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Sample GSM2648923 Query DataSets for GSM2648923
Status Public on Dec 31, 2017
Title ER_ChIP-seq_MCF7_45min_R5020
Sample type SRA
 
Source name MCF7 cells
Organism Homo sapiens
Characteristics cell line: MCF7
er/pr status: ER+/PR+
drug treatment: 10 nM R5020
hormone exposure time: 45 minutes
protocol: Cell models ChIP-seq
chip antibody: anti-ER (SC biotech HC-20, cat# SC-543, lot# L1911)
Treatment protocol Steroid-deprived cell models were treated with 10 nM estradiol, 10 nM NR3C ligand (progesterone, dexamethasone, DHT or aldosterone) or 10 nM of both the hormones for 45 minutes or 4 hours.
Growth protocol 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)
ChIP-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) of the paper.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
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.
Genome_build: HG19
Supplementary_files_format_and_content: BED files
 
Submission date Jun 02, 2017
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 GPL18573
Series (1)
GSE99626 Combinatorial Reprogramming of Estrogen Signaling by the Nuclear Receptor Family 3C
Relations
BioSample SAMN07190082
SRA SRX2881008

Supplementary file Size Download File type/resource
GSM2648923_ERPR_ER_R5020_sort_peaks.narrowPeak.gz 15.5 Kb (ftp)(http) NARROWPEAK
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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