characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2013-12-12T17:01:17Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2018-03-08T16:41:37Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA2177590
characteristics.characteristic: External Id
characteristics.text: Cancer Research UK Cambridge Institute
characteristics.characteristic: INSDC center name
characteristics.text: 2013-12-12T17:01:17Z
characteristics.characteristic: INSDC first public
characteristics.text: 2018-03-08T16:41:37Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS345684
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-1827:MDA-MB-231
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009737
characteristics.characteristic: broker name
characteristics.text: MDA-MB-231
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0001209
characteristics.characteristic: cell line
characteristics.text: epithelial
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/CL_0000066
characteristics.characteristic: cell type
characteristics.text: human
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_9606
characteristics.characteristic: common name
characteristics.text: Protocols: 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.
characteristics.characteristic: description
characteristics.text: Homo sapiens
characteristics.characteristic: organism
characteristics.text: Homo sapiens
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_9606
characteristics.characteristic: organism
characteristics.text: Homo sapiens
characteristics.characteristic: scientific_name
characteristics.text: female
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/PATO_0000383
characteristics.characteristic: sex
characteristics.text: fresh specimen
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/OBI_0000971
characteristics.characteristic: specimen with known storage state
characteristics.text: MDA-MB-231
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0001209
characteristics.characteristic: title