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
2014-01-14
ENA last update
2018-03-08
External Id
SAMEA2163244
INSDC center alias
Cancer Research UK Cambridge Institute
INSDC center name
Cancer Research UK Cambridge Institute
INSDC first public
2014-01-14T17:00:44Z
INSDC last update
2018-03-08T16:35:52Z
INSDC status
public
Submitter Id
E-MTAB-1749:MDA-MB-453
broker name
ArrayExpress
cell line
MDA-MB-453
cell type
epithelial
common name
human
sample name
E-MTAB-1749:MDA-MB-453
sex
female
specimen with known storage state
fresh specimen

Sequenced DNA Library

library_name
jc1041
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
The LNCaP prostate cancer cell line and the ER-AR+ molecular apocrine breast cancer cell line, MDA-MB-453, were obtained from American Type Culture Collection (ATCC). Cells were grown in RPMI or DMEM media respectively, both supplemented with 10% Fetal Bovine Serum, 2 mM L-glutamine, 50U/ml penicillin and 50ug/ml streptomycin in 37oC incubator with 5% CO2. Cells were transfected with 3ug pcDNA3.1_FoxA1 which expresses full length FOXA1 cDNA. Cells were harvested 48hours after treatment. For all experiments, 1x10^8 cells were cross-linked with 1% formaldehyde as previously described (Schmidt et al, Methods 48(3) July 2009 doi:10.1016/j.ymeth.2009.03.001). ChIP-seq assays were performed as previously described (Schmidt 2009). Protein-bound DNA was immunoprecipitated with an antibody against androgen receptor (AR) (Santa Cruz, sc-816). Immunoprecipitated DNA was end-repaired, A-tailed and single-end Illumina sequencing adapter ligated before 18 cycles of PCR amplification. A 2% agarose gel was used to select 200-300 bp DNA fragments.

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

hg38

Number of total reads
17690596
Reads aligned (%)
83.0
Duplicates removed (%)
15.7
Number of peaks
13584 (qval < 1E-05)

hg19

Number of total reads
17690596
Reads aligned (%)
82.4
Duplicates removed (%)
16.5
Number of peaks
13833 (qval < 1E-05)

Base call quality data from DBCLS SRA