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

Description

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.

Source

Samples

From Mouse Jul. 2007 (NCBI37/mm9) Assembly.

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

Technical Notes

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

References

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Last update: 21 Oct 2016