|
Status |
Public on May 22, 2015 |
Title |
JC1556_T47D_PR_Full_Media_3hr r1 |
Sample type |
SRA |
|
|
Source name |
T47D_PR_Full_Media_3hr
|
Organism |
Homo sapiens |
Characteristics |
cell line: T47D cell type: ER+ breast cancer cell line condition: Full_Media chip antibody: PR Antibody (H-190) chip antibody vendor: Santa Cruz chip antibody cat. #: sc-7208 chip antibody lot #: H2312
|
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 PR in T47D cell line after 3hr treatment with Full_Media [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 .xls as per MACS software)
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|
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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) |
GSE68355 |
ChIP-seq of ER, PR, p300 in two ER+ breast cancer cell lines treated with 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 |
SAMN03570760 |
SRA |
SRX1012615 |