Severson 2018, ChIP-seq against several TFs and H3K4me1 in male and female breast tumors.

Description

Characterization of human breast tumors of both genders for hormonal regulation via genome-wide chromatin binding landscapes of ERα, AR, PR, GR, FOXA1, and GATA3 and enhancer-enriched histone mark H3K4me1.

Source

Samples

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

ChIP-seq data:

Filename Description Feature GEO-ID
1 GSM2797159.sga Mixed male breast tumor|Input|| Input GSM2797159
2 GSM2797156.sga Male breast tumor 3|H3K4me1|| H3K4me1 GSM2797156
3 GSM2797155.sga Male breast tumor 24|H3K4me1|| H3K4me1 GSM2797155
4 GSM2797154.sga Male breast tumor 19|H3K4me1|| H3K4me1 GSM2797154
5 GSM2797153.sga Male breast tumor 5|H3K4me1|| H3K4me1 GSM2797153
6 GSM2797152.sga Male breast tumor 14|H3K4me1|| H3K4me1 GSM2797152
7 GSM2797151.sga Male breast tumor 6|H3K4me1|| H3K4me1 GSM2797151
8 GSM2797150.sga Male breast tumor 13|H3K4me1|| H3K4me1 GSM2797150
9 GSM2797149.sga Male breast tumor 21|GATA3|| GATA3 GSM2797149
10 GSM2797148.sga Male breast tumor 16|GATA3|| GATA3 GSM2797148
11 GSM2797147.sga Male breast tumor 15|GATA3|| GATA3 GSM2797147
12 GSM2797146.sga Male breast tumor 30|PGR|| PGR GSM2797146
13 GSM2797145.sga Male breast tumor 29|PGR|| PGR GSM2797145
14 GSM2797144.sga Male breast tumor 28|PGR|| PGR GSM2797144
15 GSM2797143.sga Male breast tumor 26|PGR|| PGR GSM2797143
16 GSM2797142.sga Male breast tumor 26|NR3C1|| NR3C1 GSM2797142
17 GSM2797141.sga Male breast tumor 21|NR3C1|| NR3C1 GSM2797141
18 GSM2797140.sga Male breast tumor 15|NR3C1|| NR3C1 GSM2797140
19 GSM2797139.sga Male breast tumor 12|NR3C1|| NR3C1 GSM2797139
20 GSM2797138.sga Male breast tumor 10|NR3C1|| NR3C1 GSM2797138
21 GSM2797137.sga Male breast tumor 9|NR3C1|| NR3C1 GSM2797137
22 GSM2797136.sga Male breast tumor 1|NR3C1|| NR3C1 GSM2797136
23 GSM2797135.sga Male breast tumor 19|FOXA1|| FOXA1 GSM2797135
24 GSM2797134.sga Male breast tumor 14|FOXA1|| FOXA1 GSM2797134
25 GSM2797133.sga Male breast tumor 13|FOXA1|| FOXA1 GSM2797133
26 GSM2797132.sga Male breast tumor 6|FOXA1|| FOXA1 GSM2797132
27 GSM2797131.sga Male breast tumor 4|FOXA1|| FOXA1 GSM2797131
28 GSM2797130.sga Male breast tumor 3|FOXA1|| FOXA1 GSM2797130
29 GSM2797129.sga Male breast tumor 1|FOXA1|| FOXA1 GSM2797129
30 GSM2797128.sga Male breast tumor 30|AR|| AR GSM2797128
31 GSM2797127.sga Male breast tumor 28|AR|| AR GSM2797127
32 GSM2797126.sga Male breast tumor 26|AR|| AR GSM2797126
33 GSM2797125.sga Male breast tumor 20|AR|| AR GSM2797125
34 GSM2797124.sga Male breast tumor 18|AR|| AR GSM2797124
35 GSM2797123.sga Male breast tumor 17|AR|| AR GSM2797123
36 GSM2797122.sga Male breast tumor 10|AR|| AR GSM2797122
37 GSM2797121.sga Male breast tumor 8|AR|| AR GSM2797121
38 GSM2797120.sga Male breast tumor 7|AR|| AR GSM2797120
39 GSM2797119.sga Male breast tumor 30|ESR1|| ESR1 GSM2797119
40 GSM2797118.sga Male breast tumor 29|ESR1|| ESR1 GSM2797118
41 GSM2797117.sga Male breast tumor 28|ESR1|| ESR1 GSM2797117
42 GSM2797116.sga Male breast tumor 27|ESR1|| ESR1 GSM2797116
43 GSM2797115.sga Male breast tumor 26|ESR1|| ESR1 GSM2797115
44 GSM2797114.sga Male breast tumor 25|ESR1|| ESR1 GSM2797114
45 GSM2797113.sga Male breast tumor 24|ESR1|| ESR1 GSM2797113
46 GSM2797112.sga Male breast tumor 23|ESR1|| ESR1 GSM2797112
47 GSM2797111.sga Male breast tumor 22|ESR1|| ESR1 GSM2797111
48 GSM2797110.sga Male breast tumor 21|ESR1|| ESR1 GSM2797110
49 GSM2797109.sga Male breast tumor 20|ESR1|| ESR1 GSM2797109
50 GSM2797108.sga Male breast tumor 19|ESR1|| ESR1 GSM2797108
51 GSM2797107.sga Male breast tumor 18|ESR1|| ESR1 GSM2797107
52 GSM2797106.sga Male breast tumor 17|ESR1|| ESR1 GSM2797106
53 GSM2797105.sga Male breast tumor 16|ESR1|| ESR1 GSM2797105
54 GSM2797104.sga Male breast tumor 15|ESR1|| ESR1 GSM2797104
55 GSM2797103.sga Male breast tumor 14|ESR1|| ESR1 GSM2797103
56 GSM2797102.sga Male breast tumor 13|ESR1|| ESR1 GSM2797102
57 GSM2797101.sga Male breast tumor 12|ESR1|| ESR1 GSM2797101
58 GSM2797100.sga Male breast tumor 11|ESR1|| ESR1 GSM2797100
59 GSM2797099.sga Male breast tumor 10|ESR1|| ESR1 GSM2797099
60 GSM2797098.sga Male breast tumor 9|ESR1|| ESR1 GSM2797098
61 GSM2797097.sga Male breast tumor 8|ESR1|| ESR1 GSM2797097
62 GSM2797096.sga Male breast tumor 7|ESR1|| ESR1 GSM2797096
63 GSM2797095.sga Male breast tumor 6|ESR1|| ESR1 GSM2797095
64 GSM2797094.sga Male breast tumor 5|ESR1|| ESR1 GSM2797094
65 GSM2797093.sga Male breast tumor 4|ESR1|| ESR1 GSM2797093
66 GSM2797092.sga Male breast tumor 3|ESR1|| ESR1 GSM2797092
67 GSM2797091.sga Male breast tumor 2|ESR1|| ESR1 GSM2797091
68 GSM2797090.sga Male breast tumor 1|ESR1|| ESR1 GSM2797090
69 GSM2797089.sga MCF7|NR3C1|| NR3C1 GSM2797089
70 GSM2797088.sga MCF7|AR|| AR GSM2797088
71 GSM2797158.sga MCF7|Input|| Input GSM2797158
72 GSM2797157.sga Mixed female breast tumor|Input|| Input GSM2797157
73 GSM2797087.sga Female breast tumor 8|AR|| AR GSM2797087
74 GSM2797086.sga Female breast tumor 8|ESR1|| ESR1 GSM2797086
75 GSM2797085.sga Female breast tumor 7|FOXA1|| FOXA1 GSM2797085
76 GSM2797084.sga Female breast tumor 5|FOXA1|| FOXA1 GSM2797084
77 GSM2797083.sga Female breast tumor 6|FOXA1|| FOXA1 GSM2797083
78 GSM2797082.sga Female breast tumor 6|ESR1|| ESR1 GSM2797082
79 GSM2797081.sga Female breast tumor 5|ESR1|| ESR1 GSM2797081
80 GSM2797080.sga Female breast tumor 3|FOXA1|| FOXA1 GSM2797080
81 GSM2797079.sga Female breast tumor 4|FOXA1|| FOXA1 GSM2797079
82 GSM2797078.sga Female breast tumor 2|FOXA1|| FOXA1 GSM2797078
83 GSM2797077.sga Female breast tumor 1|FOXA1|| FOXA1 GSM2797077
84 GSM2797076.sga Female breast tumor 3|ESR1|| ESR1 GSM2797076
85 GSM2797075.sga Female breast tumor 2|ESR1|| ESR1 GSM2797075
86 GSM2797074.sga Female breast tumor 1|ESR1|| ESR1 GSM2797074

Technical Notes

FASTQ files were extracted from SRA files using fastq-dump (SRA toolkit v2.5.0) and mapped to the genome using Bowtie v1.1.1. SAM files were then converted to BAM using samtools v0.1.14 and to BED using bamToBed v2.27.0 (bedtools). BED to SGA conversion was carried out using bed2sga (ChIP-Seq v. 1.5.4).

References

Last update: 1 Jan 2019