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

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.

• Raw data was downloaded from: SRP119087
• Input file format: SRA
• Download date: 1-1-2019

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

• Strand correlation plots: severson18_strand_cor.pdf
• ESR1 ChIP-seq tag enrichment around bound ESR1 motifs: severson18_ESR1_enr.pdf

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).

• Severson TM, Kim Y, Joosten SEP, Schuurman K, van der Groep P, Moelans CB, Ter Hoeve ND, Manson QF, Martens JW, van Deurzen CHM, Barbe E, Hedenfalk I, Bult P, Smit VTHBM, Linn SC, van Diest PJ, Wessels L, Zwart W
  Characterizing steroid hormone receptor chromatin binding landscapes in male and female breast cancer. Nat Commun. 2018 Feb 2;9(1):482. doi: 10.1038/s41467-018-02856-2. 29396493
• GEO series GSE104399: Characterizing steroid hormone receptor chromatin binding landscapes in male and female breast cancer