Mcvicker13, Identification of genetic variants that affect histone modifications in human cells

Description

ChIP-seq against 4 histone variants (H3K4me1, H3K4me3, H3K27ac, H3K27me3) and RNA polymerase II (Pol II) in 10 unrelated human Yoruba lymphoblastoid cell lines (LCLs).

Source

Samples

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

ChIP-seq data:

Filename Description Feature GEO-ID
1 GSM1164203.sga GM18505 - H3K4me1 H3K4me1 GSM1164203
2 GSM1164204.sga GM18507 - H3K4me1 H3K4me1 GSM1164204
3 GSM1164205.sga GM18508 - H3K4me1 H3K4me1 GSM1164205
4 GSM1164206.sga GM18516 - H3K4me1 H3K4me1 GSM1164206
5 GSM1164207.sga GM18522 - H3K4me1 H3K4me1 GSM1164207
6 GSM1164208.sga GM19141 - H3K4me1 H3K4me1 GSM1164208
7 GSM1164209.sga GM19193 - H3K4me1 H3K4me1 GSM1164209
8 GSM1164210.sga GM19204 - H3K4me1 H3K4me1 GSM1164210
9 GSM1164211.sga GM19238 - H3K4me1 H3K4me1 GSM1164211
10 GSM1164212.sga GM19239 - H3K4me1 H3K4me1 GSM1164212
11 GSM1164213.sga GM18505 - H3K4me3 H3K4me3 GSM1164213
12 GSM1164214.sga GM18507 - H3K4me3 H3K4me3 GSM1164214
13 GSM1164215.sga GM18508 - H3K4me3 H3K4me3 GSM1164215
14 GSM1164216.sga GM18516 - H3K4me3 H3K4me3 GSM1164216
15 GSM1164217.sga GM18522 - H3K4me3 H3K4me3 GSM1164217
16 GSM1164218.sga GM19141 - H3K4me3 H3K4me3 GSM1164218
17 GSM1164219.sga GM19193 - H3K4me3 H3K4me3 GSM1164219
18 GSM1164220.sga GM19204 - H3K4me3 H3K4me3 GSM1164220
19 GSM1164221.sga GM19238 - H3K4me3 H3K4me3 GSM1164221
20 GSM1164222.sga GM19239 - H3K4me3 H3K4me3 GSM1164222
21 GSM1164223.sga GM18505 - H3K27ac H3K27ac GSM1164223
22 GSM1164224.sga GM18507 - H3K27ac H3K27ac GSM1164224
23 GSM1164225.sga GM18508 - H3K27ac H3K27ac GSM1164225
24 GSM1164226.sga GM18516 - H3K27ac H3K27ac GSM1164226
25 GSM1164227.sga GM18522 - H3K27ac H3K27ac GSM1164227
26 GSM1164228.sga GM19141 - H3K27ac H3K27ac GSM1164228
27 GSM1164229.sga GM19193 - H3K27ac H3K27ac GSM1164229
28 GSM1164230.sga GM19204 - H3K27ac H3K27ac GSM1164230
29 GSM1164231.sga GM19238 - H3K27ac H3K27ac GSM1164231
30 GSM1164232.sga GM19239 - H3K27ac H3K27ac GSM1164232
31 GSM1164233.sga GM18505 - H3K27me3 H3K27me3 GSM1164233
32 GSM1164234.sga GM18507 - H3K27me3 H3K27me3 GSM1164234
33 GSM1164235.sga GM18508 - H3K27me3 H3K27me3 GSM1164235
34 GSM1164236.sga GM18516 - H3K27me3 H3K27me3 GSM1164236
35 GSM1164237.sga GM18522 - H3K27me3 H3K27me3 GSM1164237
36 GSM1164238.sga GM19141 - H3K27me3 H3K27me3 GSM1164238
37 GSM1164239.sga GM19193 - H3K27me3 H3K27me3 GSM1164239
38 GSM1164240.sga GM19204 - H3K27me3 H3K27me3 GSM1164240
39 GSM1164241.sga GM19238 - H3K27me3 H3K27me3 GSM1164241
40 GSM1164242.sga GM19239 - H3K27me3 H3K27me3 GSM1164242
41 GSM1164243.sga GM18505 - PolII PolII GSM1164243
42 GSM1164244.sga GM18507 - PolII PolII GSM1164244
43 GSM1164245.sga GM18508 - PolII PolII GSM1164245
44 GSM1164246.sga GM18516 - PolII PolII GSM1164246
45 GSM1164247.sga GM18522 - PolII PolII GSM1164247
46 GSM1164248.sga GM19141 - PolII PolII GSM1164248
47 GSM1164249.sga GM19193 - PolII PolII GSM1164249
48 GSM1164250.sga GM19204 - PolII PolII GSM1164250
49 GSM1164251.sga GM19238 - PolII PolII GSM1164251
50 GSM1164252.sga GM19239 - PolII PolII GSM1164252

Technical Notes

FASTQ files were extracted from SRA files using fastq-dump (SRA toolkit v2.5.0) and mapped to the hg19 genome using Bowtie v0.12.8. SAM files were then converted into bam using samtools v0.1.14 and to bed using bamToBed v2.12.0 (bedtools). SGA conversion was carried out using bed2sga.pl (ChIP-Seq v. 1.5.2).

References

Last update:23 Mar 2016