Thurman 2012, Histone Modifications by ChIP-seq from ENCODE/Stanford/Yale/Davis/Harvard

Description:

This samples serie was produced as part of the ENCODE Project. This serie contains histone modification ChIP-seq data for several cell lines. Some of the samples have been treated or are genetically modified.

Source

Files downloaded from the UCSC Genome Browser via URL: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhHistone
Input file format: BAM Alternatively, files can be downloaded from GEO serie GSE31755.

Samples

From Human Feb. 2009 (GRCh37/hg19) Assembly

Filename Description Feature GEO-ID
1 wgEncodeSydhHistoneHct116H3k04me1UcdAlnRep1.sga HCT-116 - H3K4me1 - None - rep1 H3K4me1 -
2 wgEncodeSydhHistoneHct116H3k04me1UcdAlnRep2.sga HCT-116 - H3K4me1 - None - rep2 H3K4me1 -
3 wgEncodeSydhHistoneHct116H3k27acUcdAlnRep1.sga HCT-116 - H3K27ac - None - rep1 H3K27ac -
4 wgEncodeSydhHistoneHct116H3k27acUcdAlnRep2.sga HCT-116 - H3K27ac - None - rep2 H3K27ac -
5 wgEncodeSydhHistoneHct116InputUcdAlnRep1.sga HCT-116 - Input - None - rep1 Input -
6 wgEncodeSydhHistoneK562H3k27me3bUcdAlnRep1.sga K562 - H3K27me3B - None - rep1 H3K27me3B GSM788088
7 wgEncodeSydhHistoneK562H3k27me3bUcdAlnRep2.sga K562 - H3K27me3B - None - rep2 H3K27me3B GSM788088
8 wgEncodeSydhHistoneK562H3k4me1UcdAlnRep1.sga K562 - H3K4me1 - None - rep1 H3K4me1 GSM788085
9 wgEncodeSydhHistoneK562H3k4me1UcdAlnRep2.sga K562 - H3K4me1 - None - rep2 H3K4me1 GSM788085
10 wgEncodeSydhHistoneK562H3k4me3bUcdAlnRep1.sga K562 - H3K4me3B - None - rep1 H3K4me3B GSM788087
11 wgEncodeSydhHistoneK562H3k4me3bUcdAlnRep2.sga K562 - H3K4me3B - None - rep2 H3K4me3B GSM788087
12 wgEncodeSydhHistoneK562H3k9acbUcdAlnRep1.sga K562 - H3K9acB - None - rep1 H3K9acB GSM788082
13 wgEncodeSydhHistoneK562H3k9acbUcdAlnRep2.sga K562 - H3K9acB - None - rep2 H3K9acB GSM788082
14 wgEncodeSydhHistoneK562InputUcdAln.sga K562 - Input - None - rep1 Input GSM788074
15 wgEncodeSydhHistoneK562bH3k27me3bUcdAlnRep1.sga K562 - H3K27me3B - None - rep1 H3K27me3B GSM788088
16 wgEncodeSydhHistoneK562bH3k27me3bUcdAlnRep2.sga K562 - H3K27me3B - None - rep2 H3K27me3B GSM788088
17 wgEncodeSydhHistoneK562bH3k4me1UcdAlnRep1.sga K562 - H3K4me1 - None - rep1 H3K4me1 GSM788085
18 wgEncodeSydhHistoneK562bH3k4me1UcdAlnRep2.sga K562 - H3K4me1 - None - rep2 H3K4me1 GSM788085
19 wgEncodeSydhHistoneK562bH3k4me3bUcdAlnRep1.sga K562 - H3K4me3B - None - rep1 H3K4me3B GSM788087
20 wgEncodeSydhHistoneK562bH3k4me3bUcdAlnRep2.sga K562 - H3K4me3B - None - rep2 H3K4me3B GSM788087
21 wgEncodeSydhHistoneK562bH3k9acbUcdAlnRep1.sga K562 - H3K9acB - None - rep1 H3K9acB GSM788082
22 wgEncodeSydhHistoneK562bH3k9acbUcdAlnRep2.sga K562 - H3K9acB - None - rep2 H3K9acB GSM788082
23 wgEncodeSydhHistoneK562bInputUcdAln.sga K562 - Input - None - rep1 Input GSM788074
24 wgEncodeSydhHistoneMcf7H3k09me3UcdAlnRep1.sga MCF-7 - H3K9me3 - None - rep1 H3K9me3 -
25 wgEncodeSydhHistoneMcf7H3k09me3UcdAlnRep2.sga MCF-7 - H3K9me3 - None - rep2 H3K9me3 -
26 wgEncodeSydhHistoneMcf7H3k27acUcdAlnRep1.sga MCF-7 - H3K27ac - None - rep1 H3K27ac -
27 wgEncodeSydhHistoneMcf7H3k27acUcdAlnRep2.sga MCF-7 - H3K27ac - None - rep2 H3K27ac -
28 wgEncodeSydhHistoneMcf7H3k27me3bUcdAlnRep1.sga MCF-7 - H3K27me3B - None - rep1 H3K27me3B -
29 wgEncodeSydhHistoneMcf7H3k27me3bUcdAlnRep2.sga MCF-7 - H3K27me3B - None - rep2 H3K27me3B -
30 wgEncodeSydhHistoneMcf7H3k36me3bUcdAlnRep1.sga MCF-7 - H3K36me3B - None - rep1 H3K36me3B -
31 wgEncodeSydhHistoneMcf7H3k36me3bUcdAlnRep2.sga MCF-7 - H3K36me3B - None - rep2 H3K36me3B -
32 wgEncodeSydhHistoneMcf7InputUcdAlnRep1.sga MCF-7 - Input - None - rep1 Input -
33 wgEncodeSydhHistoneMcf7InputUcdAlnRep2.sga MCF-7 - Input - None - rep2 Input -
34 wgEncodeSydhHistoneNt2d1H3k09me3UcdAlnRep1.sga NT2-D1 - H3K9me3 - None - rep1 H3K9me3 GSM788080
35 wgEncodeSydhHistoneNt2d1H3k09me3UcdAlnRep2.sga NT2-D1 - H3K9me3 - None - rep2 H3K9me3 GSM788080
36 wgEncodeSydhHistoneNt2d1H3k27me3bUcdAlnRep1.sga NT2-D1 - H3K27me3B - None - rep1 H3K27me3B GSM788071
37 wgEncodeSydhHistoneNt2d1H3k27me3bUcdAlnRep2.sga NT2-D1 - H3K27me3B - None - rep2 H3K27me3B GSM788071
38 wgEncodeSydhHistoneNt2d1H3k36me3bUcdAlnRep1.sga NT2-D1 - H3K36me3B - None - rep1 H3K36me3B GSM788081
39 wgEncodeSydhHistoneNt2d1H3k36me3bUcdAlnRep2.sga NT2-D1 - H3K36me3B - None - rep2 H3K36me3B GSM788081
40 wgEncodeSydhHistoneNt2d1H3k4me1UcdAlnRep1.sga NT2-D1 - H3K4me1 - None - rep1 H3K4me1 GSM788083
41 wgEncodeSydhHistoneNt2d1H3k4me1UcdAlnRep2.sga NT2-D1 - H3K4me1 - None - rep2 H3K4me1 GSM788083
42 wgEncodeSydhHistoneNt2d1H3k4me3bUcdAlnRep1.sga NT2-D1 - H3K4me3B - None - rep1 H3K4me3B GSM788072
43 wgEncodeSydhHistoneNt2d1H3k4me3bUcdAlnRep2.sga NT2-D1 - H3K4me3B - None - rep2 H3K4me3B GSM788072
44 wgEncodeSydhHistoneNt2d1H3k9acbUcdAlnRep1.sga NT2-D1 - H3K9acB - None - rep1 H3K9acB GSM788086
45 wgEncodeSydhHistoneNt2d1H3k9acbUcdAlnRep2.sga NT2-D1 - H3K9acB - None - rep2 H3K9acB GSM788086
46 wgEncodeSydhHistoneNt2d1InputUcdAln.sga NT2-D1 - Input - None - rep1 Input GSM788077
47 wgEncodeSydhHistonePanc1H3k04me1bUcdAlnRep1.sga PANC-1 - H3K4me1_(pAb-037-050) - None - rep1 H3K4me1_(pAb-037-050) -
48 wgEncodeSydhHistonePanc1H3k04me1bUcdAlnRep2.sga PANC-1 - H3K4me1_(pAb-037-050) - None - rep2 H3K4me1_(pAb-037-050) -
49 wgEncodeSydhHistonePanc1H3k04me3bUcdAlnRep1.sga PANC-1 - H3K4me3B - None - rep1 H3K4me3B -
50 wgEncodeSydhHistonePanc1H3k04me3bUcdAlnRep2.sga PANC-1 - H3K4me3B - None - rep2 H3K4me3B -
51 wgEncodeSydhHistonePanc1H3k27acUcdAlnRep1.sga PANC-1 - H3K27ac - None - rep1 H3K27ac -
52 wgEncodeSydhHistonePanc1H3k27acUcdAlnRep2.sga PANC-1 - H3K27ac - None - rep2 H3K27ac -
53 wgEncodeSydhHistonePanc1InputUcdAlnRep1.sga PANC-1 - Input - None - rep1 Input -
54 wgEncodeSydhHistonePbmcH3k04me3bUcdAlnRep1.sga PBMC - H3K4me3B - None - rep1 H3K4me3B GSM788075
55 wgEncodeSydhHistonePbmcH3k04me3bUcdAlnRep2.sga PBMC - H3K4me3B - None - rep2 H3K4me3B GSM788075
56 wgEncodeSydhHistonePbmcH3k27me3bUcdAlnRep1.sga PBMC - H3K27me3B - None - rep1 H3K27me3B GSM788073
57 wgEncodeSydhHistonePbmcH3k27me3bUcdAlnRep2.sga PBMC - H3K27me3B - None - rep2 H3K27me3B GSM788073
58 wgEncodeSydhHistonePbmcH3k4me1UcdAlnRep1.sga PBMC - H3K4me1 - None - rep1 H3K4me1 GSM788084
59 wgEncodeSydhHistonePbmcH3k4me1UcdAlnRep2.sga PBMC - H3K4me1 - None - rep2 H3K4me1 GSM788084
60 wgEncodeSydhHistonePbmcH3k9me3UcdAlnRep1.sga PBMC - H3K9me3 - None - rep1 H3K9me3 GSM788079
61 wgEncodeSydhHistonePbmcH3k9me3UcdAlnRep2.sga PBMC - H3K9me3 - None - rep2 H3K9me3 GSM788079
62 wgEncodeSydhHistonePbmcInputUcdAlnRep1.sga PBMC - Input - None - rep1 Input GSM788070
63 wgEncodeSydhHistoneU2osH3k36me3bUcdAlnRep1.sga U2OS - H3K36me3B - None - rep1 H3K36me3B GSM788076
64 wgEncodeSydhHistoneU2osH3k36me3bUcdAlnRep2.sga U2OS - H3K36me3B - None - rep2 H3K36me3B GSM788076
65 wgEncodeSydhHistoneU2osH3k9me3UcdAlnRep1.sga U2OS - H3K9me3 - None - rep1 H3K9me3 GSM788078
66 wgEncodeSydhHistoneU2osH3k9me3UcdAlnRep2.sga U2OS - H3K9me3 - None - rep2 H3K9me3 GSM788078
67 wgEncodeSydhHistoneU2osInputUcdAln.sga U2OS - Input - None - rep1 Input GSM788069

Technical Notes

BAM files were downloaded from UCSC and converted in sga format using bamToBed (SamTools) and bed2sga (ChIP-seq).

References

  1. Thurman RE, Rynes E, Humbert R, Vierstra J et al.
    The accessible chromatin landscape of the human genome.
    Nature 2012 Sep 6;489(7414):75-82-90
    PMID: 22955617

  2. GEO series GSE31755 Histone Modifications by ChIP-seq from ENCODE/University of Washington.