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.



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:

Quality Control and Analysis

Technical Notes

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).


Last update: 5 Jul 2019