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
2011-10-24
ENA last update
2018-03-08
External Id
SAMEA1094184
INSDC center alias
CRI
INSDC center name
Cancer Research UK Cambridge Research Institute
INSDC first public
2011-10-24T15:04:21Z
INSDC last update
2018-03-08T15:29:33Z
INSDC status
public
Submitter Id
E-MTAB-785:MCF-7
broker name
ArrayExpress
cell line
MCF-7
cell type
epithelial
common name
human
organism part
breast
sample name
E-MTAB-785:MCF-7
sex
female

Sequenced DNA Library

library_name
jc490
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
MCF7 cells were grown in DMEM medium, supplemented with 8% FBS and standard antibiotics. Three days prior to hormonal treatment, cells were switched to phenolred-free DMEM, supplemented with 5% charcoal-treated FBS and standard antibiotics. Medium was replaced daily. Serum-deprived MCF7 cells were treated with 20ml Ethanol control for 2 hours and 50 minutes, after which cells were fixed with 1% PFA and processed as described (Schmidt et al., Methods 48:3 pp240-248 2009). Cell lysis and precipitation procedures were performed as described (Schmidt et al., Methods 48:3 pp240-248 2009).

Sequencing Platform

instrument_model
Illumina Genome Analyzer II

hg38

Number of total reads
27885785
Reads aligned (%)
98.6
Duplicates removed (%)
12.9
Number of peaks
584 (qval < 1E-05)

hg19

Number of total reads
27885785
Reads aligned (%)
97.8
Duplicates removed (%)
14.5
Number of peaks
1081 (qval < 1E-05)

Base call quality data from DBCLS SRA