Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
NRIP1

Cell type

Cell type Class
Breast
Cell type
MCF-7
Primary Tissue
Breast
Site of Extraction
Pleura
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

ENA checklist
ERC000011
INSDC center alias
CR-UK Cambridge Institute
INSDC center name
CR-UK Cambridge Institute
INSDC first public
2015-03-16T17:04:47Z
INSDC last update
2018-03-08T17:40:18Z
INSDC status
public
SRA accession
ERS456736
Sample Name
ERS456736
alias
E-MTAB-2576:MCF-7-3
broker name
ArrayExpress
cell line
MCF-7
cell type
epithelial
organism
Homo sapiens
sex
female
specimen with known storage state
frozen specimen
title
MCF-7-3
transcription factor
RIP140

Sequenced DNA Library

library_name
jc607
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
MCF7 cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% antibiotics. For hormone depletion, cells were grown in phenol red-free DMEM with 5% charcoal-treated FBS and 1% antibiotics for 3 days. Hormone-deprived cells were treated for 3 hours with 0.01% DMSO. Cells were fixed with 1% PFA for 10 minutes and processed as described (Schmidt et al., Methods 48:3 pp240-248 2009). For each ChIP, 10ug of antibody was used, and 100ul of Protein A magnetic beads (Invitrogen). The antibody used was raised to detect RIP140 (6D7). ChIP was performed and libaries were contructed as described (Schmidt et al., Methods 48:3 pp240-248 2009).

Sequencing Platform

instrument_model
Illumina Genome Analyzer II

hg19

Number of total reads
27122677
Reads aligned (%)
84.7
Duplicates removed (%)
13.6
Number of peaks
7531 (qval < 1E-05)

hg38

Number of total reads
27122677
Reads aligned (%)
87.1
Duplicates removed (%)
12.0
Number of peaks
7472 (qval < 1E-05)

Base call quality data from DBCLS SRA