713.001	117	187206	70.3	87.94	23291090	12829989	23291090	12829989	84.78	85.47	23291090	15474290	23291090	12469715	155948220	8.73	1.00	0	15.66	0	0.15	0	0.11	0	0.00	0	21.69	0	18251477	0	100	0	99.09	0	1.45	0	0.00	0	1.17	0	0.00	0	483.76	0	0.20	0	234402	0	23381624	0	3661895	0	34653	0	25136	0	0	0	5070358	0	1148	0	0	0	15195	0	2924101	0	5658	0	2946102	0	62.40	0	14589582	0	124577	2972008	23.856795395619	23381624.0	18251477.0	234402.0	3661895.0	34653.0	25136.0	0.0	5070358.0	14589582.0	78.1	1.0	15.7	0.1	0.1	0.0	21.7	62.4	50	50	50.00	38	1169081200	19.6	28.0	30.2	22.2	0.0	37.4	23.4	bulk
3827891	SRR5277345	SRP100479	SRS1995331	SRX2581275	SRA539333	GEO		Pancreatic alpha and beta-cellular clocks have distinct molecular properties and impact on islet hormone secretion and gene expression	We performed a parallel analysis of the molecular properties of a- and ß-cell oscillators, using a mouse model expressing three reporter genes: one labeling a-cells, one specific for ß-cells, and a third monitoring circadian gene expression. Diurnal transcriptome analysis in separated a- and ß-cells revealed that a high number of genes with key roles in islet physiology, including regulators of glucose sensing and hormone secretion, are differentially expressed in these cell types. This study represents the first parallel large-scale circadian in vivo transcriptome analysis in separated a- and ß-cells. Overall design: 24 samples in duplicates (time course design)		GSM2497929: ZT8 alpha_2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			RNeasy Plus Micro Kit Qiagen Libraries were prepared according to the Illumina TruSeq Stranded Total RNA kit (with  Ribo-Zero TM gold probes) according to manufacturer's specifications. Input material was from 80 to 100 ng.	Illumina HiSeq 2500	cell type;;pancreatic alpha cell|source_name;;mouse alpha cell|strain;;triple reporter mouse|time;;islet isolation time ZT8 (3PM)	GEO Accession;;GSM2497929		GSM2497929	ZT8 alpha_2	2236613800	22366138	2017-02-23 15:30:41	1380349716	2236613800	22366138	2	22366138	index:0,count:22366138,average:50,stdev:0|index:1,count:22366138,average:50,stdev:0	GSM2497929_r1				in_mesa	28275001	1.85	3.17	0.06	1764397222	1746273595	1590771614	1580495173	98.97	99.35	18076846	15488264	180.017	926.944	118	149917	73.35	81.33	20904225	13259114	20904225	13259114	79.34	79.02	20904225	14341431	20904225	12883468	288737665	16.36	0.98	0	7.93	0	0.21	0	0.19	0	0.00	0	18.78	0	18076846	0	100	0	99.01	0	1.42	0	0.00	0	1.19	0	0.00	0	204.88	0	0.19	0	219070	0	22366138	0	1773373	0	46946	0	42798	0	0	0	4199548	0	1252	0	0	0	15074	0	2644295	0	4120	0	2664741	0	72.89	0	16303473	0	133376	2682012	20.108655230326	22366138.0	18076846.0	219070.0	1773373.0	46946.0	42798.0	0.0	4199548.0	16303473.0	80.8	1.0	7.9	0.2	0.2	0.0	18.8	72.9	50	50	50.00	38	1118306900	21.4	26.7	28.0	23.9	0.0	37.6	23.7	bulk
3827924	SRR5277346	SRP100479	SRS1995333	SRX2581276	SRA539333	GEO		Pancreatic alpha and beta-cellular clocks have distinct molecular properties and impact on islet hormone secretion and gene expression	We performed a parallel analysis of the molecular properties of a- and ß-cell oscillators, using a mouse model expressing three reporter genes: one labeling a-cells, one specific for ß-cells, and a third monitoring circadian gene expression. Diurnal transcriptome analysis in separated a- and ß-cells revealed that a high number of genes with key roles in islet physiology, including regulators of glucose sensing and hormone secretion, are differentially expressed in these cell types. This study represents the first parallel large-scale circadian in vivo transcriptome analysis in separated a- and ß-cells. Overall design: 24 samples in duplicates (time course design)		GSM2497930: ZT8 alpha_1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			RNeasy Plus Micro Kit Qiagen Libraries were prepared according to the Illumina TruSeq Stranded Total RNA kit (with  Ribo-Zero TM gold probes) according to manufacturer's specifications. Input material was from 80 to 100 ng.	Illumina HiSeq 2500	cell type;;pancreatic alpha cell|source_name;;mouse alpha cell|strain;;triple reporter mouse|time;;islet isolation time ZT8 (3PM)	GEO Accession;;GSM2497930		GSM2497930	ZT8 alpha_1	1706242600	17062426	2017-02-23 15:30:41	1056363876	1706242600	17062426	2	17062426	index:0,count:17062426,average:50,stdev:0|index:1,count:17062426,average:50,stdev:0	GSM2497930_r1				in_mesa	28275001	1.91	3.22	0.05	1334001557	1319383582	1217372707	1209138395	98.9	99.32	13708693	11576078	182.098	984.985	118	110853	77.05	84.41	15701305	10562498	15701305	10562498	82.13	82.16	15701305	11259232	15701305	10280882	180371755	13.52	1.10	0	7.00	0	0.19	0	0.17	0	0.00	0	19.30	0	13708693	0	100	0	98.93	0	1.39	0	0.00	0	1.18	0	0.00	0	333.83	0	0.21	0	188244	0	17062426	0	1195078	0	32389	0	29011	0	0	0	3292333	0	974	0	0	0	10905	0	2171948	0	3150	0	2186977	0	73.34	0	12513615	0	125735	2200626	17.502095677417	17062426.0	13708693.0	188244.0	1195078.0	32389.0	29011.0	0.0	3292333.0	12513615.0	80.3	1.1	7.0	0.2	0.2	0.0	19.3	73.3	50	50	50.00	38	853121300	21.3	26.6	28.1	24.0	0.0	37.5	23.5	bulk
3827957	SRR5277347	SRP100479	SRS1995335	SRX2581277	SRA539333	GEO		Pancreatic alpha and beta-cellular clocks have distinct molecular properties and impact on islet hormone secretion and gene expression	We performed a parallel analysis of the molecular properties of a- and ß-cell oscillators, using a mouse model expressing three reporter genes: one labeling a-cells, one specific for ß-cells, and a third monitoring circadian gene expression. Diurnal transcriptome analysis in separated a- and ß-cells revealed that a high number of genes with key roles in islet physiology, including regulators of glucose sensing and hormone secretion, are differentially expressed in these cell types. This study represents the first parallel large-scale circadian in vivo transcriptome analysis in separated a- and ß-cells. Overall design: 24 samples in duplicates (time course design)		GSM2497931: ZT4 beta_2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			RNeasy Plus Micro Kit Qiagen Libraries were prepared according to the Illumina TruSeq Stranded Total RNA kit (with  Ribo-Zero TM gold probes) according to manufacturer's specifications. Input material was from 80 to 100 ng.	Illumina HiSeq 2500	cell type;;pancreatic beta cell|source_name;;mouse beta cell|strain;;triple reporter mouse|time;;islet isolation time ZT4 (11AM)	GEO Accession;;GSM2497931		GSM2497931	ZT4 beta_2	2067947400	20679474	2017-02-23 15:30:41	1298917874	2067947400	20679474	2	20679474	index:0,count:20679474,average:50,stdev:0|index:1,count:20679474,average:50,stdev:0	GSM2497931_r1				in_mesa	28275001	3.39	2.15	0.03	1616250919	1600801489	1292831769	1283898508	99.04	99.31	16431468	15048947	180.330	759.803	117	157439	70.73	88.34	20888999	11621615	20888999	11621615	85.44	85.73	20888999	14039341	20888999	11279204	136083837	8.42	1.09	0	15.84	0	0.16	0	0.10	0	0.00	0	20.28	0	16431468	0	100	0	99.08	0	1.45	0	0.00	0	1.18	0	0.00	0	372.23	0	0.22	0	225534	0	20679474	0	3275253	0	32880	0	20740	0	0	0	4194386	0	1064	0	0	0	11882	0	2690226	0	5145	0	2708317	0	63.62	0	13156215	0	119431	2731946	22.874680778022	20679474.0	16431468.0	225534.0	3275253.0	32880.0	20740.0	0.0	4194386.0	13156215.0	79.5	1.1	15.8	0.2	0.1	0.0	20.3	63.6	50	50	50.00	38	1033973700	19.8	27.8	30.0	22.5	0.0	37.4	23.4	bulk
3827989	SRR5277348	SRP100479	SRS1995336	SRX2581278	SRA539333	GEO		Pancreatic alpha and beta-cellular clocks have distinct molecular properties and impact on islet hormone secretion and gene expression	We performed a parallel analysis of the molecular properties of a- and ß-cell oscillators, using a mouse model expressing three reporter genes: one labeling a-cells, one specific for ß-cells, and a third monitoring circadian gene expression. Diurnal transcriptome analysis in separated a- and ß-cells revealed that a high number of genes with key roles in islet physiology, including regulators of glucose sensing and hormone secretion, are differentially expressed in these cell types. This study represents the first parallel large-scale circadian in vivo transcriptome analysis in separated a- and ß-cells. Overall design: 24 samples in duplicates (time course design)		GSM2497932: ZT4 beta_1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			RNeasy Plus Micro Kit Qiagen Libraries were prepared according to the Illumina TruSeq Stranded Total RNA kit (with  Ribo-Zero TM gold probes) according to manufacturer's specifications. Input material was from 80 to 100 ng.	Illumina HiSeq 2500	cell type;;pancreatic beta cell|source_name;;mouse beta cell|strain;;triple reporter mouse|time;;islet isolation time ZT4 (11AM)	GEO Accession;;GSM2497932		GSM2497932	ZT4 beta_1	2013792000	20137920	2017-02-23 15:30:41	1260690508	2013792000	20137920	2	20137920	index:0,count:20137920,average:50,stdev:0|index:1,count:20137920,average:50,stdev:0	GSM2497932_r1				in_mesa	28275001	3.01	2.41	0.05	1614035703	1592371262	1413936943	1399037461	98.66	98.95	16400533	14893299	182.505	818.172	117	150436	71.36	81.42	19281859	11702677	19281859	11702677	79.67	79.25	19281859	13066886	19281859	11391242	249804920	15.48	0.99	0	10.07	0	0.20	0	0.18	0	0.00	0	18.17	0	16400533	0	100	0	99.17	0	1.48	0	0.00	0	1.19	0	0.01	0	337.19	0	0.20	0	198496	0	20137920	0	2026998	0	40603	0	36870	0	0	0	3659914	0	1079	0	0	0	14207	0	2561168	0	5217	0	2581671	0	71.38	0	14373535	0	129732	2610720	20.123947830913	20137920.0	16400533.0	198496.0	2026998.0	40603.0	36870.0	0.0	3659914.0	14373535.0	81.4	1.0	10.1	0.2	0.2	0.0	18.2	71.4	50	50	50.00	38	1006896000	20.9	27.1	28.8	23.2	0.0	37.5	23.6	bulk
3828019	SRR5277349	SRP100479	SRS1995337	SRX2581279	SRA539333	GEO		Pancreatic alpha and beta-cellular clocks have distinct molecular properties and impact on islet hormone secretion and gene expression	We performed a parallel analysis of the molecular properties of a- and ß-cell oscillators, using a mouse model expressing three reporter genes: one labeling a-cells, one specific for ß-cells, and a third monitoring circadian gene expression. Diurnal transcriptome analysis in separated a- and ß-cells revealed that a high number of genes with key roles in islet physiology, including regulators of glucose sensing and hormone secretion, are differentially expressed in these cell types. This study represents the first parallel large-scale circadian in vivo transcriptome analysis in separated a- and ß-cells. Overall design: 24 samples in duplicates (time course design)		GSM2497933: ZT4 alpha_2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			RNeasy Plus Micro Kit Qiagen Libraries were prepared according to the Illumina TruSeq Stranded Total RNA kit (with  Ribo-Zero TM gold probes) according to manufacturer's specifications. Input material was from 80 to 100 ng.	Illumina HiSeq 2500	cell type;;pancreatic alpha cell|source_name;;mouse alpha cell|strain;;triple reporter mouse|time;;islet isolation time ZT4 (11AM)	GEO Accession;;GSM2497933		GSM2497933	ZT4 alpha_2	2239798800	22397988	2017-02-23 15:30:41	1389188522	2239798800	22397988	2	22397988	index:0,count:22397988,average:50,stdev:0|index:1,count:22397988,average:50,stdev:0	GSM2497933_r1				in_mesa	28275001	1.81	3.18	0.06	1668555098	1641811785	1538771406	1520251367	98.4	98.8	17217662	15056794	169.892	842.899	118	143847	69.47	75.33	19462618	11961035	19462618	11961035	73.56	73.15	19462618	12665503	19462618	11615749	363833356	21.81	1.01	0	5.98	0	0.19	0	0.25	0	0.00	0	22.69	0	17217662	0	100	0	99.01	0	1.43	0	0.00	0	1.20	0	0.01	0	179.98	0	0.22	0	226030	0	22397988	0	1338716	0	42559	0	56180	0	0	0	5081587	0	1069	0	0	0	11551	0	2362113	0	3794	0	2378527	0	70.89	0	15878946	0	126740	2388714	18.847356793435	22397988.0	17217662.0	226030.0	1338716.0	42559.0	56180.0	0.0	5081587.0	15878946.0	76.9	1.0	6.0	0.2	0.3	0.0	22.7	70.9	50	50	50.00	38	1119899400	21.1	27.1	28.7	23.0	0.0	37.4	23.1	bulk
3828246	SRR5277350	SRP100479	SRS1995338	SRX2581280	SRA539333	GEO		Pancreatic alpha and beta-cellular clocks have distinct molecular properties and impact on islet hormone secretion and gene expression	We performed a parallel analysis of the molecular properties of a- and ß-cell oscillators, using a mouse model expressing three reporter genes: one labeling a-cells, one specific for ß-cells, and a third monitoring circadian gene expression. Diurnal transcriptome analysis in separated a- and ß-cells revealed that a high number of genes with key roles in islet physiology, including regulators of glucose sensing and hormone secretion, are differentially expressed in these cell types. This study represents the first parallel large-scale circadian in vivo transcriptome analysis in separated a- and ß-cells. Overall design: 24 samples in duplicates (time course design)		GSM2497934: ZT4 alpha_1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			RNeasy Plus Micro Kit Qiagen Libraries were prepared according to the Illumina TruSeq Stranded Total RNA kit (with  Ribo-Zero TM gold probes) according to manufacturer's specifications. Input material was from 80 to 100 ng.	Illumina HiSeq 2500	cell type;;pancreatic alpha cell|source_name;;mouse alpha cell|strain;;triple reporter mouse|time;;islet isolation time ZT4 (11AM)	GEO Accession;;GSM2497934		GSM2497934	ZT4 alpha_1	1871513200	18715132	2017-02-23 15:30:41	1148468864	1871513200	18715132	2	18715132	index:0,count:18715132,average:50,stdev:0|index:1,count:18715132,average:50,stdev:0	GSM2497934_r1				in_mesa	28275001	1.62	3.28	0.07	1521781037	1500777335	1429863107	1415674982	98.62	99.01	15611162	13751592	173.714	836.726	118	132456	70.29	74.81	17214728	10973864	17214728	10973864	73.05	72.74	17214728	11403401	17214728	10669236	353910067	23.26	0.84	0	5.04	0	0.22	0	0.26	0	0.00	0	16.10	0	15611162	0	100	0	99.13	0	1.46	0	0.00	0	1.21	0	0.01	0	178.71	0	0.18	0	156533	0	18715132	0	942999	0	42004	0	48626	0	0	0	3013340	0	1096	0	0	0	11910	0	2114501	0	3838	0	2131345	0	78.38	0	14668163	0	131929	2145150	16.259882209370	18715132.0	15611162.0	156533.0	942999.0	42004.0	48626.0	0.0	3013340.0	14668163.0	83.4	0.8	5.0	0.2	0.3	0.0	16.1	78.4	50	50	50.00	38	935756600	22.4	26.1	27.1	24.3	0.0	37.7	24.2	bulk
3828278	SRR5277351	SRP100479	SRS1995340	SRX2581281	SRA539333	GEO		Pancreatic alpha and beta-cellular clocks have distinct molecular properties and impact on islet hormone secretion and gene expression	We performed a parallel analysis of the molecular properties of a- and ß-cell oscillators, using a mouse model expressing three reporter genes: one labeling a-cells, one specific for ß-cells, and a third monitoring circadian gene expression. Diurnal transcriptome analysis in separated a- and ß-cells revealed that a high number of genes with key roles in islet physiology, including regulators of glucose sensing and hormone secretion, are differentially expressed in these cell types. This study represents the first parallel large-scale circadian in vivo transcriptome analysis in separated a- and ß-cells. Overall design: 24 samples in duplicates (time course design)		GSM2497935: ZT20 beta_2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			RNeasy Plus Micro Kit Qiagen Libraries were prepared according to the Illumina TruSeq Stranded Total RNA kit (with  Ribo-Zero TM gold probes) according to manufacturer's specifications. Input material was from 80 to 100 ng.	Illumina HiSeq 2500	cell type;;pancreatic beta cell|source_name;;mouse beta cell|strain;;triple reporter mouse|time;;islet isolation time ZT20 (3AM)	GEO Accession;;GSM2497935		GSM2497935	ZT20 beta_2	2015797400	20157974	2017-02-23 15:30:41	1268779925	2015797400	20157974	2	20157974	index:0,count:20157974,average:50,stdev:0|index:1,count:20157974,average:50,stdev:0	GSM2497935_r1				in_mesa	28275001	2.49	2.23	0.05	1563672234	1542231821	1331042486	1316329248	98.63	98.89	16045839	14879661	164.024	664.612	117	167521	64.52	75.76	19385174	10352125	19385174	10352125	74.3	73.57	19385174	11922809	19385174	10052343	311230115	19.90	0.85	0	11.81	0	0.22	0	0.27	0	0.00	0	19.92	0	16045839	0	100	0	99.19	0	1.49	0	0.00	0	1.19	0	0.01	0	199.36	0	0.19	0	171775	0	20157974	0	2381518	0	43454	0	53648	0	0	0	4015033	0	931	0	0	0	13605	0	2170998	0	5233	0	2190767	0	67.79	0	13664321	0	124127	2211054	17.812836852578	20157974.0	16045839.0	171775.0	2381518.0	43454.0	53648.0	0.0	4015033.0	13664321.0	79.6	0.9	11.8	0.2	0.3	0.0	19.9	67.8	50	50	50.00	38	1007898700	20.5	27.7	29.2	22.6	0.0	37.4	23.5	bulk
3828309	SRR5277352	SRP100479	SRS1995339	SRX2581282	SRA539333	GEO		Pancreatic alpha and beta-cellular clocks have distinct molecular properties and impact on islet hormone secretion and gene expression	We performed a parallel analysis of the molecular properties of a- and ß-cell oscillators, using a mouse model expressing three reporter genes: one labeling a-cells, one specific for ß-cells, and a third monitoring circadian gene expression. Diurnal transcriptome analysis in separated a- and ß-cells revealed that a high number of genes with key roles in islet physiology, including regulators of glucose sensing and hormone secretion, are differentially expressed in these cell types. This study represents the first parallel large-scale circadian in vivo transcriptome analysis in separated a- and ß-cells. Overall design: 24 samples in duplicates (time course design)		GSM2497936: ZT20 beta_1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			RNeasy Plus Micro Kit Qiagen Libraries were prepared according to the Illumina TruSeq Stranded Total RNA kit (with  Ribo-Zero TM gold probes) according to manufacturer's specifications. Input material was from 80 to 100 ng.	Illumina HiSeq 2500	cell type;;pancreatic beta cell|source_name;;mouse beta cell|strain;;triple reporter mouse|time;;islet isolation time ZT20 (3AM)	GEO Accession;;GSM2497936		GSM2497936	ZT20 beta_1	2230623100	22306231	2017-02-23 15:30:41	1401882897	2230623100	22306231	2	22306231	index:0,count:22306231,average:50,stdev:0|index:1,count:22306231,average:50,stdev:0	GSM2497936_r1				in_mesa	28275001	2.87	2.16	0.04	1680416805	1659902290	1389794133	1376221456	98.78	99.02	17242052	16014949	165.086	658.265	117	182024	66.1	79.88	21396202	11397576	21396202	11397576	77.86	77.59	21396202	13423851	21396202	11070582	265847137	15.82	0.92	0	13.33	0	0.18	0	0.20	0	0.00	0	22.32	0	17242052	0	100	0	99.15	0	1.47	0	0.00	0	1.18	0	0.00	0	399.51	0	0.20	0	205881	0	22306231	0	2973839	0	39510	0	45352	0	0	0	4979317	0	987	0	0	0	13469	0	2520854	0	5380	0	2540690	0	63.97	0	14268213	0	122799	2564621	20.884705901514	22306231.0	17242052.0	205881.0	2973839.0	39510.0	45352.0	0.0	4979317.0	14268213.0	77.3	0.9	13.3	0.2	0.2	0.0	22.3	64.0	50	50	50.00	38	1115311550	19.8	28.1	30.1	22.0	0.0	37.3	23.3	bulk
3828341	SRR5277353	SRP100479	SRS1995345	SRX2581283	SRA539333	GEO		Pancreatic alpha and beta-cellular clocks have distinct molecular properties and impact on islet hormone secretion and gene expression	We performed a parallel analysis of the molecular properties of a- and ß-cell oscillators, using a mouse model expressing three reporter genes: one labeling a-cells, one specific for ß-cells, and a third monitoring circadian gene expression. Diurnal transcriptome analysis in separated a- and ß-cells revealed that a high number of genes with key roles in islet physiology, including regulators of glucose sensing and hormone secretion, are differentially expressed in these cell types. This study represents the first parallel large-scale circadian in vivo transcriptome analysis in separated a- and ß-cells. Overall design: 24 samples in duplicates (time course design)		GSM2497937: ZT20 alpha_2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			RNeasy Plus Micro Kit Qiagen Libraries were prepared according to the Illumina TruSeq Stranded Total RNA kit (with  Ribo-Zero TM gold probes) according to manufacturer's specifications. Input material was from 80 to 100 ng.	Illumina HiSeq 2500	cell type;;pancreatic alpha cell|source_name;;mouse alpha cell|strain;;triple reporter mouse|time;;islet isolation time ZT20 (3AM)	GEO Accession;;GSM2497937		GSM2497937	ZT20 alpha_2	2045627600	20456276	2017-02-23 15:30:41	1278277596	2045627600	20456276	2	20456276	index:0,count:20456276,average:50,stdev:0|index:1,count:20456276,average:50,stdev:0	GSM2497937_r1				in_mesa	28275001	1.4	3.19	0.07	1690743565	1667870907	1567945313	1552655483	98.65	99.02	17200807	15107759	175.935	840.898	118	163002	66.27	71.45	19263073	11399271	19263073	11399271	70.11	69.32	19263073	12059877	19263073	11060022	442611185	26.18	0.88	0	6.09	0	0.21	0	0.33	0	0.00	0	15.37	0	17200807	0	100	0	99.13	0	1.45	0	0.00	0	1.20	0	0.00	0	184.57	0	0.19	0	180137	0	20456276	0	1246050	0	43924	0	66842	0	0	0	3144703	0	1138	0	0	0	12516	0	2172587	0	4688	0	2190929	0	77.99	0	15954757	0	132519	2210150	16.677985798263	20456276.0	17200807.0	180137.0	1246050.0	43924.0	66842.0	0.0	3144703.0	15954757.0	84.1	0.9	6.1	0.2	0.3	0.0	15.4	78.0	50	50	50.00	38	1022813800	22.4	26.1	27.0	24.5	0.0	37.6	23.9	bulk
3828373	SRR5277354	SRP100479	SRS1995341	SRX2581284	SRA539333	GEO		Pancreatic alpha and beta-cellular clocks have distinct molecular properties and impact on islet hormone secretion and gene expression	We performed a parallel analysis of the molecular properties of a- and ß-cell oscillators, using a mouse model expressing three reporter genes: one labeling a-cells, one specific for ß-cells, and a third monitoring circadian gene expression. Diurnal transcriptome analysis in separated a- and ß-cells revealed that a high number of genes with key roles in islet physiology, including regulators of glucose sensing and hormone secretion, are differentially expressed in these cell types. This study represents the first parallel large-scale circadian in vivo transcriptome analysis in separated a- and ß-cells. Overall design: 24 samples in duplicates (time course design)		GSM2497938: ZT20 alpha_1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			RNeasy Plus Micro Kit Qiagen Libraries were prepared according to the Illumina TruSeq Stranded Total RNA kit (with  Ribo-Zero TM gold probes) according to manufacturer's specifications. Input material was from 80 to 100 ng.	Illumina HiSeq 2500	cell type;;pancreatic alpha cell|source_name;;mouse alpha cell|strain;;triple reporter mouse|time;;islet isolation time ZT20 (3AM)	GEO Accession;;GSM2497938		GSM2497938	ZT20 alpha_1	2118051100	21180511	2017-02-23 15:30:41	1303929290	2118051100	21180511	2	21180511	index:0,count:21180511,average:50,stdev:0|index:1,count:21180511,average:50,stdev:0	GSM2497938_r1				in_mesa	28275001	1.31	3.09	0.09	1836287130	1805893937	1709348924	1686810307	98.34	98.68	18640777	16778300	171.520	748.854	118	182239	57.63	61.9	20736135	10743201	20736135	10743201	61.31	59.98	20736135	11428371	20736135	10410040	645105534	35.13	0.91	0	6.07	0	0.22	0	0.51	0	0.00	0	11.26	0	18640777	0	100	0	99.24	0	1.52	0	0.00	0	1.21	0	0.00	0	533.22	0	0.18	0	192511	0	21180511	0	1285863	0	46448	0	108639	0	0	0	2384647	0	1025	0	0	0	11960	0	1986040	0	6788	0	2005813	0	81.94	0	17354914	0	130968	2020607	15.428249648769	21180511.0	18640777.0	192511.0	1285863.0	46448.0	108639.0	0.0	2384647.0	17354914.0	88.0	0.9	6.1	0.2	0.5	0.0	11.3	81.9	50	50	50.00	38	1059025550	23.2	25.7	26.0	25.1	0.0	37.9	24.9	bulk
3828404	SRR5277355	SRP100479	SRS1995342	SRX2581285	SRA539333	GEO		Pancreatic alpha and beta-cellular clocks have distinct molecular properties and impact on islet hormone secretion and gene expression	We performed a parallel analysis of the molecular properties of a- and ß-cell oscillators, using a mouse model expressing three reporter genes: one labeling a-cells, one specific for ß-cells, and a third monitoring circadian gene expression. Diurnal transcriptome analysis in separated a- and ß-cells revealed that a high number of genes with key roles in islet physiology, including regulators of glucose sensing and hormone secretion, are differentially expressed in these cell types. This study represents the first parallel large-scale circadian in vivo transcriptome analysis in separated a- and ß-cells. Overall design: 24 samples in duplicates (time course design)		GSM2497939: ZT16 beta_2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			RNeasy Plus Micro Kit Qiagen Libraries were prepared according to the Illumina TruSeq Stranded Total RNA kit (with  Ribo-Zero TM gold probes) according to manufacturer's specifications. Input material was from 80 to 100 ng.	Illumina HiSeq 2500	cell type;;pancreatic beta cell|source_name;;mouse beta cell|strain;;triple reporter mouse|time;;islet isolation time ZT16 (11PM)	GEO Accession;;GSM2497939		GSM2497939	ZT16 beta_2	2333755800	23337558	2017-02-23 15:30:41	1460154506	2333755800	23337558	2	23337558	index:0,count:23337558,average:50,stdev:0|index:1,count:23337558,average:50,stdev:0	GSM2497939_r1				in_mesa	28275001	2.08	2.22	0.06	1802530065	1777551077	1553626223	1536317001	98.61	98.89	18528963	17224786	163.664	666.145	117	191633	61.54	71.37	22136990	11402863	22136990	11402863	70.4	69.22	22136990	13043705	22136990	11059342	434155663	24.09	0.92	0	10.94	0	0.22	0	0.33	0	0.00	0	20.06	0	18528963	0	100	0	99.19	0	1.50	0	0.00	0	1.20	0	0.01	0	199.09	0	0.20	0	214736	0	23337558	0	2552330	0	50235	0	76961	0	0	0	4681399	0	1151	0	0	0	14704	0	2346152	0	6634	0	2368641	0	68.46	0	15976633	0	128047	2391033	18.673088787711	23337558.0	18528963.0	214736.0	2552330.0	50235.0	76961.0	0.0	4681399.0	15976633.0	79.4	0.9	10.9	0.2	0.3	0.0	20.1	68.5	50	50	50.00	38	1166877900	20.5	27.9	29.1	22.4	0.0	37.4	23.6	bulk
3828436	SRR5277356	SRP100479	SRS1995343	SRX2581286	SRA539333	GEO		Pancreatic alpha and beta-cellular clocks have distinct molecular properties and impact on islet hormone secretion and gene expression	We performed a parallel analysis of the molecular properties of a- and ß-cell oscillators, using a mouse model expressing three reporter genes: one labeling a-cells, one specific for ß-cells, and a third monitoring circadian gene expression. Diurnal transcriptome analysis in separated a- and ß-cells revealed that a high number of genes with key roles in islet physiology, including regulators of glucose sensing and hormone secretion, are differentially expressed in these cell types. This study represents the first parallel large-scale circadian in vivo transcriptome analysis in separated a- and ß-cells. Overall design: 24 samples in duplicates (time course design)		GSM2497940: ZT16 beta_1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			RNeasy Plus Micro Kit Qiagen Libraries were prepared according to the Illumina TruSeq Stranded Total RNA kit (with  Ribo-Zero TM gold probes) according to manufacturer's specifications. Input material was from 80 to 100 ng.	Illumina HiSeq 2500	cell type;;pancreatic beta cell|source_name;;mouse beta cell|strain;;triple reporter mouse|time;;islet isolation time ZT16 (11PM)	GEO Accession;;GSM2497940		GSM2497940	ZT16 beta_1	2337421300	23374213	2017-02-23 15:30:41	1456838700	2337421300	23374213	2	23374213	index:0,count:23374213,average:50,stdev:0|index:1,count:23374213,average:50,stdev:0	GSM2497940_r1				in_mesa	28275001	2.31	2.3	0.07	1892615334	1864385878	1658869759	1638596892	98.51	98.78	19407514	18036664	165.499	671.195	117	197331	61.05	69.64	22815068	11848438	22815068	11848438	68.88	67.6	22815068	13366991	22815068	11502643	492557653	26.03	0.89	0	10.24	0	0.21	0	0.37	0	0.00	0	16.39	0	19407514	0	100	0	99.23	0	1.49	0	0.00	0	1.21	0	0.01	0	464.90	0	0.19	0	207175	0	23374213	0	2392478	0	50072	0	85732	0	0	0	3830895	0	1179	0	0	0	14141	0	2409553	0	6621	0	2431494	0	72.79	0	17015036	0	129517	2455631	18.959912598346	23374213.0	19407514.0	207175.0	2392478.0	50072.0	85732.0	0.0	3830895.0	17015036.0	83.0	0.9	10.2	0.2	0.4	0.0	16.4	72.8	50	50	50.00	38	1168710650	21.4	27.2	28.2	23.2	0.0	37.6	24.0	bulk
3828466	SRR5277357	SRP100479	SRS1995344	SRX2581287	SRA539333	GEO		Pancreatic alpha and beta-cellular clocks have distinct molecular properties and impact on islet hormone secretion and gene expression	We performed a parallel analysis of the molecular properties of a- and ß-cell oscillators, using a mouse model expressing three reporter genes: one labeling a-cells, one specific for ß-cells, and a third monitoring circadian gene expression. Diurnal transcriptome analysis in separated a- and ß-cells revealed that a high number of genes with key roles in islet physiology, including regulators of glucose sensing and hormone secretion, are differentially expressed in these cell types. This study represents the first parallel large-scale circadian in vivo transcriptome analysis in separated a- and ß-cells. Overall design: 24 samples in duplicates (time course design)		GSM2497941: ZT16 alpha_2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			RNeasy Plus Micro Kit Qiagen Libraries were prepared according to the Illumina TruSeq Stranded Total RNA kit (with  Ribo-Zero TM gold probes) according to manufacturer's specifications. Input material was from 80 to 100 ng.	Illumina HiSeq 2500	cell type;;pancreatic alpha cell|source_name;;mouse alpha cell|strain;;triple reporter mouse|time;;islet isolation time ZT16 (11PM)	GEO Accession;;GSM2497941		GSM2497941	ZT16 alpha_2	2380123700	23801237	2017-02-23 15:30:41	1479422780	2380123700	23801237	2	23801237	index:0,count:23801237,average:50,stdev:0|index:1,count:23801237,average:50,stdev:0	GSM2497941_r1				in_mesa	28275001	1.62	3.06	0.09	1891125603	1857328700	1772076607	1748159153	98.21	98.65	19235750	17233730	171.930	774.051	118	191582	61.09	65.19	21298257	11751809	21298257	11751809	64.03	63.19	21298257	12316296	21298257	11391654	608870037	32.20	1.17	0	5.08	0	0.21	0	0.41	0	0.00	0	18.57	0	19235750	0	100	0	99.15	0	1.50	0	0.01	0	1.23	0	0.01	0	202.56	0	0.22	0	277593	0	23801237	0	1208692	0	50148	0	96492	0	0	0	4418847	0	1137	0	0	0	12366	0	2157650	0	6127	0	2177280	0	75.74	0	18027058	0	135066	2195900	16.257977581331	23801237.0	19235750.0	277593.0	1208692.0	50148.0	96492.0	0.0	4418847.0	18027058.0	80.8	1.2	5.1	0.2	0.4	0.0	18.6	75.7	50	50	50.00	38	1190061850	21.8	26.9	27.5	23.8	0.0	37.6	23.6	bulk
3828500	SRR5277358	SRP100479	SRS1995346	SRX2581288	SRA539333	GEO		Pancreatic alpha and beta-cellular clocks have distinct molecular properties and impact on islet hormone secretion and gene expression	We performed a parallel analysis of the molecular properties of a- and ß-cell oscillators, using a mouse model expressing three reporter genes: one labeling a-cells, one specific for ß-cells, and a third monitoring circadian gene expression. Diurnal transcriptome analysis in separated a- and ß-cells revealed that a high number of genes with key roles in islet physiology, including regulators of glucose sensing and hormone secretion, are differentially expressed in these cell types. This study represents the first parallel large-scale circadian in vivo transcriptome analysis in separated a- and ß-cells. Overall design: 24 samples in duplicates (time course design)		GSM2497942: ZT16 alpha_1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			RNeasy Plus Micro Kit Qiagen Libraries were prepared according to the Illumina TruSeq Stranded Total RNA kit (with  Ribo-Zero TM gold probes) according to manufacturer's specifications. Input material was from 80 to 100 ng.	Illumina HiSeq 2500	cell type;;pancreatic alpha cell|source_name;;mouse alpha cell|strain;;triple reporter mouse|time;;islet isolation time ZT16 (11PM)	GEO Accession;;GSM2497942		GSM2497942	ZT16 alpha_1	2257182200	22571822	2017-02-23 15:30:41	1391284438	2257182200	22571822	2	22571822	index:0,count:22571822,average:50,stdev:0|index:1,count:22571822,average:50,stdev:0	GSM2497942_r1				in_mesa	28275001	1.33	3.13	0.1	1924284999	1892317694	1808886705	1785559699	98.34	98.71	19567853	17718845	170.311	722.398	118	192388	57.45	61.12	21547703	11242611	21547703	11242611	60.27	59.21	21547703	11794302	21547703	10891428	700800004	36.42	0.88	0	5.19	0	0.22	0	0.49	0	0.00	0	12.60	0	19567853	0	100	0	99.25	0	1.48	0	0.01	0	1.21	0	0.01	0	408.33	0	0.19	0	197753	0	22571822	0	1172209	0	48907	0	110360	0	0	0	2844702	0	1061	0	0	0	11601	0	2000542	0	6378	0	2019582	0	81.50	0	18395644	0	135815	2035317	14.985951478114	22571822.0	19567853.0	197753.0	1172209.0	48907.0	110360.0	0.0	2844702.0	18395644.0	86.7	0.9	5.2	0.2	0.5	0.0	12.6	81.5	50	50	50.00	38	1128591100	23.3	25.8	26.1	24.8	0.0	37.8	24.7	bulk
3828532	SRR5277359	SRP100479	SRS1995348	SRX2581289	SRA539333	GEO		Pancreatic alpha and beta-cellular clocks have distinct molecular properties and impact on islet hormone secretion and gene expression	We performed a parallel analysis of the molecular properties of a- and ß-cell oscillators, using a mouse model expressing three reporter genes: one labeling a-cells, one specific for ß-cells, and a third monitoring circadian gene expression. Diurnal transcriptome analysis in separated a- and ß-cells revealed that a high number of genes with key roles in islet physiology, including regulators of glucose sensing and hormone secretion, are differentially expressed in these cell types. This study represents the first parallel large-scale circadian in vivo transcriptome analysis in separated a- and ß-cells. Overall design: 24 samples in duplicates (time course design)		GSM2497943: ZT12 beta_2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			RNeasy Plus Micro Kit Qiagen Libraries were prepared according to the Illumina TruSeq Stranded Total RNA kit (with  Ribo-Zero TM gold probes) according to manufacturer's specifications. Input material was from 80 to 100 ng.	Illumina HiSeq 2500	cell type;;pancreatic beta cell|source_name;;mouse beta cell|strain;;triple reporter mouse|time;;islet isolation time ZT12 (7PM)	GEO Accession;;GSM2497943		GSM2497943	ZT12 beta_2	2027242200	20272422	2017-02-23 15:30:41	1271174297	2027242200	20272422	2	20272422	index:0,count:20272422,average:50,stdev:0|index:1,count:20272422,average:50,stdev:0	GSM2497943_r1				in_mesa	28275001	2.6	2.33	0.05	1578006897	1562972385	1333526707	1324733397	99.05	99.34	16154770	14791084	172.218	751.287	117	160231	72.62	85.9	19677146	11731770	19677146	11731770	83.1	83.58	19677146	13423828	19677146	11415214	177050965	11.22	0.88	0	12.32	0	0.21	0	0.15	0	0.00	0	19.96	0	16154770	0	100	0	99.13	0	1.48	0	0.00	0	1.18	0	0.00	0	477.00	0	0.18	0	178212	0	20272422	0	2496744	0	42121	0	29418	0	0	0	4046113	0	1120	0	0	0	14036	0	2650089	0	5438	0	2670683	0	67.37	0	13658026	0	128060	2693013	21.029306575043	20272422.0	16154770.0	178212.0	2496744.0	42121.0	29418.0	0.0	4046113.0	13658026.0	79.7	0.9	12.3	0.2	0.1	0.0	20.0	67.4	50	50	50.00	38	1013621100	20.1	27.7	29.8	22.4	0.0	37.4	23.6	bulk
3828756	SRR5277360	SRP100479	SRS1995347	SRX2581290	SRA539333	GEO		Pancreatic alpha and beta-cellular clocks have distinct molecular properties and impact on islet hormone secretion and gene expression	We performed a parallel analysis of the molecular properties of a- and ß-cell oscillators, using a mouse model expressing three reporter genes: one labeling a-cells, one specific for ß-cells, and a third monitoring circadian gene expression. Diurnal transcriptome analysis in separated a- and ß-cells revealed that a high number of genes with key roles in islet physiology, including regulators of glucose sensing and hormone secretion, are differentially expressed in these cell types. This study represents the first parallel large-scale circadian in vivo transcriptome analysis in separated a- and ß-cells. Overall design: 24 samples in duplicates (time course design)		GSM2497944: ZT12 beta_1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			RNeasy Plus Micro Kit Qiagen Libraries were prepared according to the Illumina TruSeq Stranded Total RNA kit (with  Ribo-Zero TM gold probes) according to manufacturer's specifications. Input material was from 80 to 100 ng.	Illumina HiSeq 2500	cell type;;pancreatic beta cell|source_name;;mouse beta cell|strain;;triple reporter mouse|time;;islet isolation time ZT12 (7PM)	GEO Accession;;GSM2497944		GSM2497944	ZT12 beta_1	1629226300	16292263	2017-02-23 15:30:41	1022695664	1629226300	16292263	2	16292263	index:0,count:16292263,average:50,stdev:0|index:1,count:16292263,average:50,stdev:0	GSM2497944_r1				in_mesa	28275001	2.44	2.29	0.05	1251774261	1242238409	1040252687	1035345067	99.24	99.53	12819932	11780210	169.750	716.862	117	131526	71.1	85.51	15833708	9114676	15833708	9114676	82.65	83.1	15833708	10595549	15833708	8857511	144044140	11.51	0.79	0	13.26	0	0.19	0	0.14	0	0.00	0	20.99	0	12819932	0	100	0	99.15	0	1.46	0	0.00	0	1.18	0	0.00	0	519.05	0	0.18	0	128629	0	16292263	0	2160544	0	30444	0	22107	0	0	0	3419780	0	841	0	0	0	10623	0	2033638	0	4013	0	2049115	0	65.43	0	10659388	0	120189	2062755	17.162593914585	16292263.0	12819932.0	128629.0	2160544.0	30444.0	22107.0	0.0	3419780.0	10659388.0	78.7	0.8	13.3	0.2	0.1	0.0	21.0	65.4	50	50	50.00	38	814613150	19.9	28.0	29.9	22.3	0.0	37.4	23.4	bulk
3828787	SRR5277361	SRP100479	SRS1995350	SRX2581291	SRA539333	GEO		Pancreatic alpha and beta-cellular clocks have distinct molecular properties and impact on islet hormone secretion and gene expression	We performed a parallel analysis of the molecular properties of a- and ß-cell oscillators, using a mouse model expressing three reporter genes: one labeling a-cells, one specific for ß-cells, and a third monitoring circadian gene expression. Diurnal transcriptome analysis in separated a- and ß-cells revealed that a high number of genes with key roles in islet physiology, including regulators of glucose sensing and hormone secretion, are differentially expressed in these cell types. This study represents the first parallel large-scale circadian in vivo transcriptome analysis in separated a- and ß-cells. Overall design: 24 samples in duplicates (time course design)		GSM2497945: ZT12 alpha_2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			RNeasy Plus Micro Kit Qiagen Libraries were prepared according to the Illumina TruSeq Stranded Total RNA kit (with  Ribo-Zero TM gold probes) according to manufacturer's specifications. Input material was from 80 to 100 ng.	Illumina HiSeq 2500	cell type;;pancreatic alpha cell|source_name;;mouse alpha cell|strain;;triple reporter mouse|time;;islet isolation time ZT12 (7PM)	GEO Accession;;GSM2497945		GSM2497945	ZT12 alpha_2	1757538400	17575384	2017-02-23 15:30:41	1097651024	1757538400	17575384	2	17575384	index:0,count:17575384,average:50,stdev:0|index:1,count:17575384,average:50,stdev:0	GSM2497945_r1				in_mesa	28275001	1.24	1.86	0.04	1198080391	1248032449	1055990048	1128136504	104.17	106.83	12481438	11450906	162.186	597.561	109	114779	63.16	71.84	15484457	7883514	15484457	7883514	52.03	53.69	15484457	6493640	15484457	5891642	234289649	19.56	5.54	0	8.58	0	0.14	0	0.11	0	0.00	0	28.74	0	12481438	0	100	0	98.05	0	1.46	0	0.01	0	1.30	0	0.01	0	204.76	0	0.70	0	973666	0	17575384	0	1507313	0	23997	0	19241	0	0	0	5050708	0	517	0	0	0	5971	0	1044304	0	4213	0	1055005	0	62.44	0	10974125	0	110029	1059324	9.627679975279	17575384.0	12481438.0	973666.0	1507313.0	23997.0	19241.0	0.0	5050708.0	10974125.0	71.0	5.5	8.6	0.1	0.1	0.0	28.7	62.4	50	50	50.00	38	878769200	21.7	26.4	29.6	22.3	0.0	37.5	24.0	bulk
3828820	SRR5277362	SRP100479	SRS1995349	SRX2581292	SRA539333	GEO		Pancreatic alpha and beta-cellular clocks have distinct molecular properties and impact on islet hormone secretion and gene expression	We performed a parallel analysis of the molecular properties of a- and ß-cell oscillators, using a mouse model expressing three reporter genes: one labeling a-cells, one specific for ß-cells, and a third monitoring circadian gene expression. Diurnal transcriptome analysis in separated a- and ß-cells revealed that a high number of genes with key roles in islet physiology, including regulators of glucose sensing and hormone secretion, are differentially expressed in these cell types. This study represents the first parallel large-scale circadian in vivo transcriptome analysis in separated a- and ß-cells. Overall design: 24 samples in duplicates (time course design)		GSM2497946: ZT12 alpha_1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			RNeasy Plus Micro Kit Qiagen Libraries were prepared according to the Illumina TruSeq Stranded Total RNA kit (with  Ribo-Zero TM gold probes) according to manufacturer's specifications. Input material was from 80 to 100 ng.	Illumina HiSeq 2500	cell type;;pancreatic alpha cell|source_name;;mouse alpha cell|strain;;triple reporter mouse|time;;islet isolation time ZT12 (7PM)	GEO Accession;;GSM2497946		GSM2497946	ZT12 alpha_1	1953639100	19536391	2017-02-23 15:30:41	1196343584	1953639100	19536391	2	19536391	index:0,count:19536391,average:50,stdev:0|index:1,count:19536391,average:50,stdev:0	GSM2497946_r1				in_mesa	28275001	1.39	3.17	0.07	1652242795	1637050620	1514810700	1506581146	99.08	99.46	16875931	14429576	186.525	957.528	118	130154	71.95	78.46	19156245	12142464	19156245	12142464	76.71	76.22	19156245	12945412	19156245	11794965	325908950	19.73	0.86	0	7.17	0	0.23	0	0.23	0	0.00	0	13.16	0	16875931	0	100	0	99.09	0	1.42	0	0.00	0	1.19	0	0.00	0	358.83	0	0.18	0	167549	0	19536391	0	1400124	0	44029	0	45003	0	0	0	2571428	0	1160	0	0	0	12935	0	2394544	0	3761	0	2412400	0	79.22	0	15475807	0	134505	2432629	18.085788632393	19536391.0	16875931.0	167549.0	1400124.0	44029.0	45003.0	0.0	2571428.0	15475807.0	86.4	0.9	7.2	0.2	0.2	0.0	13.2	79.2	50	50	50.00	38	976819550	22.6	25.9	26.6	24.9	0.0	37.9	24.6	bulk
3828851	SRR5277363	SRP100479	SRS1995351	SRX2581293	SRA539333	GEO		Pancreatic alpha and beta-cellular clocks have distinct molecular properties and impact on islet hormone secretion and gene expression	We performed a parallel analysis of the molecular properties of a- and ß-cell oscillators, using a mouse model expressing three reporter genes: one labeling a-cells, one specific for ß-cells, and a third monitoring circadian gene expression. Diurnal transcriptome analysis in separated a- and ß-cells revealed that a high number of genes with key roles in islet physiology, including regulators of glucose sensing and hormone secretion, are differentially expressed in these cell types. This study represents the first parallel large-scale circadian in vivo transcriptome analysis in separated a- and ß-cells. Overall design: 24 samples in duplicates (time course design)		GSM2497947: ZT0 beta_2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			RNeasy Plus Micro Kit Qiagen Libraries were prepared according to the Illumina TruSeq Stranded Total RNA kit (with  Ribo-Zero TM gold probes) according to manufacturer's specifications. Input material was from 80 to 100 ng.	Illumina HiSeq 2500	cell type;;pancreatic beta cell|source_name;;mouse beta cell|strain;;triple reporter mouse|time;;islet isolation time ZT0 (7AM)	GEO Accession;;GSM2497947		GSM2497947	ZT0 beta_2	2040599300	20405993	2017-02-23 15:30:41	1280496524	2040599300	20405993	2	20405993	index:0,count:20405993,average:50,stdev:0|index:1,count:20405993,average:50,stdev:0	GSM2497947_r1				in_mesa	28275001	2.37	2.06	0.05	1601248899	1575047974	1350268232	1331116032	98.36	98.58	16284380	15013915	174.049	733.140	117	164017	61.17	72.48	19754552	9960409	19754552	9960409	71.97	70.16	19754552	11720420	19754552	9641336	357275717	22.31	1.13	0	12.46	0	0.20	0	0.32	0	0.00	0	19.68	0	16284380	0	100	0	99.16	0	1.54	0	0.00	0	1.21	0	0.01	0	434.68	0	0.23	0	231308	0	20405993	0	2542887	0	41228	0	64734	0	0	0	4015651	0	1015	0	0	0	12844	0	2052772	0	6161	0	2072792	0	67.34	0	13741493	0	126769	2095383	16.529143560334	20405993.0	16284380.0	231308.0	2542887.0	41228.0	64734.0	0.0	4015651.0	13741493.0	79.8	1.1	12.5	0.2	0.3	0.0	19.7	67.3	50	50	50.00	38	1020299650	20.1	28.2	29.1	22.5	0.0	37.4	23.3	bulk
3828882	SRR5277364	SRP100479	SRS1995352	SRX2581294	SRA539333	GEO		Pancreatic alpha and beta-cellular clocks have distinct molecular properties and impact on islet hormone secretion and gene expression	We performed a parallel analysis of the molecular properties of a- and ß-cell oscillators, using a mouse model expressing three reporter genes: one labeling a-cells, one specific for ß-cells, and a third monitoring circadian gene expression. Diurnal transcriptome analysis in separated a- and ß-cells revealed that a high number of genes with key roles in islet physiology, including regulators of glucose sensing and hormone secretion, are differentially expressed in these cell types. This study represents the first parallel large-scale circadian in vivo transcriptome analysis in separated a- and ß-cells. Overall design: 24 samples in duplicates (time course design)		GSM2497948: ZT0 beta_1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			RNeasy Plus Micro Kit Qiagen Libraries were prepared according to the Illumina TruSeq Stranded Total RNA kit (with  Ribo-Zero TM gold probes) according to manufacturer's specifications. Input material was from 80 to 100 ng.	Illumina HiSeq 2500	cell type;;pancreatic beta cell|source_name;;mouse beta cell|strain;;triple reporter mouse|time;;islet isolation time ZT0 (7AM)	GEO Accession;;GSM2497948		GSM2497948	ZT0 beta_1	2021504100	20215041	2017-02-23 15:30:41	1280055641	2021504100	20215041	2	20215041	index:0,count:20215041,average:50,stdev:0|index:1,count:20215041,average:50,stdev:0	GSM2497948_r1				in_mesa	28275001	3.25	2.28	0.04	1553665031	1537643574	1274384259	1265052826	98.97	99.27	15939251	14695920	168.267	692.759	117	162403	71.15	86.69	19962296	11340432	19962296	11340432	83.52	84.26	19962296	13312920	19962296	11022212	156499002	10.07	0.98	0	14.14	0	0.17	0	0.13	0	0.00	0	20.85	0	15939251	0	100	0	99.12	0	1.45	0	0.00	0	1.18	0	0.00	0	360.27	0	0.21	0	198830	0	20215041	0	2857757	0	33846	0	26432	0	0	0	4215512	0	1072	0	0	0	13225	0	2569514	0	4992	0	2588803	0	64.71	0	13081494	0	120460	2610093	21.667715424207	20215041.0	15939251.0	198830.0	2857757.0	33846.0	26432.0	0.0	4215512.0	13081494.0	78.8	1.0	14.1	0.2	0.1	0.0	20.9	64.7	50	50	50.00	38	1010752050	20.0	27.7	30.0	22.4	0.0	37.3	23.0	bulk
3828914	SRR5277365	SRP100479	SRS1995354	SRX2581295	SRA539333	GEO		Pancreatic alpha and beta-cellular clocks have distinct molecular properties and impact on islet hormone secretion and gene expression	We performed a parallel analysis of the molecular properties of a- and ß-cell oscillators, using a mouse model expressing three reporter genes: one labeling a-cells, one specific for ß-cells, and a third monitoring circadian gene expression. Diurnal transcriptome analysis in separated a- and ß-cells revealed that a high number of genes with key roles in islet physiology, including regulators of glucose sensing and hormone secretion, are differentially expressed in these cell types. This study represents the first parallel large-scale circadian in vivo transcriptome analysis in separated a- and ß-cells. Overall design: 24 samples in duplicates (time course design)		GSM2497949: ZT0 alpha_2; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			RNeasy Plus Micro Kit Qiagen Libraries were prepared according to the Illumina TruSeq Stranded Total RNA kit (with  Ribo-Zero TM gold probes) according to manufacturer's specifications. Input material was from 80 to 100 ng.	Illumina HiSeq 2500	cell type;;pancreatic alpha cell|source_name;;mouse alpha cell|strain;;triple reporter mouse|time;;islet isolation time ZT0 (7AM)	GEO Accession;;GSM2497949		GSM2497949	ZT0 alpha_2	2349769400	23497694	2017-02-23 15:30:42	1450330654	2349769400	23497694	2	23497694	index:0,count:23497694,average:50,stdev:0|index:1,count:23497694,average:50,stdev:0	GSM2497949_r1				in_mesa	28275001	1.28	3.13	0.08	1881435647	1849037498	1756253931	1731915454	98.28	98.61	19264974	17131221	173.646	817.861	118	164406	62.59	67.04	21377233	12057572	21377233	12057572	65.87	65.01	21377233	12690606	21377233	11690885	569231097	30.26	1.06	0	5.45	0	0.22	0	0.40	0	0.00	0	17.40	0	19264974	0	100	0	99.15	0	1.49	0	0.00	0	1.22	0	0.01	0	431.59	0	0.21	0	249090	0	23497694	0	1280472	0	52354	0	92925	0	0	0	4087441	0	1140	0	0	0	13520	0	2240197	0	6702	0	2261559	0	76.54	0	17984502	0	136769	2276543	16.645168130205	23497694.0	19264974.0	249090.0	1280472.0	52354.0	92925.0	0.0	4087441.0	17984502.0	82.0	1.1	5.4	0.2	0.4	0.0	17.4	76.5	50	50	50.00	38	1174884700	22.0	26.8	27.3	24.0	0.0	37.7	23.7	bulk
3828946	SRR5277366	SRP100479	SRS1995353	SRX2581296	SRA539333	GEO		Pancreatic alpha and beta-cellular clocks have distinct molecular properties and impact on islet hormone secretion and gene expression	We performed a parallel analysis of the molecular properties of a- and ß-cell oscillators, using a mouse model expressing three reporter genes: one labeling a-cells, one specific for ß-cells, and a third monitoring circadian gene expression. Diurnal transcriptome analysis in separated a- and ß-cells revealed that a high number of genes with key roles in islet physiology, including regulators of glucose sensing and hormone secretion, are differentially expressed in these cell types. This study represents the first parallel large-scale circadian in vivo transcriptome analysis in separated a- and ß-cells. Overall design: 24 samples in duplicates (time course design)		GSM2497950: ZT0 alpha_1; Mus musculus; RNA-Seq				RNA-Seq	TRANSCRIPTOMIC	cDNA	paired			RNeasy Plus Micro Kit Qiagen Libraries were prepared according to the Illumina TruSeq Stranded Total RNA kit (with  Ribo-Zero TM gold probes) according to manufacturer's specifications. Input material was from 80 to 100 ng.	Illumina HiSeq 2500	cell type;;pancreatic alpha cell|source_name;;mouse alpha cell|strain;;triple reporter mouse|time;;islet isolation time ZT0 (7AM)	GEO Accession;;GSM2497950		GSM2497950	ZT0 alpha_1	2251849000	22518490	2017-02-23 15:30:42	1389252949	2251849000	22518490	2	22518490	index:0,count:22518490,average:50,stdev:0|index:1,count:22518490,average:50,stdev:0	GSM2497950_r1				in_mesa	28275001	1.75	3.14	0.05	1780368483	1760694605	1604298089	1592488425	98.89	99.26	18226562	15653938	178.731	904.264	118	160455	72.06	79.94	21058223	13133483	21058223	13133483	78.0	77.6	21058223	14217269	21058223	12750255	312577546	17.56	1.02	0	7.98	0	0.19	0	0.19	0	0.00	0	18.67	0	18226562	0	100	0	98.99	0	1.42	0	0.00	0	1.19	0	0.01	0	292.66	0	0.21	0	228942	0	22518490	0	1796781	0	43021	0	43722	0	0	0	4205185	0	1292	0	0	0	14162	0	2610109	0	4206	0	2629769	0	72.96	0	16429781	0	130837	2649027	20.246772701912	22518490.0	18226562.0	228942.0	1796781.0	43021.0	43722.0	0.0	4205185.0	16429781.0	80.9	1.0	8.0	0.2	0.2	0.0	18.7	73.0	50	50	50.00	38	1125924500	21.5	26.7	27.9	23.9	0.0	37.6	23.7	bulk
2769684	SRR5590218	SRP107891	SRS2220297	SRX2847326	SRA565436	University of Rochester	Center for Musculoskeletal Research	Adult/aged diaphragm and gastrocnemius RNA seq	To evaluate whether aged muscles share similar molecular features as muscles after denervation/reinnervation.		RNA-Seq of mus musculus: adult extrasynaptic diaphragm	Illumina-compatible library construction was performed using the TruSeq Stranded Total RNA Sample Preparation Kit (Illumina, San Diego, California) per manufacturerŐs protocols. The amplified libraries were hybridized to the Illumina single-end flow cell and amplified using the cBot (Illumina) at a concentration of 8 pM per lane. Single-end reads of 100 nt were generated for each sample. Sequenced reads were cleaned according to a rigorous pre-processing workflow (Trimmomatic-0.32) before mapping some of them to the mouse reference genome (GRCm38.p4) with STAR-2.4.2a. Cufflinks2.0.2 with the gencode-M6 mouse gene annotations was then used to perform differential expression analysis.		Adult_ExS	RNA-Seq	TRANSCRIPTOMIC	cDNA	single				Illumina HiSeq 2500	age;;6 months|BioSampleModel;;Model organism or animal|breed;;C57BL/6|sample_type;;Adult extrasynaptic diaphragm|sex;;male|tissue;;Diaphragm			Adult_ExS		9941935001	105213337	2017-05-26 00:00:53	1585323125	9941935001	105213337	1	105213337	index:0,count:105213337,average:94.49,stdev:17.82	clt_Adult_ExS-2_R1.bam				in_mesa	28583253	43.88	1.2	0.04	9847729324	9798296873	8797146106	8786986352	99.5	99.88	0	0	0	0	0	0	75.93	85.58	122154056	79703678	122154056	79703678	81.53	83.72	122154056	85589590	122154056	77972026	1224989048	12.44	0.10	0	11.25	0	0.05	0	0.00	0	0.00	0	0.18	0	104973631	0	94	0	94.46	0	1.40	0	0.00	0	1.08	0	0.00	0	855.01	0	0.11	0	107259	0	105213337	0	11841666	0	48796	0	432	0	0	0	190478	0	4066	0	0	0	50757	0	8501330	0	15837	0	8571990	0	88.52	0	93131965	0	189083	9124106	48.254501991189	105213337.0	104973631.0	107259.0	11841666.0	48796.0	432.0	0.0	190478.0	93131965.0	99.8	0.1	11.3	0.0	0.0	0.0	0.2	88.5	15	101	94.49	6	9941935001	25.3	20.7	22.3	31.7	0.0	35.8	29.6	bulk
2769713	SRR5590219	SRP107891	SRS2220296	SRX2847325	SRA565436	University of Rochester	Center for Musculoskeletal Research	Adult/aged diaphragm and gastrocnemius RNA seq	To evaluate whether aged muscles share similar molecular features as muscles after denervation/reinnervation.		RNA-Seq of mus musculus: adult synaptic diaphragm	Illumina-compatible library construction was performed using the TruSeq Stranded Total RNA Sample Preparation Kit (Illumina, San Diego, California) per manufacturerŐs protocols. The amplified libraries were hybridized to the Illumina single-end flow cell and amplified using the cBot (Illumina) at a concentration of 8 pM per lane. Single-end reads of 100 nt were generated for each sample. Sequenced reads were cleaned according to a rigorous pre-processing workflow (Trimmomatic-0.32) before mapping some of them to the mouse reference genome (GRCm38.p4) with STAR-2.4.2a. Cufflinks2.0.2 with the gencode-M6 mouse gene annotations was then used to perform differential expression analysis.		Adult_Syn	RNA-Seq	TRANSCRIPTOMIC	cDNA	single				Illumina HiSeq 2500	age;;6 months|BioSampleModel;;Model organism or animal|breed;;C57BL/6|sample_type;;Adult synaptic diaphragm|sex;;male|tissue;;Diaphragm			Adult_Syn		9462807342	100314326	2017-05-26 00:00:53	1531343609	9462807342	100314326	1	100314326	index:0,count:100314326,average:94.33,stdev:17.90	clt_Adult_Syn_R1.bam				in_mesa	28583253	39.74	1.25	0.04	9367198051	9297666566	8471740750	8444367188	99.26	99.68	0	0	0	0	0	0	74.05	82.41	114645226	74129504	114645226	74129504	79.38	80.53	114645226	79469456	114645226	72430430	1435036393	15.32	0.12	0	10.13	0	0.04	0	0.00	0	0.00	0	0.16	0	100109061	0	94	0	94.19	0	1.40	0	0.00	0	1.11	0	0.00	0	815.20	0	0.11	0	121850	0	100314326	0	10161498	0	41736	0	361	0	0	0	163168	0	3936	0	0	0	53749	0	8891872	0	16866	0	8966423	0	89.67	0	89947563	0	186105	9474513	50.909502700089	100314326.0	100109061.0	121850.0	10161498.0	41736.0	361.0	0.0	163168.0	89947563.0	99.8	0.1	10.1	0.0	0.0	0.0	0.2	89.7	15	101	94.33	6	9462807342	25.6	20.7	22.2	31.5	0.0	35.8	29.5	bulk
2769939	SRR5590220	SRP107891	SRS2220295	SRX2847324	SRA565436	University of Rochester	Center for Musculoskeletal Research	Adult/aged diaphragm and gastrocnemius RNA seq	To evaluate whether aged muscles share similar molecular features as muscles after denervation/reinnervation.		RNA-Seq of mus musculus: sciatic nerve transection-treated adult gastrocnemius	Illumina-compatible library construction was performed using the TruSeq Stranded Total RNA Sample Preparation Kit (Illumina, San Diego, California) per manufacturerŐs protocols. The amplified libraries were hybridized to the Illumina single-end flow cell and amplified using the cBot (Illumina) at a concentration of 8 pM per lane. Single-end reads of 100 nt were generated for each sample. Sequenced reads were cleaned according to a rigorous pre-processing workflow (Trimmomatic-0.32) before mapping some of them to the mouse reference genome (GRCm38.p4) with STAR-2.4.2a. Cufflinks2.0.2 with the gencode-M6 mouse gene annotations was then used to perform differential expression analysis.		Adult_nc	RNA-Seq	TRANSCRIPTOMIC	cDNA	single				Illumina HiSeq 2500	age;;6 months|BioSampleModel;;Model organism or animal|breed;;C57BL/6|sample_type;;Adult sciatic nerve transection-treated gastrocnemius|sex;;male|tissue;;Gastrocnemius			Adult_nc		15985312528	168420195	2017-05-26 00:00:53	2532826007	15985312528	168420195	1	168420195	index:0,count:168420195,average:94.91,stdev:16.80	clt_7M-1-nc_R1.bam				in_mesa	28583253	43.46	1.38	0.04	15799289110	15703813164	13509201735	13472159831	99.4	99.73	0	0	0	0	0	0	73.03	85.95	207405212	122771877	207405212	122771877	79.44	84.2	207405212	133550149	207405212	120265898	1831239112	11.59	0.15	0	15.01	0	0.05	0	0.00	0	0.00	0	0.13	0	168116506	0	94	0	94.58	0	1.40	0	0.00	0	1.11	0	0.00	0	894.27	0	0.13	0	255853	0	168420195	0	25283715	0	83932	0	976	0	0	0	218781	0	4546	0	0	0	63208	0	9956974	0	35742	0	10060470	0	84.81	0	142832791	0	201568	10788930	53.525013891094	168420195.0	168116506.0	255853.0	25283715.0	83932.0	976.0	0.0	218781.0	142832791.0	99.8	0.2	15.0	0.0	0.0	0.0	0.1	84.8	15	101	94.91	6	15985312528	25.7	20.2	21.8	32.3	0.0	35.9	29.9	bulk
2769971	SRR5590221	SRP107891	SRS2220298	SRX2847323	SRA565436	University of Rochester	Center for Musculoskeletal Research	Adult/aged diaphragm and gastrocnemius RNA seq	To evaluate whether aged muscles share similar molecular features as muscles after denervation/reinnervation.		RNA-Seq of mus musculus: adult gastrocnemius	Illumina-compatible library construction was performed using the TruSeq Stranded Total RNA Sample Preparation Kit (Illumina, San Diego, California) per manufacturerŐs protocols. The amplified libraries were hybridized to the Illumina single-end flow cell and amplified using the cBot (Illumina) at a concentration of 8 pM per lane. Single-end reads of 100 nt were generated for each sample. Sequenced reads were cleaned according to a rigorous pre-processing workflow (Trimmomatic-0.32) before mapping some of them to the mouse reference genome (GRCm38.p4) with STAR-2.4.2a. Cufflinks2.0.2 with the gencode-M6 mouse gene annotations was then used to perform differential expression analysis.		Adult_Ctrl	RNA-Seq	TRANSCRIPTOMIC	cDNA	single				Illumina HiSeq 2500	age;;6 months|BioSampleModel;;Model organism or animal|breed;;C57BL/6|sample_type;;Adult control gastrocnemius|sex;;male|tissue;;Gastrocnemius			Adult_Ctrl		16000620211	167197992	2017-05-26 00:00:53	2303817578	16000620211	167197992	1	167197992	index:0,count:167197992,average:95.70,stdev:15.88	clt_5M-3-Ctrl_R1.bam				in_mesa	28583253	34.81	1.72	0.05	15815628944	15661361640	13905743834	13812500064	99.02	99.33	0	0	0	0	0	0	69.21	79.11	198785262	115416577	198785262	115416577	74.13	77.33	198785262	123629578	198785262	112829487	2803468087	17.73	0.15	0	12.48	0	0.05	0	0.00	0	0.00	0	0.20	0	166765073	0	95	0	95.31	0	1.41	0	0.00	0	1.14	0	0.00	0	887.78	0	0.10	0	253175	0	167197992	0	20864077	0	89373	0	1398	0	0	0	342148	0	5458	0	0	0	86568	0	13414617	0	36228	0	13542871	0	87.26	0	145900996	0	207270	14347735	69.222439330342	167197992.0	166765073.0	253175.0	20864077.0	89373.0	1398.0	0.0	342148.0	145900996.0	99.7	0.2	12.5	0.1	0.0	0.0	0.2	87.3	15	101	95.70	6	16000620211	25.7	21.1	22.2	31.1	0.0	36.0	30.5	bulk