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:



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

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).


Last update: 24 Mar 2020, Philipp Bucher