GSE29611, Histone Modifications by ChIP-seq

Description

ChIP-seq experiment investigating 15 different cell types for 25 different histone modifications. 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.

Source

Files downloaded from: UCSC
Input file format: BAM

Sample

From Human Mar. 2006 (NCBI36/hg18) Assembly

Filename Description Feature GEO-ID
1 Dnd41-CTCF.sga Dnd41 CTCF CTCF -
2 Dnd41-H2A.Z.sga Dnd41 H2A.Z H2A.Z -
3 Dnd41-H3K27ac.sga Dnd41 H3K27ac H3K27ac -
4 Dnd41-H3K36me3.sga Dnd41 H3K36me3 H3K36me3 -
5 Dnd41-H3K4me1.sga Dnd41 H3K4me1 H3K4me1 -
6 Dnd41-H3K4me2.sga Dnd41 H3K4me2 H3K4me2 -
7 Dnd41-H3K4me3.sga Dnd41 H3K4me3 H3K4me3 -
8 Dnd41-H3K79me2.sga Dnd41 H3K79me2 H3K79me2 -
9 Dnd41-H3K9ac.sga Dnd41 H3K9ac H3K9ac -
10 Dnd41-H3K9me3.sga Dnd41 H3K9me3 H3K9me3 -
11 Dnd41-H4K20me1.sga Dnd41 H4K20me1 H4K20me1 -
12 Dnd41-Input.sga Dnd41 Input Input -
13 GM12878-CTCF.sga GM12878 CTCF CTCF -
14 GM12878-EZH2.sga GM12878 EZH2 EZH2 -
15 GM12878-H2A.Z.sga GM12878 H2A.Z H2A.Z -
16 GM12878-H3K27ac.sga GM12878 H3K27ac H3K27ac -
17 GM12878-H3K27me3.sga GM12878 H3K27me3 H3K27me3 -
18 GM12878-H3K36me3.sga GM12878 H3K36me3 H3K36me3 -
19 GM12878-H3K4me1.sga GM12878 H3K4me1 H3K4me1 -
20 GM12878-H3K4me2.sga GM12878 H3K4me2 H3K4me2 -
21 GM12878-H3K4me3.sga GM12878 H3K4me3 H3K4me3 -
22 GM12878-H3K79me2.sga GM12878 H3K79me2 H3K79me2 -
23 GM12878-H3K9ac.sga GM12878 H3K9ac H3K9ac -
24 GM12878-H3K9me3.sga GM12878 H3K9me3 H3K9me3 -
25 GM12878-H4K20me1.sga GM12878 H4K20me1 H4K20me1 -
26 GM12878-Input.sga GM12878 Input Input -
27 H1-hESC-CHD1.sga H1-hESC CHD1 CHD1 -
28 H1-hESC-CTCF.sga H1-hESC CTCF CTCF -
29 H1-hESC-H2A.Z.sga H1-hESC H2A.Z H2A.Z -
30 H1-hESC-H3K27ac.sga H1-hESC H3K27ac H3K27ac -
31 H1-hESC-H3K27me3.sga H1-hESC H3K27me3 H3K27me3 -
32 H1-hESC-H3K36me3.sga H1-hESC H3K36me3 H3K36me3 -
33 H1-hESC-H3K4me1.sga H1-hESC H3K4me1 H3K4me1 -
34 H1-hESC-H3K4me2.sga H1-hESC H3K4me2 H3K4me2 -
35 H1-hESC-H3K4me3.sga H1-hESC H3K4me3 H3K4me3 -
36 H1-hESC-H3K79me2.sga H1-hESC H3K79me2 H3K79me2 -
37 H1-hESC-H3K9ac.sga H1-hESC H3K9ac H3K9ac -
38 H1-hESC-H3K9me3.sga H1-hESC H3K9me3 H3K9me3 -
39 H1-hESC-H4K20me1.sga H1-hESC H4K20me1 H4K20me1 -
40 H1-hESC-Input.sga H1-hESC Input Input -
41 H1-hESC-JARID1A.sga H1-hESC JARID1A JARID1A -
42 H1-hESC-RBBP5.sga H1-hESC RBBP5 RBBP5 -
43 HMEC-CTCF.sga HMEC CTCF CTCF -
44 HMEC-EZH2.sga HMEC EZH2 EZH2 -
45 HMEC-H2A.Z.sga HMEC H2A.Z H2A.Z -
46 HMEC-H3K27ac.sga HMEC H3K27ac H3K27ac -
47 HMEC-H3K27me3.sga HMEC H3K27me3 H3K27me3 -
48 HMEC-H3K36me3.sga HMEC H3K36me3 H3K36me3 -
49 HMEC-H3K4me1.sga HMEC H3K4me1 H3K4me1 -
50 HMEC-H3K4me2.sga HMEC H3K4me2 H3K4me2 -
51 HMEC-H3K4me3.sga HMEC H3K4me3 H3K4me3 -
52 HMEC-H3K79me2.sga HMEC H3K79me2 H3K79me2 -
53 HMEC-H3K9ac.sga HMEC H3K9ac H3K9ac -
54 HMEC-H3K9me3.sga HMEC H3K9me3 H3K9me3 -
55 HMEC-H4K20me1.sga HMEC H4K20me1 H4K20me1 -
56 HMEC-Input.sga HMEC Input Input -
57 HSMM-CTCF.sga HSMM CTCF CTCF -
58 HSMM-EZH2.sga HSMM EZH2 EZH2 -
59 HSMM-H2A.Z.sga HSMM H2A.Z H2A.Z -
60 HSMM-H3K27ac.sga HSMM H3K27ac H3K27ac -
61 HSMM-H3K27me3.sga HSMM H3K27me3 H3K27me3 -
62 HSMM-H3K36me3.sga HSMM H3K36me3 H3K36me3 -
63 HSMM-H3K4me1.sga HSMM H3K4me1 H3K4me1 -
64 HSMM-H3K4me2.sga HSMM H3K4me2 H3K4me2 -
65 HSMM-H3K4me3.sga HSMM H3K4me3 H3K4me3 -
66 HSMM-H3K79me2.sga HSMM H3K79me2 H3K79me2 -
67 HSMM-H3K9ac.sga HSMM H3K9ac H3K9ac -
68 HSMM-H3K9me3.sga HSMM H3K9me3 H3K9me3 -
69 HSMM-H4K20me1.sga HSMM H4K20me1 H4K20me1 -
70 HSMM-Input.sga HSMM Input Input -
71 HSMMtube-CTCF.sga HSMMtube CTCF CTCF -
72 HSMMtube-H2A.Z.sga HSMMtube H2A.Z H2A.Z -
73 HSMMtube-H3K27ac.sga HSMMtube H3K27ac H3K27ac -
74 HSMMtube-H3K36me3.sga HSMMtube H3K36me3 H3K36me3 -
75 HSMMtube-H3K4me1.sga HSMMtube H3K4me1 H3K4me1 -
76 HSMMtube-H3K4me2.sga HSMMtube H3K4me2 H3K4me2 -
77 HSMMtube-H3K4me3.sga HSMMtube H3K4me3 H3K4me3 -
78 HSMMtube-H3K79me2.sga HSMMtube H3K79me2 H3K79me2 -
79 HSMMtube-H3K9ac.sga HSMMtube H3K9ac H3K9ac -
80 HSMMtube-H3K9me3.sga HSMMtube H3K9me3 H3K9me3 -
81 HSMMtube-H4K20me1.sga HSMMtube H4K20me1 H4K20me1 -
82 HSMMtube-Input.sga HSMMtube Input Input -
83 HUVEC-CTCF.sga HUVEC CTCF CTCF -
84 HUVEC-H2A.Z.sga HUVEC H2A.Z H2A.Z -
85 HUVEC-H3K27ac.sga HUVEC H3K27ac H3K27ac -
86 HUVEC-H3K27me3.sga HUVEC H3K27me3 H3K27me3 -
87 HUVEC-H3K36me3.sga HUVEC H3K36me3 H3K36me3 -
88 HUVEC-H3K4me1.sga HUVEC H3K4me1 H3K4me1 -
89 HUVEC-H3K4me2.sga HUVEC H3K4me2 H3K4me2 -
90 HUVEC-H3K4me3.sga HUVEC H3K4me3 H3K4me3 -
91 HUVEC-H3K79me2.sga HUVEC H3K79me2 H3K79me2 -
92 HUVEC-H3K9ac.sga HUVEC H3K9ac H3K9ac -
93 HUVEC-H3K9me1.sga HUVEC H3K9me1 H3K9me1 -
94 HUVEC-H4K20me1.sga HUVEC H4K20me1 H4K20me1 -
95 HUVEC-Input.sga HUVEC Input Input -
96 HUVEC-Pol2.sga HUVEC Pol2 Pol2 -
97 HeLa-S3-CTCF.sga HeLa-S3 CTCF CTCF -
98 HeLa-S3-H2A.Z.sga HeLa-S3 H2A.Z H2A.Z -
99 HeLa-S3-H3K27ac.sga HeLa-S3 H3K27ac H3K27ac -
100 HeLa-S3-H3K27me3.sga HeLa-S3 H3K27me3 H3K27me3 -
101 HeLa-S3-H3K36me3.sga HeLa-S3 H3K36me3 H3K36me3 -
102 HeLa-S3-H3K4me1.sga HeLa-S3 H3K4me1 H3K4me1 -
103 HeLa-S3-H3K4me2.sga HeLa-S3 H3K4me2 H3K4me2 -
104 HeLa-S3-H3K4me3.sga HeLa-S3 H3K4me3 H3K4me3 -
105 HeLa-S3-H3K79me2.sga HeLa-S3 H3K79me2 H3K79me2 -
106 HeLa-S3-H3K9ac.sga HeLa-S3 H3K9ac H3K9ac -
107 HeLa-S3-H3K9me3.sga HeLa-S3 H3K9me3 H3K9me3 -
108 HeLa-S3-H4K20me1.sga HeLa-S3 H4K20me1 H4K20me1 -
109 HeLa-S3-Input.sga HeLa-S3 Input Input -
110 HepG2-CTCF.sga HepG2 CTCF CTCF -
111 HepG2-EZH2.sga HepG2 EZH2 EZH2 -
112 HepG2-H2A.Z.sga HepG2 H2A.Z H2A.Z -
113 HepG2-H3K27ac.sga HepG2 H3K27ac H3K27ac -
114 HepG2-H3K27me3.sga HepG2 H3K27me3 H3K27me3 -
115 HepG2-H3K36me3.sga HepG2 H3K36me3 H3K36me3 -
116 HepG2-H3K4me1.sga HepG2 H3K4me1 H3K4me1 -
117 HepG2-H3K4me2.sga HepG2 H3K4me2 H3K4me2 -
118 HepG2-H3K4me3.sga HepG2 H3K4me3 H3K4me3 -
119 HepG2-H3K79me2.sga HepG2 H3K79me2 H3K79me2 -
120 HepG2-H3K9ac.sga HepG2 H3K9ac H3K9ac -
121 HepG2-H4K20me1.sga HepG2 H4K20me1 H4K20me1 -
122 HepG2-Input.sga HepG2 Input Input -
123 K562-CHD1.sga K562 CHD1 CHD1 -
124 K562-CTCF.sga K562 CTCF CTCF -
125 K562-EZH2.sga K562 EZH2 EZH2 -
126 K562-H2A.Z.sga K562 H2A.Z H2A.Z -
127 K562-H3K27ac.sga K562 H3K27ac H3K27ac -
128 K562-H3K27me3.sga K562 H3K27me3 H3K27me3 -
129 K562-H3K36me3.sga K562 H3K36me3 H3K36me3 -
130 K562-H3K4me1.sga K562 H3K4me1 H3K4me1 -
131 K562-H3K4me2.sga K562 H3K4me2 H3K4me2 -
132 K562-H3K4me3.sga K562 H3K4me3 H3K4me3 -
133 K562-H3K79me2.sga K562 H3K79me2 H3K79me2 -
134 K562-H3K9ac.sga K562 H3K9ac H3K9ac -
135 K562-H3K9me1.sga K562 H3K9me1 H3K9me1 -
136 K562-H3K9me3.sga K562 H3K9me3 H3K9me3 -
137 K562-H4K20me1.sga K562 H4K20me1 H4K20me1 -
138 K562-HDAC1.sga K562 HDAC1 HDAC1 -
139 K562-HDAC2.sga K562 HDAC2 HDAC2 -
140 K562-Input.sga K562 Input Input -
141 K562-PHF8.sga K562 PHF8 PHF8 -
142 K562-PLU1.sga K562 PLU1 PLU1 -
143 K562-Pol2.sga K562 Pol2 Pol2 -
144 K562-RBBP5.sga K562 RBBP5 RBBP5 -
145 K562-SAP30.sga K562 SAP30 SAP30 -
146 K562-p300.sga K562 p300 p300 -
147 NH-A-CTCF.sga NH-A CTCF CTCF -
148 NH-A-EZH2.sga NH-A EZH2 EZH2 -
149 NH-A-H2A.Z.sga NH-A H2A.Z H2A.Z -
150 NH-A-H3K27ac.sga NH-A H3K27ac H3K27ac -
151 NH-A-H3K27me3.sga NH-A H3K27me3 H3K27me3 -
152 NH-A-H3K36me3.sga NH-A H3K36me3 H3K36me3 -
153 NH-A-H3K4me1.sga NH-A H3K4me1 H3K4me1 -
154 NH-A-H3K4me2.sga NH-A H3K4me2 H3K4me2 -
155 NH-A-H3K4me3.sga NH-A H3K4me3 H3K4me3 -
156 NH-A-H3K79me2.sga NH-A H3K79me2 H3K79me2 -
157 NH-A-H3K9ac.sga NH-A H3K9ac H3K9ac -
158 NH-A-H3K9me3.sga NH-A H3K9me3 H3K9me3 -
159 NH-A-H4K20me1.sga NH-A H4K20me1 H4K20me1 -
160 NH-A-Input.sga NH-A Input Input -
161 NHDF-Ad-CTCF.sga NHDF-Ad CTCF CTCF -
162 NHDF-Ad-EZH2.sga NHDF-Ad EZH2 EZH2 -
163 NHDF-Ad-H3K27ac.sga NHDF-Ad H3K27ac H3K27ac -
164 NHDF-Ad-H3K27me3.sga NHDF-Ad H3K27me3 H3K27me3 -
165 NHDF-Ad-H3K36me3.sga NHDF-Ad H3K36me3 H3K36me3 -
166 NHDF-Ad-H3K4me1.sga NHDF-Ad H3K4me1 H3K4me1 -
167 NHDF-Ad-H3K4me2.sga NHDF-Ad H3K4me2 H3K4me2 -
168 NHDF-Ad-H3K4me3.sga NHDF-Ad H3K4me3 H3K4me3 -
169 NHDF-Ad-H3K79me2.sga NHDF-Ad H3K79me2 H3K79me2 -
170 NHDF-Ad-H3K9ac.sga NHDF-Ad H3K9ac H3K9ac -
171 NHDF-Ad-H3K9me3.sga NHDF-Ad H3K9me3 H3K9me3 -
172 NHDF-Ad-H4K20me1.sga NHDF-Ad H4K20me1 H4K20me1 -
173 NHDF-Ad-Input.sga NHDF-Ad Input Input -
174 NHEK-CTCF.sga NHEK CTCF CTCF -
175 NHEK-EZH2.sga NHEK EZH2 EZH2 -
176 NHEK-H2A.Z.sga NHEK H2A.Z H2A.Z -
177 NHEK-H3K27ac.sga NHEK H3K27ac H3K27ac -
178 NHEK-H3K27me3.sga NHEK H3K27me3 H3K27me3 -
179 NHEK-H3K36me3.sga NHEK H3K36me3 H3K36me3 -
180 NHEK-H3K4me1.sga NHEK H3K4me1 H3K4me1 -
181 NHEK-H3K4me2.sga NHEK H3K4me2 H3K4me2 -
182 NHEK-H3K4me3.sga NHEK H3K4me3 H3K4me3 -
183 NHEK-H3K79me2.sga NHEK H3K79me2 H3K79me2 -
184 NHEK-H3K9ac.sga NHEK H3K9ac H3K9ac -
185 NHEK-H3K9me1.sga NHEK H3K9me1 H3K9me1 -
186 NHEK-H3K9me3.sga NHEK H3K9me3 H3K9me3 -
187 NHEK-H4K20me1.sga NHEK H4K20me1 H4K20me1 -
188 NHEK-Input.sga NHEK Input Input -
189 NHEK-Pol2.sga NHEK Pol2 Pol2 -
190 NHLF-CTCF.sga NHLF CTCF CTCF -
191 NHLF-EZH2.sga NHLF EZH2 EZH2 -
192 NHLF-H2A.Z.sga NHLF H2A.Z H2A.Z -
193 NHLF-H3K27ac.sga NHLF H3K27ac H3K27ac -
194 NHLF-H3K27me3.sga NHLF H3K27me3 H3K27me3 -
195 NHLF-H3K36me3.sga NHLF H3K36me3 H3K36me3 -
196 NHLF-H3K4me1.sga NHLF H3K4me1 H3K4me1 -
197 NHLF-H3K4me2.sga NHLF H3K4me2 H3K4me2 -
198 NHLF-H3K4me3.sga NHLF H3K4me3 H3K4me3 -
199 NHLF-H3K79me2.sga NHLF H3K79me2 H3K79me2 -
200 NHLF-H3K9ac.sga NHLF H3K9ac H3K9ac -
201 NHLF-H3K9me3.sga NHLF H3K9me3 H3K9me3 -
202 NHLF-H4K20me1.sga NHLF H4K20me1 H4K20me1 -
203 NHLF-Input.sga NHLF Input Input -
204 Osteobl-CTCF.sga Osteobl CTCF CTCF -
205 Osteobl-H2A.Z.sga Osteobl H2A.Z H2A.Z -
206 Osteobl-H3K27ac.sga Osteobl H3K27ac H3K27ac -
207 Osteobl-H3K27me3.sga Osteobl H3K27me3 H3K27me3 -
208 Osteobl-H3K36me3.sga Osteobl H3K36me3 H3K36me3 -
209 Osteobl-H3K4me1.sga Osteobl H3K4me1 H3K4me1 -
210 Osteobl-H3K4me2.sga Osteobl H3K4me2 H3K4me2 -
211 Osteobl-H3K79me2.sga Osteobl H3K79me2 H3K79me2 -
212 Osteobl-H3K9me3.sga Osteobl H3K9me3 H3K9me3 -
213 Osteobl-H4K20me1.sga Osteobl H4K20me1 H4K20me1 -
214 Osteobl-Input.sga Osteobl Input Input -

Technical Notes:

BAM files were downloaded from UCSC and converted to BED files. These were lifted over to hg 18 from hg19 and converted into SGA files using in-house software

References:

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