GSE29611, Histone Modifications by ChIP-seq

Description:

This track displays maps of chromatin state generated by the Broad/MGH ENCODE group using ChIP-seq. Chemical modifications (methylation, acetylation) to the histone proteins present in chromatin influence gene expression by changing how accessible the chromatin is to transcription.

The ChIP-seq method involves first using formaldehyde to cross-link histones and other DNA-associated proteins to genomic DNA within cells. The cross-linked chromatin is subsequently extracted, mechanically sheared, and immunoprecipitated using specific antibodies. After reversal of cross-links, the immunoprecipitated DNA is sequenced and mapped to the human reference genome. The relative enrichment of each antibody-target (epitope) across the genome is inferred from the density of mapped fragments.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Overall design

ChIP-seq: Cells were grown according to the approved ENCODE cell culture protocols. Cells were fixed in 1% formaldehyde and resuspended in lysis buffer. Chromatin was sheared to 200-700 bp using a Diagenode Bioruptor. Solubilized chromatin was immunoprecipitated with antibodies against each of the histone antibodies listed above. Antibody-chromatin complexes were pulled-down using protein A-sepharose (or anti-IgM-conjugated agarose for RNA polymerase II), washed and then eluted. After cross-link reversal and proteinase K treatment, immunoprecipitated DNA was extracted with phenol-chloroform, ethanol precipitated, treated with RNAse and purified. One to ten nanograms of DNA were end-repaired, adapter-ligated and sequenced by Illumina Genome Analyzers as recommended by the manufacturer.

Alignment: Sequence reads from each IP experiment were aligned to the human reference genome (GRCh37/hg19) using MAQ with default parameters, except '-C 11' and '-H output_file', which outputs up to 11 additional best matches for each read (if any are found) to a file. This information was used to filter out any read that had more than 10 best matches on the genome. Note: It is likely that instances where multiple reads align to the same position and with the same orientation are due to enhanced PCR amplification of a single DNA fragment. No attempt has been made, however, to remove such artifacts from the data, following ENCODE practices.

Signal: Fragment densities were computed by counting the number of reads overlapping each 25 bp bin along the genome. Densities were computed using igvtools count with default parameters (in particular, '-w 25' to set window size of 25 bp and '-f mean' to report the mean value across the window), except for '-e' set to extend the reads to 200 bp, and the .wig output was converted to bigWig using wigToBigWig from the UCSC Kent software package.

Peaks: Discrete intervals of ChIP-seq fragment enrichment were identified using Scripture, a scan statistics approach, under the assumption of uniform background signal. All data sets where processed with '-task chip', and with '-windows 100,200,500,1000,5000,10000,100000'. (No mask file nor the '-trim' option have been used.) The resulting called segments were then further filtered to remove intervals that are significantly enriched only because they contain smaller enriched intervals within them. This post-processing step has been implemented using Matlab. The use of the post-processing step allowed very large enriched intervals (of the order of Mbps for H3K27me3, for instance) to be detected, as well as much smaller intervals, without the need to tailor the parameters of Scripture based on prior expectations.

Source

Files downloaded from GEO series: GSE29611
Input file format: BAM

Samples

From Human Feb. 2009 (GRCh37/hg19) Assembly

Filename Description Feature GEO-ID
1 GSM733752.sga GM12878 CTCF CTCF GSM733752
2 GSM733742.sga GM12878 Control Control GSM733742
3 GSM733767.sga GM12878 H2A.Z H2A.Z GSM733767
4 GSM733771.sga GM12878 H3K27ac H3K27ac GSM733771
5 GSM733758.sga GM12878 H3K27me3 H3K27me3 GSM733758
6 GSM733679.sga GM12878 H3K36me3 H3K36me3 GSM733679
7 GSM733772.sga GM12878 H3K4me1 H3K4me1 GSM733772
8 GSM733769.sga GM12878 H3K4me2 H3K4me2 GSM733769
9 GSM733708.sga GM12878 H3K4me3 H3K4me3 GSM733708
10 GSM733736.sga GM12878 H3K79me2 H3K79me2 GSM733736
11 GSM733677.sga GM12878 H3K9ac H3K9ac GSM733677
12 GSM733664.sga GM12878 H3K9me3 H3K9me3 GSM733664
13 GSM733642.sga GM12878 H4K20me1 H4K20me1 GSM733642
14 GSM733672.sga H1-hESC CTCF CTCF GSM733672
15 GSM733770.sga H1-hESC Control Control GSM733770
16 GSM733718.sga H1-hESC H3K27ac H3K27ac GSM733718
17 GSM733748.sga H1-hESC H3K27me3 H3K27me3 GSM733748
18 GSM733725.sga H1-hESC H3K36me3 H3K36me3 GSM733725
19 GSM733782.sga H1-hESC H3K4me1 H3K4me1 GSM733782
20 GSM733670.sga H1-hESC H3K4me2 H3K4me2 GSM733670
21 GSM733657.sga H1-hESC H3K4me3 H3K4me3 GSM733657
22 GSM733773.sga H1-hESC H3K9ac H3K9ac GSM733773
23 GSM733687.sga H1-hESC H4K20me1 H4K20me1 GSM733687
24 GSM733724.sga HMEC CTCF CTCF GSM733724
25 GSM733668.sga HMEC Control Control GSM733668
26 GSM733660.sga HMEC H3K27ac H3K27ac GSM733660
27 GSM733722.sga HMEC H3K27me3 H3K27me3 GSM733722
28 GSM733707.sga HMEC H3K36me3 H3K36me3 GSM733707
29 GSM733705.sga HMEC H3K4me1 H3K4me1 GSM733705
30 GSM733654.sga HMEC H3K4me2 H3K4me2 GSM733654
31 GSM733712.sga HMEC H3K4me3 H3K4me3 GSM733712
32 GSM733713.sga HMEC H3K9ac H3K9ac GSM733713
33 GSM733647.sga HMEC H4K20me1 H4K20me1 GSM733647
34 GSM733762.sga HSMM CTCF CTCF GSM733762
35 GSM733663.sga HSMM Control Control GSM733663
36 GSM733760.sga HSMM H2A.Z H2A.Z GSM733760
37 GSM733755.sga HSMM H3K27ac H3K27ac GSM733755
38 GSM733667.sga HSMM H3K27me3 H3K27me3 GSM733667
39 GSM733702.sga HSMM H3K36me3 H3K36me3 GSM733702
40 GSM733761.sga HSMM H3K4me1 H3K4me1 GSM733761
41 GSM733768.sga HSMM H3K4me2 H3K4me2 GSM733768
42 GSM733637.sga HSMM H3K4me3 H3K4me3 GSM733637
43 GSM733741.sga HSMM H3K79me2 H3K79me2 GSM733741
44 GSM733775.sga HSMM H3K9ac H3K9ac GSM733775
45 GSM733730.sga HSMM H3K9me3 H3K9me3 GSM733730
46 GSM733676.sga HSMM H4K20me1 H4K20me1 GSM733676
47 GSM733783.sga HSMMtube CTCF CTCF GSM733783
48 GSM733648.sga HSMMtube Control Control GSM733648
49 GSM733746.sga HSMMtube H2A.Z H2A.Z GSM733746
50 GSM733666.sga HSMMtube H3K27ac H3K27ac GSM733666
51 GSM733717.sga HSMMtube H3K36me3 H3K36me3 GSM733717
52 GSM733661.sga HSMMtube H3K4me1 H3K4me1 GSM733661
53 GSM733700.sga HSMMtube H3K4me2 H3K4me2 GSM733700
54 GSM733738.sga HSMMtube H3K4me3 H3K4me3 GSM733738
55 GSM733727.sga HSMMtube H3K79me2 H3K79me2 GSM733727
56 GSM733639.sga HSMMtube H3K9ac H3K9ac GSM733639
57 GSM733644.sga HSMMtube H4K20me1 H4K20me1 GSM733644
58 GSM733716.sga HUVEC CTCF CTCF GSM733716
59 GSM733715.sga HUVEC Control Control GSM733715
60 GSM733691.sga HUVEC H3K27ac H3K27ac GSM733691
61 GSM733688.sga HUVEC H3K27me3 H3K27me3 GSM733688
62 GSM733757.sga HUVEC H3K36me3 H3K36me3 GSM733757
63 GSM733690.sga HUVEC H3K4me1 H3K4me1 GSM733690
64 GSM733683.sga HUVEC H3K4me2 H3K4me2 GSM733683
65 GSM733673.sga HUVEC H3K4me3 H3K4me3 GSM733673
66 GSM733735.sga HUVEC H3K9ac H3K9ac GSM733735
67 GSM733703.sga HUVEC H3K9me1 H3K9me1 GSM733703
68 GSM733640.sga HUVEC H4K20me1 H4K20me1 GSM733640
69 GSM733749.sga HUVEC Pol2(b) Pol2(b) GSM733749
70 GSM733785.sga HeLa-S3 CTCF CTCF GSM733785
71 GSM733659.sga HeLa-S3 Control Control GSM733659
72 GSM733684.sga HeLa-S3 H3K27ac H3K27ac GSM733684
73 GSM733696.sga HeLa-S3 H3K27me3 H3K27me3 GSM733696
74 GSM733711.sga HeLa-S3 H3K36me3 H3K36me3 GSM733711
75 GSM733734.sga HeLa-S3 H3K4me2 H3K4me2 GSM733734
76 GSM733682.sga HeLa-S3 H3K4me3 H3K4me3 GSM733682
77 GSM733669.sga HeLa-S3 H3K79me2 H3K79me2 GSM733669
78 GSM733756.sga HeLa-S3 H3K9ac H3K9ac GSM733756
79 GSM733689.sga HeLa-S3 H4K20me1 H4K20me1 GSM733689
80 GSM733759.sga HeLa-S3 Pol2(b) Pol2(b) GSM733759
81 GSM733645.sga HepG2 CTCF CTCF GSM733645
82 GSM733732.sga HepG2 Control Control GSM733732
83 GSM733774.sga HepG2 H2A.Z H2A.Z GSM733774
84 GSM733743.sga HepG2 H3K27ac H3K27ac GSM733743
85 GSM733754.sga HepG2 H3K27me3 H3K27me3 GSM733754
86 GSM733685.sga HepG2 H3K36me3 H3K36me3 GSM733685
87 GSM733693.sga HepG2 H3K4me2 H3K4me2 GSM733693
88 GSM733737.sga HepG2 H3K4me3 H3K4me3 GSM733737
89 GSM733641.sga HepG2 H3K79me2 H3K79me2 GSM733641
90 GSM733638.sga HepG2 H3K9ac H3K9ac GSM733638
91 GSM733694.sga HepG2 H4K20me1 H4K20me1 GSM733694
92 GSM733719.sga K562 CTCF CTCF GSM733719
93 GSM733780.sga K562 Control Control GSM733780
94 GSM733786.sga K562 H2A.Z H2A.Z GSM733786
95 GSM733656.sga K562 H3K27ac H3K27ac GSM733656
96 GSM733658.sga K562 H3K27me3 H3K27me3 GSM733658
97 GSM733714.sga K562 H3K36me3 H3K36me3 GSM733714
98 GSM733692.sga K562 H3K4me1 H3K4me1 GSM733692
99 GSM733651.sga K562 H3K4me2 H3K4me2 GSM733651
100 GSM733680.sga K562 H3K4me3 H3K4me3 GSM733680
101 GSM733653.sga K562 H3K79me2 H3K79me2 GSM733653
102 GSM733778.sga K562 H3K9ac H3K9ac GSM733778
103 GSM733777.sga K562 H3K9me1 H3K9me1 GSM733777
104 GSM733776.sga K562 H3K9me3 H3K9me3 GSM733776
105 GSM733675.sga K562 H4K20me1 H4K20me1 GSM733675
106 GSM733643.sga K562 Pol2(b) Pol2(b) GSM733643
107 GSM733765.sga NH-A CTCF CTCF GSM733765
108 GSM733678.sga NH-A Control Control GSM733678
109 GSM733763.sga NH-A H3K27ac H3K27ac GSM733763
110 GSM733729.sga NH-A H3K27me3 H3K27me3 GSM733729
111 GSM733751.sga NH-A H3K36me3 H3K36me3 GSM733751
112 GSM733710.sga NH-A H3K4me1 H3K4me1 GSM733710
113 GSM733747.sga NH-A H3K4me3 H3K4me3 GSM733747
114 GSM733744.sga NHDF-Ad CTCF CTCF GSM733744
115 GSM733750.sga NHDF-Ad Control Control GSM733750
116 GSM733662.sga NHDF-Ad H3K27ac H3K27ac GSM733662
117 GSM733745.sga NHDF-Ad H3K27me3 H3K27me3 GSM733745
118 GSM733733.sga NHDF-Ad H3K36me3 H3K36me3 GSM733733
119 GSM733753.sga NHDF-Ad H3K4me2 H3K4me2 GSM733753
120 GSM733650.sga NHDF-Ad H3K4me3 H3K4me3 GSM733650
121 GSM733709.sga NHDF-Ad H3K9ac H3K9ac GSM733709
122 GSM733636.sga NHEK CTCF CTCF GSM733636
123 GSM733740.sga NHEK Control Control GSM733740
124 GSM733674.sga NHEK H3K27ac H3K27ac GSM733674
125 GSM733701.sga NHEK H3K27me3 H3K27me3 GSM733701
126 GSM733726.sga NHEK H3K36me3 H3K36me3 GSM733726
127 GSM733698.sga NHEK H3K4me1 H3K4me1 GSM733698
128 GSM733686.sga NHEK H3K4me2 H3K4me2 GSM733686
129 GSM733720.sga NHEK H3K4me3 H3K4me3 GSM733720
130 GSM733665.sga NHEK H3K9ac H3K9ac GSM733665
131 GSM733655.sga NHEK H3K9me1 H3K9me1 GSM733655
132 GSM733728.sga NHEK H4K20me1 H4K20me1 GSM733728
133 GSM733671.sga NHEK Pol2(b) Pol2(b) GSM733671
134 GSM733695.sga NHLF CTCF CTCF GSM733695
135 GSM733731.sga NHLF Control Control GSM733731
136 GSM733646.sga NHLF H3K27ac H3K27ac GSM733646
137 GSM733764.sga NHLF H3K27me3 H3K27me3 GSM733764
138 GSM733699.sga NHLF H3K36me3 H3K36me3 GSM733699
139 GSM733649.sga NHLF H3K4me1 H3K4me1 GSM733649
140 GSM733781.sga NHLF H3K4me2 H3K4me2 GSM733781
141 GSM733723.sga NHLF H3K4me3 H3K4me3 GSM733723
142 GSM733652.sga NHLF H3K9ac H3K9ac GSM733652
143 GSM733706.sga NHLF H4K20me1 H4K20me1 GSM733706
144 GSM733784.sga Osteobl CTCF CTCF GSM733784
145 GSM733697.sga Osteobl Control Control GSM733697
146 GSM733766.sga Osteobl H2A.Z H2A.Z GSM733766
147 GSM733739.sga Osteobl H3K27ac H3K27ac GSM733739
148 GSM733721.sga Osteobl H3K36me3 H3K36me3 GSM733721
149 GSM733704.sga Osteobl H3K4me1 H3K4me1 GSM733704
150 GSM733779.sga Osteobl H3K4me2 H3K4me2 GSM733779
151 GSM733681.sga Osteobl H3K9me3 H3K9me3 GSM733681

Technical Notes

BAM files were downloaded from GEO and processed using the following bash commands:

  1. Make BED file:
    bamToBed -i SAMPLE_sorted.bam > SAMPLE.bed
    
  2. Make SGA file:
    bed2sga.pl -s hg19 -f FEATURE < SAMPLE.bed | sort -s -k1,1 -k3,3n -k4,4 | compactsga > SAMPLE.sga
    

References

  1. GEO series GSE29611 Histone Modifications by ChIP-seq from ENCODE/Broad Institute.