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.

• Raw data was downloaded from GEO series: GSE11431
• Input file format: BED

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
7	ES_CTCF.sga	ES CTCF	CTCF	GSM288351
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

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.

• Chen X, Xu H, Yuan P, Fang F, Huss M, Vega VB, Wong E, Orlov YL, Zhang W, Jiang J, Loh YH, Yeo HC, Yeo ZX, Narang V, Govindarajan KR, Leong B, Shahab A, Ruan Y, Bourque G, Sung WK, Clarke ND, Wei CL, Ng HH
  Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell. 2008 Jun 13;133(6):1106-17. doi: 10.1016/j.cell.2008.04.043. 18555785
• GEO series GSE11431: Mapping of transcription factor binding sites in mouse embryonic stem cells