Mohammed 2015, Progesterone receptor modulates estrogen receptor-α action in breast cancer.

The series includes the following experiements (subSeries):

• ChIP-seq of ER-α, PR, p300 in two ER+ breast cancer cell lines (MCF7 and T47D) treated with estrogen and with and without progestins;
• ChIP-seq of ER-α and PR in two ER+ breast cancer cell lines treated with and without estrogen and with and without progestins;
• ChIP-seq of ER and PR in xenografted MCF7 tumors grown in mice [xenograft].

• Raw data was downloaded from: SRP057755, SRP057756,SRP057757
• Input file format: SRA
• Download date: 26-10-2018

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

ChIP-seq data:

	Filename	Description	Feature	GEO-ID
1	GSM1669011.sga	T47D|ESR1|Full_Media 3hr|rep1	ESR1	GSM1669011
2	GSM1669012.sga	T47D|ESR1|Full_Media 3hr|rep2	ESR1	GSM1669012
3	GSM1669013.sga	T47D|ESR1|Full_Media 3hr|rep3	ESR1	GSM1669013
4	GSM1669014.sga	T47D|ESR1|Progesterone 3hr|rep1	ESR1	GSM1669014
5	GSM1669015.sga	T47D|ESR1|Progesterone 3hr|rep2	ESR1	GSM1669015
6	GSM1669016.sga	T47D|ESR1|Progesterone 3hr|rep3	ESR1	GSM1669016
7	GSM1669017.sga	T47D|ESR1|R5020 3hr|rep1	ESR1	GSM1669017
8	GSM1669018.sga	T47D|ESR1|R5020 3hr|rep2	ESR1	GSM1669018
9	GSM1669019.sga	T47D|ESR1|R5020 3hr|rep3	ESR1	GSM1669019
10	GSM1669020.sga	T47D|input|Full_Media 3hr|rep1	input	GSM1669020
11	GSM1669021.sga	T47D|input|Full_Media 3hr|rep2	input	GSM1669021
12	GSM1669022.sga	T47D|input|Full_Media 3hr|rep3	input	GSM1669022
13	GSM1669023.sga	T47D|EP300|Full_Media 3hr|rep1	EP300	GSM1669023
14	GSM1669024.sga	T47D|EP300|Full_Media 3hr|rep2	EP300	GSM1669024
15	GSM1669025.sga	T47D|EP300|Full_Media 3hr|rep3	EP300	GSM1669025
16	GSM1669026.sga	T47D|EP300|Progesterone 3hr|rep1	EP300	GSM1669026
17	GSM1669027.sga	T47D|EP300|Progesterone 3hr|rep2	EP300	GSM1669027
18	GSM1669028.sga	T47D|EP300|Progesterone 3hr|rep3	EP300	GSM1669028
19	GSM1669029.sga	T47D|EP300|R5020 3hr|rep1	EP300	GSM1669029
20	GSM1669030.sga	T47D|EP300|R5020 3hr|rep2	EP300	GSM1669030
21	GSM1669031.sga	T47D|EP300|R5020 3hr|rep3	EP300	GSM1669031
22	GSM1669032.sga	T47D|PGR|Full_Media 3hr|rep1	PGR	GSM1669032
23	GSM1669033.sga	T47D|PGR|Full_Media 3hr|rep2	PGR	GSM1669033
24	GSM1669034.sga	T47D|PGR|Full_Media 3hr|rep3	PGR	GSM1669034
25	GSM1669035.sga	T47D|PGR|Progesterone 3hr|rep1	PGR	GSM1669035
26	GSM1669036.sga	T47D|PGR|Progesterone 3hr|rep2	PGR	GSM1669036
27	GSM1669037.sga	T47D|PGR|Progesterone 3hr|rep3	PGR	GSM1669037
28	GSM1669038.sga	T47D|PGR|R5020 3hr|rep1	PGR	GSM1669038
29	GSM1669039.sga	T47D|PGR|R5020 3hr|rep2	PGR	GSM1669039
30	GSM1669040.sga	T47D|PGR|R5020 3hr|rep3	PGR	GSM1669040
31	GSM1669041.sga	MCF7|EP300|Progesterone 3hr|	EP300	GSM1669041
32	GSM1669042.sga	MCF7|ESR1|Full_Media 3hr|rep1	ESR1	GSM1669042
33	GSM1669043.sga	MCF7|ESR1|Full_Media 3hr|rep2	ESR1	GSM1669043
34	GSM1669044.sga	MCF7|ESR1|Full_Media 3hr|rep3	ESR1	GSM1669044
35	GSM1669045.sga	MCF7|ESR1|Progesterone 3hr|rep1	ESR1	GSM1669045
36	GSM1669046.sga	MCF7|ESR1|Progesterone 3hr|rep2	ESR1	GSM1669046
37	GSM1669047.sga	MCF7|ESR1|Progesterone 3hr|rep3	ESR1	GSM1669047
38	GSM1669048.sga	MCF7|ESR1|R5020 3hr|rep1	ESR1	GSM1669048
39	GSM1669049.sga	MCF7|ESR1|R5020 3hr|rep2	ESR1	GSM1669049
40	GSM1669050.sga	MCF7|ESR1|R5020 3hr|rep3	ESR1	GSM1669050
41	GSM1669051.sga	MCF7|input|Full_Media 3hr|rep1	input	GSM1669051
42	GSM1669052.sga	MCF7|input|Full_Media 3hr|rep2	input	GSM1669052
43	GSM1669053.sga	MCF7|input|Full_Media 3hr|rep3	input	GSM1669053
44	GSM1669054.sga	MCF7|EP300|Full_Media 3hr|	EP300	GSM1669054
45	GSM1669055.sga	MCF7|EP300|Full_Media 3hr|rep1	EP300	GSM1669055
46	GSM1669056.sga	MCF7|EP300|Full_Media 3hr|rep2	EP300	GSM1669056
47	GSM1669057.sga	MCF7|EP300|Full_Media 3hr|rep3	EP300	GSM1669057
48	GSM1669058.sga	MCF7|EP300|Progesterone 24hr|	EP300	GSM1669058
49	GSM1669059.sga	MCF7|EP300|Progesterone 3hr|rep1	EP300	GSM1669059
50	GSM1669060.sga	MCF7|EP300|Progesterone 3hr|rep2	EP300	GSM1669060
51	GSM1669061.sga	MCF7|EP300|Progesterone 3hr|rep3	EP300	GSM1669061
52	GSM1669062.sga	MCF7|EP300|R5020 3hr|	EP300	GSM1669062
53	GSM1669063.sga	MCF7|EP300|R5020 24hr|	EP300	GSM1669063
54	GSM1669064.sga	MCF7|EP300|R5020 3hr|rep1	EP300	GSM1669064
55	GSM1669065.sga	MCF7|EP300|R5020 3hr|rep2	EP300	GSM1669065
56	GSM1669066.sga	MCF7|EP300|R5020 3hr|rep3	EP300	GSM1669066
57	GSM1669067.sga	MCF7|PGR|Full_Media 3hr|rep1	PGR	GSM1669067
58	GSM1669068.sga	MCF7|PGR|Full_Media 3hr|rep2	PGR	GSM1669068
59	GSM1669069.sga	MCF7|PGR|Full_Media 3hr|rep3	PGR	GSM1669069
60	GSM1669070.sga	MCF7|PGR|Progesterone 3hr|rep1	PGR	GSM1669070
61	GSM1669071.sga	MCF7|PGR|Progesterone 3hr|rep2	PGR	GSM1669071
62	GSM1669072.sga	MCF7|PGR|Progesterone 3hr|rep3	PGR	GSM1669072
63	GSM1669073.sga	MCF7|PGR|R5020 3hr|	PGR	GSM1669073
64	GSM1669074.sga	MCF7|PGR|R5020 24hr|	PGR	GSM1669074
65	GSM1669075.sga	MCF7|PGR|R5020 3hr|rep1	PGR	GSM1669075
66	GSM1669076.sga	MCF7|PGR|R5020 3hr|rep2	PGR	GSM1669076
67	GSM1669077.sga	MCF7|PGR|R5020 3hr|rep3	PGR	GSM1669077
68	GSM1669078.sga	MCF7|ESR1|Vehicle 3hr|rep1	ESR1	GSM1669078
69	GSM1669079.sga	MCF7|ESR1|E2 3hr|rep1	ESR1	GSM1669079
70	GSM1669080.sga	MCF7|ESR1|PG 3hr|rep1	ESR1	GSM1669080
71	GSM1669081.sga	MCF7|ESR1|E2+PG 3hr|rep1	ESR1	GSM1669081
72	GSM1669082.sga	MCF7|ESR1|Vehicle 3hr|rep2	ESR1	GSM1669082
73	GSM1669083.sga	MCF7|ESR1|E2 3hr|rep2	ESR1	GSM1669083
74	GSM1669084.sga	MCF7|ESR1|PG 3hr|rep2	ESR1	GSM1669084
75	GSM1669085.sga	MCF7|ESR1|E2+PG 3hr|rep2	ESR1	GSM1669085
76	GSM1669086.sga	MCF7|ESR1|Vehicle 3hr|rep3	ESR1	GSM1669086
77	GSM1669087.sga	MCF7|ESR1|E2 3hr|rep3	ESR1	GSM1669087
78	GSM1669088.sga	MCF7|ESR1|PG 3hr|rep3	ESR1	GSM1669088
79	GSM1669089.sga	MCF7|ESR1|E2+PG 3hr|rep3	ESR1	GSM1669089
80	GSM1669090.sga	MCF7|PGR|Vehicle 3hr|rep1	PGR	GSM1669090
81	GSM1669091.sga	MCF7|PGR|E2 3hr|rep1	PGR	GSM1669091
82	GSM1669092.sga	MCF7|PGR|PG 3hr|rep1	PGR	GSM1669092
83	GSM1669093.sga	MCF7|PGR|E2+PG 3hr|rep1	PGR	GSM1669093
84	GSM1669094.sga	MCF7|PGR|Vehicle 3hr|rep2	PGR	GSM1669094
85	GSM1669095.sga	MCF7|PGR|E2 3hr|rep2	PGR	GSM1669095
86	GSM1669096.sga	MCF7|PGR|PG 3hr|rep2	PGR	GSM1669096
87	GSM1669097.sga	MCF7|PGR|E2+PG 3hr|rep2	PGR	GSM1669097
88	GSM1669098.sga	MCF7|PGR|Vehicle 3hr|rep3	PGR	GSM1669098
89	GSM1669099.sga	MCF7|PGR|E2 3hr|rep3	PGR	GSM1669099
90	GSM1669100.sga	MCF7|PGR|PG 3hr|rep3	PGR	GSM1669100
91	GSM1669101.sga	MCF7|PGR|E2+PG 3hr|rep3	PGR	GSM1669101
92	GSM1669102.sga	T47D|ESR1|Vehicle 3hr|rep1	ESR1	GSM1669102
93	GSM1669103.sga	T47D|ESR1|E2 3hr|rep1	ESR1	GSM1669103
94	GSM1669104.sga	T47D|ESR1|PG 3hr|rep1	ESR1	GSM1669104
95	GSM1669105.sga	T47D|ESR1|E2+PG 3hr|rep1	ESR1	GSM1669105
96	GSM1669106.sga	T47D|ESR1|Vehicle 3hr|rep2	ESR1	GSM1669106
97	GSM1669107.sga	T47D|ESR1|E2 3hr|rep2	ESR1	GSM1669107
98	GSM1669108.sga	T47D|ESR1|PG 3hr|rep2	ESR1	GSM1669108
99	GSM1669109.sga	T47D|ESR1|E2+PG 3hr|rep2	ESR1	GSM1669109
100	GSM1669110.sga	T47D|ESR1|Vehicle 3hr|rep3	ESR1	GSM1669110
101	GSM1669111.sga	T47D|ESR1|E2 3hr|rep3	ESR1	GSM1669111
102	GSM1669112.sga	T47D|ESR1|PG 3hr|rep3	ESR1	GSM1669112
103	GSM1669113.sga	T47D|ESR1|E2+PG 3hr|rep3	ESR1	GSM1669113
104	GSM1669114.sga	T47D|PGR|Vehicle 3hr|rep1	PGR	GSM1669114
105	GSM1669115.sga	T47D|PGR|E2 3hr|rep1	PGR	GSM1669115
106	GSM1669116.sga	T47D|PGR|PG 3hr|rep1	PGR	GSM1669116
107	GSM1669117.sga	T47D|PGR|E2+PG 3hr|rep1	PGR	GSM1669117
108	GSM1669118.sga	T47D|PGR|Vehicle 3hr|rep2	PGR	GSM1669118
109	GSM1669119.sga	T47D|PGR|E2 3hr|rep2	PGR	GSM1669119
110	GSM1669120.sga	T47D|PGR|PG 3hr|rep2	PGR	GSM1669120
111	GSM1669121.sga	T47D|PGR|E2+PG 3hr|rep2	PGR	GSM1669121
112	GSM1669122.sga	T47D|PGR|Vehicle 3hr|rep3	PGR	GSM1669122
113	GSM1669123.sga	T47D|PGR|E2 3hr|rep3	PGR	GSM1669123
114	GSM1669124.sga	T47D|PGR|PG 3hr|rep3	PGR	GSM1669124
115	GSM1669125.sga	T47D|PGR|E2+PG 3hr|rep3	PGR	GSM1669125
116	GSM1669126.sga	Xenograft_MCF7|input|Vehicle|rep1	input	GSM1669126
117	GSM1669127.sga	Xenograft_MCF7|input|Vehicle|rep2	input	GSM1669127
118	GSM1669128.sga	Xenograft_MCF7|input|E2+PG|rep1	input	GSM1669128
119	GSM1669129.sga	Xenograft_MCF7|input|E2+PG|rep2	input	GSM1669129
120	GSM1669130.sga	Xenograft_MCF7|input|E2|rep1	input	GSM1669130
121	GSM1669131.sga	Xenograft_MCF7|input|E2|rep2	input	GSM1669131
122	GSM1669132.sga	Xenograft_MCF7|ESR1|Vehicle|rep1	ESR1	GSM1669132
123	GSM1669133.sga	Xenograft_MCF7|ESR1|Vehicle|rep2	ESR1	GSM1669133
124	GSM1669134.sga	Xenograft_MCF7|ESR1|E2+PG|rep3	ESR1	GSM1669134
125	GSM1669135.sga	Xenograft_MCF7|ESR1|E2+PG|rep4	ESR1	GSM1669135
126	GSM1669136.sga	Xenograft_MCF7|ESR1|E2+PG|rep5	ESR1	GSM1669136
127	GSM1669137.sga	Xenograft_MCF7|ESR1|E2+PG|rep6	ESR1	GSM1669137
128	GSM1669138.sga	Xenograft_MCF7|ESR1|E2+PG|rep7	ESR1	GSM1669138
129	GSM1669139.sga	Xenograft_MCF7|ESR1|E2+PG|rep8	ESR1	GSM1669139
130	GSM1669140.sga	Xenograft_MCF7|ESR1|E2|rep9	ESR1	GSM1669140
131	GSM1669141.sga	Xenograft_MCF7|ESR1|E2|rep10	ESR1	GSM1669141
132	GSM1669142.sga	Xenograft_MCF7|ESR1|E2|rep11	ESR1	GSM1669142
133	GSM1669143.sga	Xenograft_MCF7|ESR1|E2|rep12	ESR1	GSM1669143
134	GSM1669144.sga	Xenograft_MCF7|ESR1|E2|rep13	ESR1	GSM1669144
135	GSM1669145.sga	Xenograft_MCF7|ESR1|E2|rep14	ESR1	GSM1669145
136	GSM1669146.sga	Xenograft_MCF7|PGR|Vehicle|rep1	PGR	GSM1669146
137	GSM1669147.sga	Xenograft_MCF7|PGR|Vehicle|rep2	PGR	GSM1669147
138	GSM1669148.sga	Xenograft_MCF7|PGR|E2+PG|rep3	PGR	GSM1669148
139	GSM1669149.sga	Xenograft_MCF7|PGR|E2+PG|rep4	PGR	GSM1669149
140	GSM1669150.sga	Xenograft_MCF7|PGR|E2+PG|rep5	PGR	GSM1669150
141	GSM1669151.sga	Xenograft_MCF7|PGR|E2+PG|rep6	PGR	GSM1669151
142	GSM1669152.sga	Xenograft_MCF7|PGR|E2+PG|rep7	PGR	GSM1669152
143	GSM1669153.sga	Xenograft_MCF7|PGR|E2+PG|rep8	PGR	GSM1669153
144	GSM1669154.sga	Xenograft_MCF7|PGR|E2|rep9	PGR	GSM1669154
145	GSM1669155.sga	Xenograft_MCF7|PGR|E2|rep10	PGR	GSM1669155
146	GSM1669156.sga	Xenograft_MCF7|PGR|E2|rep11	PGR	GSM1669156
147	GSM1669157.sga	Xenograft_MCF7|PGR|E2|rep12	PGR	GSM1669157
148	GSM1669158.sga	Xenograft_MCF7|PGR|E2|rep13	PGR	GSM1669158
149	GSM1669159.sga	Xenograft_MCF7|PGR|E2|rep14	PGR	GSM1669159

Quality Control and Analysis

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. 1.5.3).

• Mohammed H, Russell IA, Stark R, Rueda OM, Hickey TE, Tarulli GA, Serandour AA, Birrell SN, Bruna A, Saadi A, Menon S, Hadfield J, Pugh M, Raj GV, Brown GD, D'Santos C, Robinson JL, Silva G, Launchbury R, Perou CM, Stingl J, Caldas C, Tilley WD, Carroll JS
  Progesterone receptor modulates ERα action in breast cancer. Nature. 2015 Jul 16;523(7560):313-7. doi: 10.1038/nature14583. Epub 2015 Jul 8. 26153859
• GEO series GSE68359: Progesterone receptor directs a distinct estrogen receptor-alpha chromatin binding profile in breast cancer to elicit good clinical outcome

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