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

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

• Raw data was downloaded from: UCSC
• Input file format: BAM
• Download date: 26-9-2015

From H. sapiens (Feb 2009 GRCh37/hg19).

ChIP-seq data:

	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

BAM files were converted to bed using bamToBed v2.12.0 (bedtools). SGA conversion was carried out using bed2sga.pl (ChIP-Seq v. 1.5.3).

• Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, Sheffield NC, Stergachis AB, Wang H, Vernot B, Garg K, John S, Sandstrom R, Bates D, Boatman L, Canfield TK, Diegel M, Dunn D, Ebersol AK, Frum T, Giste E, Johnson AK, Johnson EM, Kutyavin T, Lajoie B, Lee BK, Lee K, London D, Lotakis D, Neph S, Neri F, Nguyen ED, Qu H, Reynolds AP, Roach V, Safi A, Sanchez ME, Sanyal A, Shafer A, Simon JM, Song L, Vong S, Weaver M, Yan Y, Zhang Z, Zhang Z, Lenhard B, Tewari M, Dorschner MO, Hansen RS, Navas PA, Stamatoyannopoulos G, Iyer VR, Lieb JD, Sunyaev SR, Akey JM, Sabo PJ, Kaul R, Furey TS, Dekker J, Crawford GE, Stamatoyannopoulos JA
  The accessible chromatin landscape of the human genome. Nature. 2012 Sep 6;489(7414):75-82. doi: 10.1038/nature11232. 22955617
• GEO series GSE31755: Histone Modifications by ChIP-seq from ENCODE/Stanford/Yale/Davis/Harvard