Sample information curated by ChIP-Atlas

Antigen

Antigen Class
No description
Antigen
NA

Cell type

Cell type Class
Breast
Cell type
MDA-MB-231
Primary Tissue
Breast
Site of Extraction
Effusion, Pleural
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

ENA first public
2013-12-12
ENA last update
2018-03-08
ENA-CHECKLIST
ERC000011
External Id
SAMEA2177590
INSDC center alias
Cancer Research UK Cambridge Institute
INSDC center name
Cancer Research UK Cambridge Institute
INSDC first public
2013-12-12T17:01:17Z
INSDC last update
2018-03-08T16:41:37Z
INSDC status
public
Submitter Id
E-MTAB-1827:MDA-MB-231
broker name
ArrayExpress
cell line
MDA-MB-231
cell type
epithelial
common name
human
sample name
E-MTAB-1827:MDA-MB-231
sex
female
specimen with known storage state
fresh specimen

Sequenced DNA Library

library_name
jc1345
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
The MCF-7, MDA-MB-231, MDA-MB-453, LNCaP and ZR-75-1 cell lines were obtained from American Type Culture Collection (ATCC). Cells were grown in DMEM (MCF-7, MDA-MB-231 and MDA-MB-453) or RPMI (LNCaP and ZR-75-1), both supplemented with 10% Fetal Bovine Serum, 2 mM L-glutamine, 50U/ml penicillin and 50ug/ml streptomycin in 37_C incubator with 5% CO2. 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). The ChIP assays were performed as previously described (Schmidt et al., 2009). Protein-bound DNA was immunoprecipitated with antibodies against COT2/COUP-TFII (R&D Systems, PP-H7147-00), FoxA1 (Abcam, ab5089), ER (Santa-Cruz, sc-543), FoxA2 (Santa-Cruz, sc-6554) and P300 (Santa-Cruz, sc-585). For the ChIP-exo library preparation, the immunoprecipitated chromatin was end-repaired, ligated to the TruSeq P7 exo-adapter, nick repaired, digested with the lambda and the RecJf exonucleases. The digested DNA was extracted, second-strand synthesised with the P7 primer, ligated to the TruSeq P5 exo-adapter and finally amplified with 18 PCR cycles. 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
34922228
Reads aligned (%)
72.7
Duplicates removed (%)
49.7
Number of peaks
10152 (qval < 1E-05)

hg19

Number of total reads
34922228
Reads aligned (%)
72.2
Duplicates removed (%)
51.2
Number of peaks
10693 (qval < 1E-05)

Base call quality data from DBCLS SRA