Creyghton 2010, histone marks, GSE24164.

Description

ChIP-Seq against H3, H3K4me1, H3K4me3, H3K27ac and Rfx1 in mouse embryonic stem (ES) cells, several cell types and adult tissues.

Source

Samples

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

ChIP-seq data:

Filename Description Feature GEO-ID
1 ES_WCE.sga ES WCE WCE GSM594599
2 ES_H3.sga ES H3 H3 GSM594580
3 ES_H3K4me1.sga ES H3K4me1 H3K4me1 GSM594577
4 ES_H3K4me3.sga ES H3K4me3 H3K4me3 GSM594581
5 ES_H3K27ac1.sga ES H3K27ac/rep1 H3K27ac GSM594578
6 ES_H3K27ac2.sga ES H3K27ac/rep2 H3K27ac GSM594579
7 ES_p300_1.sga ES_p300/rep1 p300 GSM594600
8 ES_p300_2.sga ES p300/rep2 p300 GSM594601
9 ES_H3K4me1_inbred.sga ES/inbred H3K4me1 H3K4me1 GSM594583
10 ES_H3K4me1_transgene.sga ES/+transgene H3K4me1 H3K4me1 GSM594582
11 iPS_H3K4me1.sga iPS H3K4me1 H3K4me1 GSM594598
12 liver_WCE.sga liver WCE WCE GSM594590
13 liver_H3.sga liver H3 H3 GSM594588
14 liver_H3K4me1.sga liver H3K4me1 H3K4me1 GSM594586
15 liver_H3K4me3.sga liver H3K4me3 H3K4me3 GSM594589
16 liver_H3K27ac.sga liver H3K27ac H3K27ac GSM594587
17 mef_H3.sga MEF H3 H3 GSM594597
18 mef_H3K4me1.sga MEF H3K4me1 H3K4me1 GSM594596
19 NPC_H3K27ac.sga NPC H3K27ac H3K27ac GSM594585
20 NPC_Rfx1.sga NPC Rfx1 Rfx1 GSM594584
21 proB_WCE.sga proB WCE WCE GSM594595
22 proB_H3.sga proB H3 H3 GSM594593
23 proB_H3K4me1.sga proB H3K4me1 H3K4me1 GSM594591
24 proB_H3K4me3.sga proB H3K4me3 H3K4me3 GSM594594
25 proB_H3K27ac.sga proB H3K27ac H3K27ac GSM594592

Technical Notes

The sga files were gerenerated from GEO accessory text files providing the starting postions of mapped sequence tags in mouse genome assembly 2006 (NCBI36/mm8).
The genome positions were remapped to mouse genome assembly July 2007 (NCBI37/mm9) using the liftOver software from UCSC. Genome positions on the minus strand were shifted 35 bp downstream.
This was based on the following assumptions:
(i) the genome positions given in the source file represent the beginning of the genome regions that match the sequence reads. For reads matching the minus strand, this position corresponds to the 3'end rather than the 5' end of the read.
(ii) according to the paper cited below, the sequence reads were of length 36.

References

Last update: 31 Jan 2017