|
| Status |
Public on Jun 01, 2016 |
| Title |
T47D_E2+R5020_45 mins_ERPRComplex_reChIP |
| Sample type |
SRA |
| |
|
| Source name |
Breast cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue type: ER+/PR+ cell models
cell line: T47D
er/pr status: ER+/PR+
drug treatment: 10nM Estradiol + 10 nM R5020
hormone exposure time: 45 minutes
|
| Treatment protocol |
Steroid-deprived cell models were treated with 10 nM estradiol, 10 nM R5020 or 10 nM of both the hormones for 45 minutes.
|
| Growth protocol |
ChIP-seq and reChIP-seq: Cells were cultured for 48 hours in charcoal-stripped serum media to deprive them of steroids.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Hormone-treated were harvested and ChIP was performed as per the directions provided in materials and method (ChIP and ChIP-sequencing; reChIP and reChIP-sequencing)
ChIP-seq and reChIP-seq libraries were prepared using Kapa ChIP-seq kits.
Details of library preparation strategy are provided in the materials and methods section (ChIP and ChIP-seq; reChIP and reChIP-seq) of the paper.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
anti-ER (SC biotech HC-20) ChIP plus anti-PR (inhouse KD68) ChIP
reChIP-seq
Processed data file: T47D(reChIP)_ERPRComplexes_E2+R5020_RC3 (subtracted Veh and IgG).bed
|
| Data processing |
The FASTQ files were filtered and good quality reads were groomed and subsequently aligned to HG19 genome build using Bowtie2
The output from Bowtie2 (BAM files) was subjected to MACS14 to call ChIP-seq peaks. Corresponding inputs for each of the treatment conditions were used as the background.
If needed, the ChIP-seq peaks thus obtained were filtered based on false discovery rates and height of the peaks.
Vehicle treated ChIP-peaksets were subtracted from the hormone-treated ChIP-peaksets. For reChIP-seq, the reChIP peaks obtained after vehicle treatment as well as the reChIP peaks observed upon second pulldown with control IgG were used as controls. Hence, both of the reChIP controls were subtracted from the reChIP-signal obtained on joint estradiol plus R5020 treatment.
Genome_build: HG19
Supplementary_files_format_and_content: BED files
|
| |
|
| Submission date |
Apr 10, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Hari Singhal |
| E-mail(s) |
hari_singhal@dfci.harvard.edu
|
| Organization name |
University of Chicago
|
| Department |
Ben May Department for Cancer Research
|
| Lab |
Geoffrey L Greene
|
| Street address |
929 E 57th St
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE80098 |
Genomic agonism and phenotypic antagonism between estrogen and progesterone receptors in breast cancer. |
| GSE80367 |
Genomic agonism and phenotypic antagonism between estrogen and progesterone receptors in breast cancer. [ChIP-seq] |
|
| Relations |
| BioSample |
SAMN04631312 |
| SRA |
SRX1688801 |
