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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
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
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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