Sample information curated by ChIP-Atlas

Antigen

Antigen Class
No description
Antigen
NA

Cell type

Cell type Class
Breast
Cell type
MDA-MB-453
Primary Tissue
Breast
Site of Extraction
Effusion, Pericardial
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

ENA first public
2012-02-18
ENA last update
2018-03-08
External Id
SAMEA1094835
INSDC center alias
CRUK-CRI
INSDC center name
CRUK-CRI
INSDC first public
2012-02-18T17:00:29Z
INSDC last update
2018-03-08T15:36:05Z
INSDC status
public
Submitter Id
E-MTAB-986:MDA-MB-453
broker name
ArrayExpress
cell line
MDAMB453
cell type
epithelial
common name
human
organism part
breast
sample name
E-MTAB-986:MDA-MB-453
sex
female

Sequenced DNA Library

library_name
jc226
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
MDA-MB-453 and MCF7 cells were grown in DMEM containing 10% heat-inactivated FBS, 2 mM L glutamine, 50 U/ml penicillin and 50 _g/ml streptomycin and LNCaP cells were grown in RPMI containing 10% heat-inactivated FBS, 2 mM L glutamine, 50 U/ml penicillin and 50 _g/ml streptomycin. The antibodies used were anti-AR (sc-816) and anti-ER (sc-543) from Santa Cruz Biotechnologies and anti-FoxA1 (ab5089) from Abcam. Four 15 cm dishes of cells were used per chromatin immunoprecipitation (ChIP) and samples were processed according to standard ChIP procedures as described in Schmidt et al, Methods 48(3) July 2009 doi:10.1016/j.ymeth.2009.03.001. The immunoprecipitated DNA was subsequently amplified as previously described for Illumina sequencing (Schmidt et al, 2009).

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

hg38

Number of total reads
20362717
Reads aligned (%)
98.8
Duplicates removed (%)
1.2
Number of peaks
545 (qval < 1E-05)

hg19

Number of total reads
20362717
Reads aligned (%)
98.1
Duplicates removed (%)
2.4
Number of peaks
839 (qval < 1E-05)

Base call quality data from DBCLS SRA