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
2014-04-17
ENA last update
2018-03-08
External Id
SAMEA2080601
INSDC center alias
CR-UK Cambridge Institute
INSDC center name
CR-UK Cambridge Institute
INSDC first public
2014-04-17T17:00:42Z
INSDC last update
2018-03-08T16:30:11Z
INSDC status
public
Submitter Id
E-MTAB-1694:MDA-MB-453
broker name
ArrayExpress
cell line
MDA-MB-453
cell type
epithelial
common name
human
sample name
E-MTAB-1694:MDA-MB-453
sex
female
specimen with known storage state
fresh specimen

Sequenced DNA Library

library_name
jc815
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
The ER-AR+ molecular apocrine breast cancer cell line, MDA-MB-453, was obtained from American Type Culture Collection (ATCC). Cells were grown in DMEM media 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 50nM siFoxA1 (either GAGAGAAAAAAUCAACAGC, siFoxA1#1 or siGenome pool, siFoxA1#2 (Dharmacon, Cat. M-010319-01). 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 antibodies against AR (Santa Cruz, sc-816), AP2alpha (Santa Cruz, sc-12726) or the histone modifications H3K27Ac (Abcam, ab4729) and H3K4me1 (Abcam, 8895). Immunoprecipitated DNA was end-repaired, A-tailed and single-end Illumina sequencing adapters 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
28050418
Reads aligned (%)
99.0
Duplicates removed (%)
1.6
Number of peaks
4551 (qval < 1E-05)

hg19

Number of total reads
28050418
Reads aligned (%)
98.4
Duplicates removed (%)
2.6
Number of peaks
4632 (qval < 1E-05)

Base call quality data from DBCLS SRA