Mendoza Parra 2016, Retinoid-induced cell fate-regulatory programs in stem cells.

Time serie data for RXRα binding (ChIP-seq), chromatin accessibility (FAIRE-seq), histone marks H3K27me3 and H3K4me3 (ChIP-seq) and RNAPII (ChIP-seq) in two mouse embryonic carcinoma cell lines (P19 and F9).
All trans retinoic acid (ATRA) induction triggers RXR isotypes (α, β and γ) and RAR isotypes (α, β and γ) to heterodimerize and activate their target genes. This triggers neuronal fate commitment (ectoderm) for P19 cells and endoderm fate commitment for F9 cells. On the other hand, ethanol (EtOH) treatment should not trigger any of these events.
These data have been used to model gene activation cascade during neuronal commitment of P19 cells by the authors.

• Raw data was downloaded from: GEO
• Input file format: BED
• Download date: 20-10-2016

From M. musculus (July 2007 NCBI37/mm9).

DNase FAIRE data:

	Filename	Description	Feature	GEO-ID
1	GSM1674792_F9_FAIRE_EtOH.sga	F9|FAIRE|48hEtOH	FAIRE	GSM1674792
2	GSM1674793_F9_FAIRE_2hATRA.sga	F9|FAIRE|2hATRA	FAIRE	GSM1674793
3	GSM1674794_F9_FAIRE_6hATRA.sga	F9|FAIRE|6hATRA	FAIRE	GSM1674794
4	GSM1674795_F9_FAIRE_24hATRA.sga	F9|FAIRE|24hATRA	FAIRE	GSM1674795
5	GSM1674796_F9_FAIRE_48hATRA.sga	F9|FAIRE|48hATRA	FAIRE	GSM1674796
6	GSM1674817_P19_FAIREseq_48h_EtOH.sga	P19|FAIRE|48hEtOH	FAIRE	GSM1674817
7	GSM1674818_P19_FAIREseq_2hATRA.sga	P19|FAIRE|2hATRA	FAIRE	GSM1674818
8	GSM1674819_P19_FAIREseq_6hATRA.sga	P19|FAIRE|6hATRA	FAIRE	GSM1674819
9	GSM1674820_P19_FAIREseq_24hATRA.sga	P19|FAIRE|24hATRA	FAIRE	GSM1674820
10	GSM1674821_P19_FAIREseq_48hATRA.sga	P19|FAIRE|48hATRA	FAIRE	GSM1674821

ChIP-seq data:

	Filename	Description	Feature	GEO-ID
1	GSM1674797_F9_H3K4me3_EtOH.sga	F9|H3K4me3|48hEtOH	H3K4me3	GSM1674797
2	GSM1674798_F9_H3K4me3_2hATRA.sga	F9|H3K4me3|2hATRA	H3K4me3	GSM1674798
3	GSM1674799_F9_H3K4me3_6hATRA.sga	F9|H3K4me3|6hATRA	H3K4me3	GSM1674799
4	GSM1674800_F9_H3K4me3_24hATRA.sga	F9|H3K4me3|24hATRA	H3K4me3	GSM1674800
5	GSM1674801_F9_H3K4me3_48hATRA.sga	F9|H3K4me3|48hATRA	H3K4me3	GSM1674801
6	GSM1674802_F9_H3K27me3_EtOH.sga	F9|H3K27me3|EtOH	H3K27me3	GSM1674802
7	GSM1674803_F9_H3K27me3_2hATRA.sga	F9|H3K27me3|2hATRA	H3K27me3	GSM1674803
8	GSM1674804_F9_H3K27me3_6hATRA.sga	F9|H3K27me3|6hATRA	H3K27me3	GSM1674804
9	GSM1674805_F9_H3K27me3_24hATRA.sga	F9|H3K27me3|24hATRA	H3K27me3	GSM1674805
10	GSM1674806_F9_H3K27me3_48hATRA.sga	F9|H3K27me3|48hATRA	H3K27me3	GSM1674806
11	GSM1674807_F9_RNAPII_EtOH.sga	F9|PolII|48hEtOH	PolII	GSM1674807
12	GSM1674808_F9_RNAPII_2hATRA.sga	F9|PolII|2hATRA	PolII	GSM1674808
13	GSM1674809_F9_RNAPII_6hATRA.sga	F9|PolII|6hATRA	PolII	GSM1674809
14	GSM1674810_F9_RNAPII_24hATRA.sga	F9|PolII|24hATRA	PolII	GSM1674810
15	GSM1674811_F9_RNAPII_48hATRA.sga	F9|PolII|48hATRA	PolII	GSM1674811
16	GSM1674812_F9_RXRa_EtOH.sga	F9|RXRa|48hEtOH	RXRa	GSM1674812
17	GSM1674813_F9_RXRa_2hATRA.sga	F9|RXRa|2hATRA	RXRa	GSM1674813
18	GSM1674814_F9_RXRa_6hATRA.sga	F9|RXRa|6hATRA	RXRa	GSM1674814
19	GSM1674815_F9_RXRa_24hATRA.sga	F9|RXRa|24hATRA	RXRa	GSM1674815
20	GSM1674816_F9_RXRa_48hATRA.sga	F9|RXRa|48hATRA	RXRa	GSM1674816
21	GSM1674822_P19_H3K4me3_48h_EtOH.sga	P19|H3K4me3|48hEtOH	H3K4me3	GSM1674822
22	GSM1674823_P19_H3K4me3_2hATRA.sga	P19|H3K4me3|2hATRA	H3K4me3	GSM1674823
23	GSM1674824_P19_H3K4me3_6hATRA.sga	P19|H3K4me3|6hATRA	H3K4me3	GSM1674824
24	GSM1674825_P19_H3K4me3_24hATRA.sga	P19|H3K4me3|24hATRA	H3K4me3	GSM1674825
25	GSM1674826_P19_H3K4me3_48hATRA.sga	P19|H3K4me3|48hATRA	H3K4me3	GSM1674826
26	GSM1674827_P19_H3K27me3_48H_EtOH.sga	P19|H3K27me3|48hEtOH	H3K27me3	GSM1674827
27	GSM1674828_P19_H3K27me3_2hATRA.sga	P19|H3K27me3|2hATRA	H3K27me3	GSM1674828
28	GSM1674829_P19_H3K27me3_6hATRA.sga	P19|H3K27me3|6hATRA	H3K27me3	GSM1674829
29	GSM1674830_P19_H3K27me3_24hATRA.sga	P19|H3K27me3|24hATRA	H3K27me3	GSM1674830
30	GSM1674831_P19_H3K27me3_48h_ATRA.sga	P19|H3K27me3|48hEtOH	H3K27me3	GSM1674831
31	GSM1674832_P19_RNAPII_EtOH.sga	P19|PolII|48hEtOH	PolII	GSM1674832
32	GSM1674833_P19_RNAPII_2hATRA.sga	P19|PolII|2hATRA	PolII	GSM1674833
33	GSM1674834_P19_RNAPII_6hATRA.sga	P19|PolII|6hATRA	PolII	GSM1674834
34	GSM1674835_P19_RNAPII_24hATRA.sga	P19|PolII|24hATRA	PolII	GSM1674835
35	GSM1674836_P19_RNAPII_48hATRA.sga	P19|PolII|48hATRA	PolII	GSM1674836
36	GSM1674837_P19_RXRa_EtOH.sga	P19|RXRa|48hEtOH	RXRa	GSM1674837
37	GSM1674838_P19_RXRa_2hATRA.sga	P19|RXRa|2hATRA	RXRa	GSM1674838
38	GSM1674839_P19_RXRa_6hATRA.sga	P19|RXRa|6hATRA	RXRa	GSM1674839
39	GSM1674840_P19_RXRa_24hATRA.sga	P19|RXRa|24hATRA	RXRa	GSM1674840
40	GSM1674841_P19_RXRa_48hATRA.sga	P19|RXRa|48hATRA	RXRa	GSM1674841
41	GSM1674842_P19_INPUT.sga	P19|INPUT|	INPUT	GSM1674842
42	GSM1674843_F9_INPUT.sga	F9|INPUT|	INPUT	GSM1674843

BED to SGA conversion was carried out using bed2sga.pl (ChIP-Seq v. 1.5.2).

• Mendoza-Parra MA, Malysheva V, Mohamed Saleem MA, Lieb M, Godel A, Gronemeyer H
  Reconstructed cell fate-regulatory programs in stem cells reveal hierarchies and key factors of neurogenesis. Genome Res. 2016 Sep 20. pii: gr.208926.116. [Epub ahead of print] 27650846
• GEO series GSE68540: Reconstructing divergent retinoid-induced cell fate-regulatory programs in stem cells [ChIP-Seq]

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