Sample information curated by ChIP-Atlas

Antigen

Antigen Class
No description
Antigen
NA

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 first public
2010-06-12
ENA last update
2018-03-08
External Id
SAMEA717111
INSDC center alias
CRUK-CRI
INSDC center name
CRUK-CRI
INSDC first public
2010-06-12T00:00:34Z
INSDC last update
2018-03-08T15:25:00Z
INSDC status
public
Submitter Id
E-TABM-828:Era_breast_sc543_hsaMCF7_vehicle
broker name
ArrayExpress
cell line
MCF7
common name
human
organism part
breast
sample name
E-TABM-828:Era_breast_sc543_hsaMCF7_vehicle
sex
female

Sequenced DNA Library

library_name
Era_breast_sc543_hsaMCF7_vehicle
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
MCF7 human breast cancer cells were grown as previously described (Neve et al. 2006). Unless otherwise stated, during all experiments oestrogen was added at a final concentration of 100 nM for 45 minutes (ChIP) or 24 hours (cell cycle analysis). HepG2 cells were grown in DMEM supplemented with 10% FBS. ChIP experiments were performed with well-characterized antibodies against CTCF (Millipore, 07-729), STAG1 (abcam, ab4457), RAD21 (abcam, ab992), ERa (santa cruz, sc-543), CEBPa (santa cruz, sc-9314) and MED12 (abcam, ab70842). ChIP-seq experiments were performed as recently described (Schmidt et al. 2009)

Sequencing Platform

instrument_model
Illumina Genome Analyzer

hg38

Number of total reads
15002382
Reads aligned (%)
88.2
Duplicates removed (%)
15.3
Number of peaks
10920 (qval < 1E-05)

hg19

Number of total reads
15002382
Reads aligned (%)
87.6
Duplicates removed (%)
16.1
Number of peaks
11005 (qval < 1E-05)

Base call quality data from DBCLS SRA