Mikkelsen 2007, histone modifications in mouse embryonic stem cells.


ChIP-seq against H3K4me3, H3K9me3, H3K27me3, H3K36me3, H4K20me3, pan-H3 or RNA polymerase II in mouse embryonic stem (ES) cells, embryonic fibroblasts (MEF) and neural progenitor (NP) cells. Whole cell extract (input DNA).



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

ChIP-seq data:

Filename Description Feature GEO-ID
1 ES.H3.sga ES pan-H3 pan-H3 GSM307624
2 ES.K20.sga ES H4K20me3 H4K20me3 GSM307622
3 ES.K27.sga ES H3K27me3 H3K27me3 GSM307619
4 ES.K36.sga ES H3K36me3 H3K36me3 GSM307620
5 ES.K4.sga ES H3K4me3 H3K4me3 GSM307618
6 ES.K9.sga ES H3K9me3 H3K9me3 GSM307621
7 ES.RPol.sga ES PolII PolII GSM307623
8 ES.WCE.sga ES WCE WCE GSM307625
9 ESHyb.K36.sga ESHyb H3K36me3 H3K36me3 GSM307606
10 ESHyb.K4.sga ESHyb H3K4me3 H3K4me3 GSM307605
11 ESHyb.K9.sga ESHyb H3K9me3 H3K9me3 GSM307607
12 MEF.K27.sga MEF H3K27me3 H3K27me3 GSM307609
13 MEF.K36.sga MEF H3K36me3 H3K36me3 GSM307610
14 MEF.K4.sga MEF H3K4me3 H3K4me3 GSM307608
15 MEF.K9.sga MEF H3K9me3 H3K9me3 GSM307611
16 MEF.WCE.sga MEF WCE WCE GSM307612
17 NP.K27.sga NP H3K27me3 H3K27me3 GSM307614
18 NP.K36.sga NP H3K36me3 H3K36me3 GSM307615
19 NP.K4.sga NP H3K4me3 H3K4me3 GSM307613
20 NP.K9.sga NP H3K9me3 H3K9me3 GSM307616
21 NP.WCE.sga NP WCE WCE GSM307617
22 ES.all_histones.sga ES histones histones -
23 ESHyb.all_histones.sga ESHyb histones histones -
24 MEF.all_histones.sga MEF histones histones -
25 NP.all_histones.sga NP histones histones -

Technical Notes

The primary sequence data for Mikkelsen et al. included files contain the SMS sequence data and their alignment coordiantes on the mouse reference genome (UCSC version mm8).

The format of each file is the same, in tab-delimited text:

The original data have been remapped to assembly mm9 using liftOver, sorted and converted to the SGA format.


Genome browser viewable files

WIG files are available at:

Last update: 14 Feb 2017