Ponnusamy 2019, ChIP-seq against ESR1, AR and FOXA1 in enobosarm treated breast cancer xenografts.

ChIP-seq was applied to two breast cancer patient-derived xenografts in order to study the relocalization of ER (ESR1), AR and FOXA1 in response to enobosarm treatment. Enobosarm is a tissue-selective AR agonist. Xenograft HCI-013 expresses mutated AR plus ER, whereas HCI-009 expresses only AR. More information about these xenografts can be found at:

http://www.pdxfinder.org/data/pdx/HCI-BCM/HCI-013

http://www.pdxfinder.org/data/pdx/HCI-BCM/HCI-009

Source

Samples

ChIP-seq data:

	Filename	Description	Feature	GEO-ID
1	GSM3660468.sga	BC PDX HCI-09\|AR\|ENOB	AR	GSM3660468
2	GSM3660469.sga	BC PDX HCI-09\|AR\|vehicle	AR	GSM3660469
3	GSM3660493.sga	BC PDX HCI-09\|Input	Input	GSM3660493
4	GSM3660488.sga	BC PDX HCI-13\|ESR1\|ENOB\|S181	ESR1	GSM3660488
5	GSM3660489.sga	BC PDX HCI-13\|ESR1\|ENOB\|S182	ESR1	GSM3660489
6	GSM3660490.sga	BC PDX HCI-13\|ESR1\|ENOB\|S186	ESR1	GSM3660490
7	GSM3660492.sga	BC PDX HCI-13\|ESR1\|ENOB\|S440	ESR1	GSM3660492
8	GSM3660485.sga	BC PDX HCI-13\|ESR1\|vehicle\|S176	ESR1	GSM3660485
9	GSM3660486.sga	BC PDX HCI-13\|ESR1\|vehicle\|S177	ESR1	GSM3660486
10	GSM3660487.sga	BC PDX HCI-13\|ESR1\|vehicle\|S179	ESR1	GSM3660487
11	GSM3660491.sga	BC PDX HCI-13\|ESR1\|vehicle\|S440	ESR1	GSM3660491
12	GSM3660470.sga	BC PDX HCI-13\|AR\|ENOB\|rep1	AR	GSM3660470
13	GSM3660471.sga	BC PDX HCI-13\|AR\|ENOB\|rep2	AR	GSM3660471
14	GSM3660472.sga	BC PDX HCI-13\|AR\|ENOB\|rep3	AR	GSM3660472
15	GSM3660473.sga	BC PDX HCI-13\|AR\|vehicle\|rep1	AR	GSM3660473
16	GSM3660474.sga	BC PDX HCI-13\|AR\|vehicle\|rep2	AR	GSM3660474
17	GSM3660475.sga	BC PDX HCI-13\|AR\|vehicle\|rep3	AR	GSM3660475
18	GSM3660476.sga	BC PDX HCI-13\|AR\|vehicle\|rep4	AR	GSM3660476
19	GSM3660477.sga	BC PDX HCI-13\|FOXA1\|ENOB\|rep1	FOXA1	GSM3660477
20	GSM3660478.sga	BC PDX HCI-13\|FOXA1\|ENBO\|rep2	FOXA1	GSM3660478
21	GSM3660479.sga	BC PDX HCI-13\|FOXA1\|ENOB\|rep3	FOXA1	GSM3660479
22	GSM3660480.sga	BC PDX HCI-13\|FOXA1\|ENOB\|rep4	FOXA1	GSM3660480
23	GSM3660481.sga	BC PDX HCI-13\|FOXA1\|vehicle\|rep1	FOXA1	GSM3660481
24	GSM3660482.sga	BC PDX HCI-13\|FOXA1\|vehicle\|rep2	FOXA1	GSM3660482
25	GSM3660483.sga	BC PDX HCI-13\|FOXA1\|vehicle\|rep3	FOXA1	GSM3660483
26	GSM3660484.sga	BC PDX HCI-13\|FOXA1\|vehicle\|rep4	FOXA1	GSM3660484
27	GSM3660494.sga	BC PDX HCI-13\|Input	Input	GSM3660494

Notes on samples nomenclature:

Abbreviations: BC, breast cancer; ENOB, enobosarm

The information contained in the sample descriptions was extracted manually from the GEO sample titles and the filenames of bigWig supplementary files provided by GEO. The fourth field, if present, contains either a replicate number (e.g. rep1) or an identifier for an individual xenograft tumor grown in a mouse (e.g S181). These identifiers correspond to the data track labels appearing in Figures S5, S7 and S8 in Ponnusamy et al. 2019 (see reference below).

Quality Control and Analysis

Technical Notes

FASTQ files were extracted from SRA files using fastq-dump (SRA toolkit v2.5.0) and mapped to the genome using Bowtie 2 v2.2.9 in paired-end mapping mode. SAM files were then converted to BAM using samtools v1.9 and to BED using bamToBed v2.27.0 (bedtools). BED to SGA conversion was carried out using bed2sga (ChIP-Seq v. 1.5.5).

References

Ponnusamy S, Asemota S, Schwartzberg LS, Guestini F, McNamara KM, Pierobon M, Font-Tello A, Qiu X, Xie Y, Rao PK, Thiyagarajan T, Grimes B, Johnson DL, Fleming MD, Pritchard FE, Berry MP, Oswaks R, Fine RE, Brown M, Sasano H, Petricoin EF, Long HW, Narayanan R
Androgen Receptor Is a Non-canonical Inhibitor of Wild-Type and Mutant Estrogen Receptors in Hormone Receptor-Positive Breast Cancers. iScience. 2019 Nov 22;21:341-358. doi: 10.1016/j.isci.2019.10.038. Epub 2019 Oct 23. 31698248
GEO series GSE128018: Androgen Receptor is a Backdoor Inhibitor of Wildtype and Mutant Estrogen Receptors in Refractory Hormone Receptor-Positive Breast Cancers