|
| Status |
Public on Jan 18, 2021 |
| Title |
ZR-75-1_xeno_Input_Veh |
| Sample type |
SRA |
| |
|
| Source name |
ZR-75-1 cell line xenograft tumour
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: ZR-75-1 cell line xenograft tumour
treatment: Vehicle
time point: Short-term (5 days treatment)
chip antibody: Pooled input
|
| Treatment protocol |
Mice were randomly assigned to treatment groups and treated for 5 days with either a vehicle, DHT, or enobosarm. Enobosarm (10mg/kg/day) was dissolved in 10% Tween80 and delivered daily by oral gavage. DHT pellets were surgically implanted subcutaneously. After 5 days, tumours were excised and snap-frozen.
|
| Growth protocol |
Athymic nude mice were subcutaneously implanted with an E2 pellet and injected with 5x10^6 (20µl) ZR-75-1 cells into the fourth inguinal mammary fat pad. Tumours were allowed to grow until reaching ~200mm3 size before beginning treatment.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tumours were cut into 30µm slices on a cryostat and fixed with formaldehyde for 10m prior to quenching. Chromatin was prepared and subsequently sheared by the Diagenode BioRuptor Pico for 8 cycles (30 sec on, 30 sec off) on ice. Sheared chromatin was immunoprecipitated with AR or ERα antibody overnight, after coupling to Protein A Dynabeads (10002D). DNA was purified using phenol:chloroform:isoamyl alcohol extraction.
Libraries were prepared according to manufacturer's instructions.
ChIP-Seq; Illumina NextSeq 500 (High Output v2) single-end 75 bp reads.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
FASTQ files were aligned to hg19 using bwa (v0.7.15; default parameters) (Li & Durbin, 2009).
Mapped reads were filtered using a minimum MAPQ quality score of 15.
Mapped reads with a minimum MAPQ <15 were removed using SAMtools and peaks were called using MACS2 (default settings).
Consensus peaksets were obtained through DiffBind.
Genome_build: hg19
Supplementary_files_format_and_content: Consensus bed files were generated corresponding to shared peaks found within any two replicate experiments. Bigwig files, representing an average enrichment signal from all replicates, were created using HOMER (Heinz et al. 2010).
|
| |
|
| Submission date |
Dec 13, 2018 |
| Last update date |
Jan 18, 2021 |
| Contact name |
Luke Selth |
| E-mail(s) |
luke.selth@flinders.edu.au
|
| Organization name |
Flinders University
|
| Department |
College of Medicine and Public Health
|
| Street address |
Flinders Drive
|
| City |
Bedford Park |
| State/province |
SA |
| ZIP/Postal code |
5042 |
| Country |
Australia |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE123764 |
The Androgen Receptor is a Tumor Suppressor in Estrogen Receptor Positive Breast Cancer [ZR-75-1 xenograft ChIP-seq] |
| GSE123770 |
The Androgen Receptor is a Tumor Suppressor in Estrogen Receptor Positive Breast Cancer |
|
| Relations |
| BioSample |
SAMN10587999 |
| SRA |
SRX5128110 |
