Kilpinen13, TF binding, chromatin structure, and transcription in HapMap cells.

Description

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.

Source

Samples

From Human Feb. 2009 (GRCh37/hg19) Assembly.

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 -

RNA-seq 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 -

Technical Notes

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

References

Last update: 19 Apr 2016