|
| Status |
Public on Jan 18, 2021 |
| Title |
T-47D ER ChIP E2 Consensus |
| Sample type |
SRA |
| |
|
| Source name |
Breast cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: T-47D
passages: 14-16 (where replicates represent sequential passages)
chip antibody: ERα (HC-20)X (Santa Cruz SC-543X)
treatment: E2
|
| Treatment protocol |
T-47D cells were treated for 4 h with either 10 nM E2 or 10 nM E2 + 10 nM DHT
|
| Growth protocol |
T-47D cells were grown in hormone-deplete conditions (phenol red-free RPMI-1640 + 5% dextran-coated charcoal-stripped FBS) for 72h
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
T-47D cells were fixed with formaldehyde for 10m prior to quenching. Chromatin was prepared and subsequently sheared by the Diagenode BioRuptor Plus for 10 cycles (30 sec on, 30 sec off) on ice. Sheared chromatin was immunoprecipitated with 10µg of 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 accompanying the Qiagen Ultralow Input Library Kit (Part# 180495).
ChIP-Seq; Illumina NextSeq500 (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 |
Basecalls performed in BaseSpace.
Trimmed FASTQ files were aligned to the hg19 genome assembly using Bowtie2 (Langmead & Salzberg, 2012).
Mapped reads with a minimum MAPQ <10 and duplicate reads were removed using SAMtools (Li et al., 2009).
Peaks were called using MACS2 (Zhang et al., 2008 & Feng et al., 2012) with a pooled input sample as the control.
Peaks found in a minimum of 2 replicates (as determined using BEDTools (Quinlan & Hall, 2010)) were kept for the consensus peakset.
Genome_build: hg19
Supplementary_files_format_and_content: Consensus bed files were generated corresponding to shared peaks found within any two of three replicate experiments. An average enrichment signal from all replicates was generated by merging mapped reads for a given condition (Picard Toolkit, 2018), followed by subsequent conversion to bigwig format using deepTools (Ramirez et al. 2016).
|
| |
|
| Submission date |
Apr 17, 2019 |
| Last update date |
Jan 19, 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) |
| GSE123770 |
The Androgen Receptor is a Tumor Suppressor in Estrogen Receptor Positive Breast Cancer |
| GSE129929 |
The Androgen Receptor is a Tumor Suppressor in Estrogen Receptor Positive Breast Cancer [T-47D cell line ChIP-seq] |
|
| Relations |
| BioSample |
SAMN11445632 |
| SRA |
SRX5702620 |
