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Sample GSM1669081 Query DataSets for GSM1669081
Status Public on May 22, 2015
Title JC2337_MCF7_ER_3hr_E2+PG r1
Sample type SRA
 
Source name MCF7_ER_3hr_E2+PG
Organism Homo sapiens
Characteristics cell line: MCF7
cell type: ER+ breast cancer cell line
condition: E2+PG
chip antibody: ERα Antibody (HC-20)
chip antibody vendor: Santa Cruz
chip antibody cat. #: sc-543
chip antibody lot #: A2213
Treatment protocol Cells were treated with progesterone (100nM) or R5020 (10nM) for 3hr and immunoprecipitated, and DNA extracted.
Growth protocol Cells grown in DMEM, supplemented with 10% FBS
Extracted molecule genomic DNA
Extraction protocol Immunoprecipitated DNA was end-repaired, A-tailed, ligated to the sequencing adapters, amplified by 18 cycles of PCR and size selected (200-300 bp) followed by single end 50bp sequencing on an Illumina HiSeq 2000 according to the manufacturer’s recommendations
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Description ChIP for ER in MCF7 cell line after 3 hours treatment with E2+PG [Replicate 1]
Data processing Single-end reads were aligned against the Human Reference Genome (assembly hg19, NCBI GRCH37) using BWA version 0.5.5. Reads were filtered by removing those with a BWA alignment quality score less than 15. A further filtration was carried out by removing reads falling into the 'blacklist' regions identified by ENCODE.
Quality was confirmed using Biocnoductor package ChIPQC. Peaks we called using MACS v 1.4.1.
The Bioconductor package DiffBind was used to determine clustering, formulate consensus peaksets, and identify differentially bound sites.
Genome_build: hg19, Genome Reference Consortium GRCh37
Supplementary_files_format_and_content: MACS peaks in .csv file format (named as .txt as per MACS software)
 
Submission date Apr 28, 2015
Last update date May 15, 2019
Contact name Chandra Chilamakuri
E-mail(s) datasubmissions@cruk.cam.ac.uk
Organization name Cancer Research UK Cambridge Institute
Street address Robinson Way
City Cambridge
ZIP/Postal code CB2 0RE
Country United Kingdom
 
Platform ID GPL11154
Series (2)
GSE68356 ChIP-seq of ERa and PR in two ER+ breast cancer cell lines treated with and without estrogen and with and without progestins
GSE68359 Progesterone receptor directs a distinct estrogen receptor-alpha chromatin binding profile in breast cancer to elicit good clinical outcome
Relations
BioSample SAMN03570691
SRA SRX1012681

Supplementary file Size Download File type/resource
GSM1669081_jc2337MCF7ERE2+PGRep1.bwa_Processed_peaks.txt.gz 371.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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