Kilpinen 2013, TF binding, chromatin structure, and transcription in HapMap cells.

ChIP-seq against five histone posttranslational modifications (H3K4me1, H3K4me3, H3K27ac, H3K27me3 and H4K20me1), three transcription factors (TFIIB, PU.1, and MYC) and the second largest RNA polymerase II subunit RPB2, in 14 lymphoblastoid cell lines (LCLs) from the 1000 Genomes sample set. Trancription analyzed also using GRO-seq technology in LCLs derived from parent-offspring trio.

• ChIP-seq files downloaded from EBI site: http://www.ebi.ac.uk/arrayexpress/files/E-MTAB-1884/
  GRO-seq files from: http://www.ebi.ac.uk/arrayexpress/files/E-MTAB-1885/
• Input file format: BAM

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

ChIP-seq data:

	Filename	Description	Feature	GEO-ID
1	IP_11830_H3K27me3_120815_1_sorted.sga	NA11830 - H3K27me3	H3K27me3	-
2	IP_11830_H3K4me1_120605_6_sorted.sga	NA11830 - H3K4me1	H3K4me1	-
3	IP_11830_H3K4me1_121019_4_sorted.sga	NA11830 - H3K4me1	H3K4me1	-
4	IP_11830_H3K4me3_120521_3_sorted.sga	NA11830 - H3K4me3	H3K4me3	-
5	IP_11830_PU1_120612_2_sorted.sga	NA11830 - PU1	PU1	-
6	IP_11830_RPB2_120726_1_sorted.sga	NA11830 - RPB2	RPB2	-
7	IP_11830_TFIIB_120815_7_sorted.sga	NA11830 - TFIIB	TFIIB	-
8	IP_11881_H3K27ac_120628_1_sorted.sga	NA11830 - H3K27ac	H3K27ac	-
9	IP_11831_H3K27me3_120815_1_sorted.sga	NA11831 - H3K27me3	H3K27me3	-
10	IP_11831_H3K4me1_120612_3_sorted.sga	NA11831 - H3K4me1	H3K4me1	-
11	IP_11831_H3K4me1_121019_4_sorted.sga	NA11831 - H3K4me1	H3K4me1	-
12	IP_11831_H3K4me3_120521_4_sorted.sga	NA11831 - H3K4me3	H3K4me3	-
13	IP_11831_PU1_120612_8_sorted.sga	NA11831 - PU1	PU1	-
14	IP_11831_RPB2_120612_2_sorted.sga	NA11831 - RPB2	RPB2	-
15	IP_11831_TFIIB_120815_8_sorted.sga	NA11831 - TFIIB	TFIIB	-
16	IP_11894_H3K27ac_120628_1_sorted.sga	NA11831 - H3K27ac	H3K27ac	-
17	IP_11840_H3K4me1_120612_3_sorted.sga	NA11840 - H3K4me1	H3K4me1	-
18	IP_11840_H3K4me1_121019_5_sorted.sga	NA11840 - H3K4me1	H3K4me1	-
19	IP_11840_H3K4me3_120605_8_sorted.sga	NA11840 - H3K4me3	H3K4me3	-
20	IP_11840_PU1_120612_3_sorted.sga	NA11840 - PU1	PU1	-
21	IP_11840_RPB2_120612_2_sorted.sga	NA11840 - RPB2	RPB2	-
22	IP_11840_TFIIB_120815_8_sorted.sga	NA11840 - TFIIB	TFIIB	-
23	IP_12043_H3K27ac_120628_3_sorted.sga	NA11840 - H3K27ac	H3K27ac	-
24	IP_11881_H3K27me3_120815_2_sorted.sga	NA11881 - H3K27me3	H3K27me3	-
25	IP_11881_H3K4me1_120612_1_sorted.sga	NA11881 - H3K4me1	H3K4me1	-
26	IP_11881_H3K4me1_121019_5_sorted.sga	NA11881 - H3K4me1	H3K4me1	-
27	IP_11881_H3K4me3_120521_5_sorted.sga	NA11881 - H3K4me3	H3K4me3	-
28	IP_11881_PU1_120612_1_sorted.sga	NA11881 - PU1	PU1	-
29	IP_11881_RPB2_120612_3_sorted.sga	NA11881 - RPB2	RPB2	-
30	IP_11881_TFIIB_120815_5_sorted.sga	NA11881 - TFIIB	TFIIB	-
31	IP_12776_H3K27ac_120628_7_sorted.sga	NA11881 - H3K27ac	H3K27ac	-
32	IP_11830_H3K27ac_120815_7_sorted.sga	NA11894 - H3K27ac	H3K27ac	-
33	IP_11894_H3K27me3_120815_2_sorted.sga	NA11894 - H3K27me3	H3K27me3	-
34	IP_11894_H3K4me1_120521_2_sorted.sga	NA11894 - H3K4me1	H3K4me1	-
35	IP_11894_H3K4me1_121019_6_sorted.sga	NA11894 - H3K4me1	H3K4me1	-
36	IP_11894_H3K4me3_120521_2_sorted.sga	NA11894 - H3K4me3	H3K4me3	-
37	IP_11894_PU1_120521_2_sorted.sga	NA11894 - PU1	PU1	-
38	IP_11894_RPB2_120612_3_sorted.sga	NA11894 - RPB2	RPB2	-
39	IP_11894_TFIIB_120815_5_sorted.sga	NA11894 - TFIIB	TFIIB	-
40	IP_11831_H3K27ac_120628_8_sorted.sga	NA12043 - H3K27ac	H3K27ac	-
41	IP_12043_H3K27me3_120815_3_sorted.sga	NA12043 - H3K27me3	H3K27me3	-
42	IP_12043_H3K4me1_120612_5_sorted.sga	NA12043 - H3K4me1	H3K4me1	-
43	IP_12043_H3K4me1_121019_7_sorted.sga	NA12043 - H3K4me1	H3K4me1	-
44	IP_12043_H3K4me3_120521_7_sorted.sga	NA12043 - H3K4me3	H3K4me3	-
45	IP_12043_PU1_120605_5_sorted.sga	NA12043 - PU1	PU1	-
46	IP_12043_RPB2_120515_1_sorted.sga	NA12043 - RPB2	RPB2	-
47	IP_12043_TFIIB_120815_6_sorted.sga	NA12043 - TFIIB	TFIIB	-
48	IP_11840_H3K27ac_120628_8_sorted.sga	NA12776 - H3K27ac	H3K27ac	-
49	IP_12776_H3K27me3_120815_3_sorted.sga	NA12776 - H3K27me3	H3K27me3	-
50	IP_12776_H3K4me1_120612_5_sorted.sga	NA12776 - H3K4me1	H3K4me1	-
51	IP_12776_H3K4me1_121019_6_sorted.sga	NA12776 - H3K4me1	H3K4me1	-
52	IP_12776_H3K4me3_120521_2_sorted.sga	NA12776 - H3K4me3	H3K4me3	-
53	IP_12776_PU1_120605_5_sorted.sga	NA12776 - PU1	PU1	-
54	IP_12776_RPB2_120612_5_sorted.sga	NA12776 - RPB2	RPB2	-
55	IP_12776_TFIIB_120815_6_sorted.sga	NA12776 - TFIIB	TFIIB	-
56	IP_12813_H3K27ac_120628_4_sorted.sga	NA12813 - H3K27ac	H3K27ac	-
57	IP_12813_H3K27me3_120815_3_sorted.sga	NA12813 - H3K27me3	H3K27me3	-
58	IP_12813_H3K4me1_120521_4_sorted.sga	NA12813 - H3K4me1	H3K4me1	-
59	IP_12813_H3K4me1_121019_7_sorted.sga	NA12813 - H3K4me1	H3K4me1	-
60	IP_12813_H3K4me3_120521_4_sorted.sga	NA12813 - H3K4me3	H3K4me3	-
61	IP_12813_PU1_120521_4_sorted.sga	NA12813 - PU1	PU1	-
62	IP_12813_RPB2_120515_7_sorted.sga	NA12813 - RPB2	RPB2	-
63	IP_12813_TFIIB_120815_7_sorted.sga	NA12813 - TFIIB	TFIIB	-
64	IP_12878_H3K27ac_120628_1_sorted.sga	NA12878 - H3K27ac	H3K27ac	-
65	IP_12878_H3K27me3_120221_4_sorted.sga	NA12878 - H3K27me3	H3K27me3	-
66	IP_12878_H3K4me1_121019_1_sorted.sga	NA12878 - H3K4me1	H3K4me1	-
67	IP_12878_H3K4me3_111122_1_sorted.sga	NA12878 - H3K4me3	H3K4me3	-
68	IP_12878_H4K20me1_120202_5_sorted.sga	NA12878 - H4K20me1	H4K20me1	-
69	IP_12878_MYC_120221_6_sorted.sga	NA12878 - MYC	MYC	-
70	IP_12878_PU1_111025_8_sorted.sga	NA12878 - PU1	PU1	-
71	IP_12878_RPB2_120221_1_sorted.sga	NA12878 - RPB2	RPB2	-
72	IP_12878_TFIIB_120202_1_sorted.sga	NA12878 - TFIIB	TFIIB	-
73	IP_12891_H3K27ac_120628_1_sorted.sga	NA12891 - H3K27ac	H3K27ac	-
74	IP_12891_H3K27me3_120221_5_sorted.sga	NA12891 - H3K27me3	H3K27me3	-
75	IP_12891_H3K4me1_121019_2_sorted.sga	NA12891 - H3K4me1	H3K4me1	-
76	IP_12891_H3K4me3_111122_2_sorted.sga	NA12891 - H3K4me3	H3K4me3	-
77	IP_12891_H4K20me1_120202_6_sorted.sga	NA12891 - H4K20me1	H4K20me1	-
78	IP_12891_MYC_120221_7_sorted.sga	NA12891 - MYC	MYC	-
79	IP_12891_PU1_110712_8_sorted.sga	NA12891 - PU1	PU1	-
80	IP_12891_RPB2_120221_2_sorted.sga	NA12891 - RPB2	RPB2	-
81	IP_12891_TFIIB_120202_2_sorted.sga	NA12891 - TFIIB	TFIIB	-
82	IP_12892_H3K27ac_120628_1_sorted.sga	NA12892 - H3K27ac	H3K27ac	-
83	IP_12892_H3K27me3_120221_6_sorted.sga	NA12892 - H3K27me3	H3K27me3	-
84	IP_12892_H3K4me1_121019_3_sorted.sga	NA12892 - H3K4me1	H3K4me1	-
85	IP_12892_H3K4me3_111220_8_sorted.sga	NA12892 - H3K4me3	H3K4me3	-
86	IP_12892_H4K20me1_120202_7_sorted.sga	NA12892 - H4K20me1	H4K20me1	-
87	IP_12892_MYC_120221_8_sorted.sga	NA12892 - MYC	MYC	-
88	IP_12892_PU1_110816_8_sorted.sga	NA12892 - PU1	PU1	-
89	IP_12892_RPB2_120221_3_sorted.sga	NA12892 - RPB2	RPB2	-
90	IP_12892_TFIIB_120202_3_sorted.sga	NA12892 - TFIIB	TFIIB	-
91	IP_19238_H3K27ac_120628_2_sorted.sga	NA19238 - H3K27ac	H3K27ac	-
92	IP_19238_H3K27me3_120221_7_sorted.sga	NA19238 - H3K27me3	H3K27me3	-
93	IP_19238_H3K4me1_120815_6_sorted.sga	NA19238 - H3K4me1	H3K4me1	-
94	IP_19238_H3K4me3_111025_1_sorted.sga	NA19238 - H3K4me3	H3K4me3	-
95	IP_19238_H4K20me1_111220_1_sorted.sga	NA19238 - H4K20me1	H4K20me1	-
96	IP_19238_MYC_111011_1_sorted.sga	NA19238 - MYC	MYC	-
97	IP_19238_PU1_110816_1_sorted.sga	NA19238 - PU1	PU1	-
98	IP_19238_RPB2_120104_6_sorted.sga	NA19238 - RPB2	RPB2	-
99	IP_19238_TFIIB_111122_6_sorted.sga	NA19238 - TFIIB	TFIIB	-
100	IP_19239_H3K27ac_120628_2_sorted.sga	NA19239 - H3K27ac	H3K27ac	-
101	IP_19239_H3K27me3_120221_8_sorted.sga	NA19239 - H3K27me3	H3K27me3	-
102	IP_19239_H3K4me1_120815_7_sorted.sga	NA19239 - H3K4me1	H3K4me1	-
103	IP_19239_H3K4me3_111025_2_sorted.sga	NA19239 - H3K4me3	H3K4me3	-
104	IP_19239_H4K20me1_111220_2_sorted.sga	NA19239 - H4K20me1	H4K20me1	-
105	IP_19239_MYC_111011_2_sorted.sga	NA19239 - MYC	MYC	-
106	IP_19239_PU1_110816_2_sorted.sga	NA19239 - PU1	PU1	-
107	IP_19239_RPB2_120104_7_sorted.sga	NA19239 - RPB2	RPB2	-
108	IP_19239_TFIIB_111122_7_sorted.sga	NA19239 - TFIIB	TFIIB	-
109	IP_19240_H3K27ac_120628_2_sorted.sga	NA19240 - H3K27ac	H3K27ac	-
110	IP_19240_H3K27me3_120221_5_sorted.sga	NA19240 - H3K27me3	H3K27me3	-
111	IP_19240_H3K4me1_120815_8_sorted.sga	NA19240 - H3K4me1	H3K4me1	-
112	IP_19240_H3K4me3_111025_3_sorted.sga	NA19240 - H3K4me3	H3K4me3	-
113	IP_19240_H4K20me1_111220_3_sorted.sga	NA19240 - H4K20me1	H4K20me1	-
114	IP_19240_MYC_111011_3_sorted.sga	NA19240 - MYC	MYC	-
115	IP_19240_PU1_110816_3_sorted.sga	NA19240 - PU1	PU1	-
116	IP_19240_RPB2_120104_8_sorted.sga	NA19240 - RPB2	RPB2	-
117	IP_19240_TFIIB_111122_8_sorted.sga	NA19240 - TFIIB	TFIIB	-

Transcription Profiling data:

	Filename	Description	Feature	GEO-ID
1	GM12878_merged_r1_mapq10.sga	NA12878 - GRO-seq	GRO	-
2	GM12891_merged_r1_mapq10.sga	NA12891 - GRO-seq	GRO	-
3	GM12892_merged_r1_mapq10.sga	NA12892 - GRO-seq	GRO	-

BAM files were converted to bed using bamToBed v2.12.0 (bedtools) and to SGA using bed2sga.pl (ChIP-Seq v. 1.5.2).

• Kilpinen H, Waszak SM, Gschwind AR, Raghav SK, Witwicki RM, Orioli A, Migliavacca E, Wiederkehr M, Gutierrez-Arcelus M, Panousis NI, Yurovsky A, Lappalainen T, Romano-Palumbo L, Planchon A, Bielser D, Bryois J, Padioleau I, Udin G, Thurnheer S, Hacker D, Core LJ, Lis JT, Hernandez N, Reymond A, Deplancke B, Dermitzakis ET
  Coordinated effects of sequence variation on DNA binding, chromatin structure, and transcription. Science. 2013 Nov 8;342(6159):744-7. doi: 10.1126/science.1242463. Epub 2013 Oct 17. 24136355