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
2013-04-01
ENA last update
2018-03-08
External Id
SAMEA1713769
INSDC center alias
Cancer Research UK Cambridge Institute
INSDC center name
Cancer Research UK Cambridge Institute
INSDC first public
2013-04-01T17:02:48Z
INSDC last update
2018-03-08T16:18:12Z
INSDC status
public
Submitter Id
E-MTAB-1534:MCF7_cells
broker name
ArrayExpress
cell line
MCF-7
cell type
epithelial
common name
human
sample name
E-MTAB-1534:MCF7_cells
sex
female

Sequenced DNA Library

library_name
jc43
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. Samples were processed and chromatin was extracted as described (Schmidt et al., Methods 48:3 pp240-248 2009) but with a number of modifications. During the immunoprecipitation, 100mg/ml glycogen (Invitrogen) or 20mg/ml recombinant histone 2B (M2505S; New England Biolabs) and 1mg/ml human mRNA (Invitrogen) was added as carriers for the ChIP. During the entire procedure, non-sticky eppendorf tubes were used (13-698-794; Fisher Scientific).

Sequencing Platform

instrument_model
Illumina Genome Analyzer II

hg38

Number of total reads
13633868
Reads aligned (%)
87.8
Duplicates removed (%)
6.6
Number of peaks
10215 (qval < 1E-05)

hg19

Number of total reads
13633868
Reads aligned (%)
87.3
Duplicates removed (%)
7.4
Number of peaks
10315 (qval < 1E-05)

Base call quality data from DBCLS SRA