Chen 2008, ES cells, 16 transcription factors, GSE11431 .


ChIP-seq against thirteen sequence specific transcription factors (Nanog, Oct4, STAT3, Smad1, Sox2, Zfx, c-Myc, n-Myc, Klf4, Esrrb, Tcfcp2l1, E2f1 and CTCF) and two transcription regulators (p300 and Suz12), in mouse embryonic stem (ES) cells. GFP library used as negative control.



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

ChIP-seq data:

Filename Description Feature GEO-ID
1 ES_Nanog.sga ES Nanog Nanog GSM288345
2 ES_Oct4.sga ES Oct4 Oct4 GSM288346
3 ES_Sox2.sga ES Sox2 Sox2 GSM288347
4 ES_Smad1.sga ES Smad1 Smad1 GSM288348
5 ES_E2f1.sga ES E2f1 E2f1 GSM288349
6 ES_Tcfcp2I1.sga ES Tcfcp2I1 Tcfcp2I1 GSM288350
8 ES_Zfx.sga ES Zfx Zfx GSM288352
9 ES_STAT3.sga ES STAT3 STAT3 GSM288353
10 ES_Klf4.sga ES Klf4 Klf4 GSM288354
11 ES_Esrrb.sga ES Esrrb Esrrb GSM288355
12 ES_c-Myc.sga ES c-Myc c-Myc GSM288356
13 ES_n-Myc.sga ES n-Myc n-Myc GSM288357
14 ES_GFP.sga ES GFP/control GFP GSM288358
15 ES_p300.sga ES p300 p300 GSM288359
16 ES_Suz12.sga ES Suz12 Suz12 GSM288360

ChIP-seq peaks files:

Filename Description Feature GEO-ID
1 ES_Nanog_peaks.sga ES Nanog peaks Nanog_P GSM288345
2 ES_Oct4_peaks.sga ES Oct4 peaks Oct4_P GSM288346
3 ES_Sox2_peaks.sga ES Sox2 peaks Sox2_P GSM288347
4 ES_Smad1_peaks.sga ES Smad1 peaks Smad1_P GSM288348
5 ES_E2f1_peaks.sga ES E2f1 peaks E2f1_P GSM288349
6 ES_Tcfcp2l1_peaks.sga ES Tcfcp2l1 peaks Tcfcp2l1_P GSM288350
7 ES_CTCF_peaks.sga ES CTCF peaks CTCF_P GSM288351
8 ES_Zfx_peaks.sga ES Zfx peaks Zfx_P GSM288352
9 ES_STAT3_peaks.sga ES STAT3 peaks STAT3_P GSM288353
10 ES_Klf4_peaks.sga ES Klf4 peaks Klf4_P GSM288354
11 ES_Esrrb_peaks.sga ES Esrrb peaks Esrrb_P GSM288355
12 ES_c-Myc_peaks.sga ES c-Myc peaks c-Myc_P GSM288356
13 ES_n-Myc_peaks.sga ES n-Myc peaks n-Myc_P GSM288357
14 ES_p300_peaks.sga ES p300 peaks p300_P GSM288359
15 ES_Suz12_peaks.sga ES Suz12 peaks Suz12_P GSM288360

Technical Notes

The sga files for the mapped sequence tags were generated from GEO accessory BED files providing the starting and ending positions of mapped sequence tags in mouse genome assembly Feb 2006 (NCBI36/mm8).
The genome positions were remapped to mouse genome assembly Jul 2007 (NCBI37/mm9) using the liftOver software from UCSC. The peak sga files were generated from GEO accessory text files providing the starting and ending positions of the peak regions. The single position recorded in the sga file corresponds to the mid-point of the peak region. The strand field (4th column) is set to 0 and the count field (5th column) is set to 1 in all lines.


Last update: 1 Oct 2018