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Sample GSM2112805 Query DataSets for GSM2112805
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

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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