Ross-Inness 2012, breast cancer, ER and FOXA1. LiftOver from hg18.

ChIP-Seq for ER and FOXA1 in breast cancer tumors and cell lines. Samples include eight primary tumors from patients with good prognosis (ER+ PR+ HER2-), seven primary tumors from patients with poor outcome (ER+ PR- HER2- or ER+ PR+ HER2+), three ER+ distant metastases, two ER- tumors, and five breast cancer cell lines grown under two different different conditions. Input used as control.

• Raw data was downloaded from GEO series: GSE322222
• Input file format: BAM

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

ChIP-seq data:

	Filename	Description	Feature	GEO-ID
1	GSM798384_BT82590_ER_Responder.sga	tumor BT82590(good) ER	ER	GSM798384
2	GSM798407_BT82590_none_Responder.sga	tumor BT82590(good) Input	Input	GSM798407
3	GSM798383_BT82597_ER_Responder.sga	tumor BT82597(good) ER	ER	GSM798383
4	GSM798406_BT82597_none_Responder.sga	tumor BT82597(good) Input	Input	GSM798406
5	GSM798385_CC106585_T3_ER_Responder.sga	tumor CC106585(good) ER	ER	GSM798385
6	GSM798386_CX627219_T4_ER_Responder.sga	tumor CX627219(good) ER	ER	GSM798386
7	GSM798408_CX627219_T4_none_Responder.sga	tumor CX627219(good) Input	Input	GSM798408
8	GSM798391_NT2289_ER_Responder.sga	tumor NT2289(good) ER	ER	GSM798391
9	GSM798412_NT2289_none_Responder.sga	tumor NT2289(good) Input	Input	GSM798412
10	GSM798389_NT2433_ER_Responder.sga	tumor NT2433(good) ER	ER	GSM798389
11	GSM798410_NT2433_none_Responder.sga	tumor NT2433(good) Input	Input	GSM798410
12	GSM798387_NT2304_ER_Responder.sga	tumor NT2304(good) ER rep1	ER	GSM798387
13	GSM798388_NT2304_ER_Responder.sga	tumor NT2304(good) ER rep2	ER	GSM798388
14	GSM798409_NT2304_none_Responder.sga	tumor NT2304(good) Input	Input	GSM798409
15	GSM798390_NT2360_ER_Responder.sga	tumor NT2360(good) ER	ER	GSM798390
16	GSM798411_NT2360_none_Responder.sga	tumor NT2360(good) Input	Input	GSM798411
17	GSM798400_BT81583_ER_Non-responder.sga	tumor BT81583(poor) ER	ER	GSM798400
18	GSM798417_BT81583_none_Non-responder.sga	tumor BT81583(poor) ER	Input	GSM798417
19	GSM798398_BT81585_ER_Non-responder.sga	tumor BT81585(poor) ER rep1	ER	GSM798398
20	GSM798399_BT81585_ER_Non-responder.sga	tumor BT81585(poor) ER rep2	ER	GSM798399
21	GSM798416_BT81585_none_Non-responder.sga	tumor BT81585(poor) Input	Input	GSM798416
22	GSM798392_CC316812_T1_ER_Non-responder.sga	tumor CC316812(poor) ER	ER	GSM798392
23	GSM798393_CC135745_T2_ER_Non-responder.sga	tumor CC135745(poor) ER	ER	GSM798393
24	GSM798394_NT2138_ER_Non-responder.sga	tumor NT2138(poor) ER	ER	GSM798394
25	GSM798413_NT2138_none_Non-responder.sga	tumor NT2138(poor) Input	Input	GSM798413
26	GSM798395_NT2171_ER_Non-responder.sga	tumor NT2171(poor) ER	ER	GSM798395
27	GSM798414_NT2171_none_Non-responder.sga	tumor NT2171(poor) Input	Input	GSM798414
28	GSM798396_NT2350_ER_Non-responder.sga	tumor NT2350(poor) ER rep1	ER	GSM798396
29	GSM798397_NT2350_ER_Non-responder.sga	tumor NT2350(poor) ER rep2	ER	GSM798397
30	GSM798415_NT2350_none_Non-responder.sga	tumor NT2350(poor) Input	Input	GSM798415
31	GSM798405_NT2079_ER_ER-.sga	tumor NT2079(ERneg) ER	ER	GSM798405
32	GSM798422_NT2079_none_ER-.sga	tumor NT2079(ERneg) Input	Input	GSM798422
33	GSM798404_NT2229_ER_ER-.sga	tumor NT2229(ERneg) ER	ER	GSM798404
34	GSM798421_NT2229_none_ER-.sga	tumor NT2229(ERneg) Input	Input	GSM798421
35	GSM798401_Met_T1_ER_Metastasis.sga	metastasis T1 ER	ER	GSM798401
36	GSM798418_Met_T1_none_Metastasis.sga	metastasis T1 Input	Input	GSM798418
37	GSM798402_Met_T3_ER_Metastasis.sga	metastasis T3 ER	ER	GSM798402
38	GSM798419_Met_T3_none_Metastasis.sga	metastasis T3 Input	Input	GSM798419
39	GSM798403_Met_T4_ER_Metastasis.sga	metastasis T4 ER	ER	GSM798403
40	GSM798420_Met_T4_none_Metastasis.sga	metastasis T4 Input	Input	GSM798420
41	GSM798423_MCF7_ER_Tam-Responsive.sga	cell-line MCF7 ER rep1	ER	GSM798423
42	GSM798424_MCF7_ER_Tam-Responsive.sga	cell-line MCF7 ER rep2	ER	GSM798424
43	GSM798425_MCF7_ER_Tam-Responsive.sga	cell-line MCF7 ER rep3	ER	GSM798425
44	GSM798434_MCF7_ER_Cocktail_90.sga	cell-line MCF7 ER Cocktail rep1	ER	GSM798434
45	GSM798435_MCF7_ER_Cocktail_90.sga	cell-line MCF7 ER Cocktail rep2	ER	GSM798435
46	GSM798437_MCF7_FOXA1_Veh_90.sga	cell-line MCF7 FOXA1 Vehicle rep1	FOXA1	GSM798437
47	GSM798439_MCF7_FOXA1_Veh_90.sga	cell-line MCF7 FOXA1 Vehicle rep2	FOXA1	GSM798439
48	GSM798436_MCF7_FOXA1_Cocktail_90.sga	cell-line MCF7 FOXA1 Cocktail rep1	FOXA1	GSM798436
49	GSM798438_MCF7_FOXA1_Cocktail_90.sga	cell-line MCF7 FOXA1 Cocktail rep2	FOXA1	GSM798438
50	GSM798440_MCF7_Input_Tam-Responsive.sga	cell-line MCF7 Input	Input	GSM798440
51	GSM798426_ZR75_ER_Tam-Responsive.sga	cell-line ZR75 ER rep1	ER	GSM798426
52	GSM798427_ZR75_ER_Tam-Responsive.sga	cell-line ZR75 ER rep2	ER	GSM798427
53	GSM798441_ZR75_Input_Tam-Responsive.sga	cell-line ZR75 Input	Input	GSM798441
54	GSM798428_T47D_ER_Tam-Responsive.sga	cell-line T47D ER rep1	ER	GSM798428
55	GSM798429_T47D_ER_Tam-Responsive.sga	cell-line T47D ER rep2	ER	GSM798429
56	GSM798442_T47D_Input_Tam-Responsive.sga	cell-line T47D Input	Input	GSM798442
57	GSM798430_BT474_ER_Tam-Resist.sga	cell-line BT474 ER rep1	ER	GSM798430
58	GSM798431_BT474_ER_Tam-Resist.sga	cell-line BT474 ER rep2	ER	GSM798431
59	GSM798443_BT474_Input_Tam-Resist.sga	cell-line BT474 Input	Input	GSM798443
60	GSM798432_TAMR_ER_Tam-Resist.sga	cell-line TAM-R ER rep1	ER	GSM798432
61	GSM798433_TAMR_ER_Tam-Resist.sga	cell-line TAM-R ER rep2	ER	GSM798433
62	GSM798444_TAMR_Input_Tam-Resist.sga	cell-line TAM-R Input	Input	GSM798444

Notes on samples nomenclature:

• Tumor identifiers were taken from GEO sample documentation.
• We were unable to match the names used in Ross-Innes et al. 2012 (G1, G2, etc.) with those provided by GEO (e.g. BT81583).
• The nomenclature of cell lines and conditions is based on Supplementary figure 2 from Ross-Innes et al. 2012.

• Strand correlation plots: ross12_strand_cor.pdf
• ESR1 ChIP-seq tag enrichment around bound ESR1 motifs: ross12_ESR1_enr.pdf

The sga files were automatically generated from the original BAM files providing the starting and ending postions of mapped sequence tags in the human genome assembly 2006 (NCBI36/hg18).

• Ross-Innes CS, Stark R, Teschendorff AE, Holmes KA, Ali HR, Dunning MJ, Brown GD, Gojis O, Ellis IO, Green AR, Ali S, Chin SF, Palmieri C, Caldas C, Carroll JS
  Differential oestrogen receptor binding is associated with clinical outcome in breast cancer. Nature. 2012 Jan 4;481(7381):389-93. doi: 10.1038/nature10730. 22217937
• GEO series GSE32222: Differential oestrogen receptor binding is associated with clinical outcome in breast cancer