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Status |
Public on Dec 31, 2017 |
Title |
ER_ChIP-seq_MCF7_45min_R5020 |
Sample type |
SRA |
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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)
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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.
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina NextSeq 500 |
|
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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
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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 |