title: Carroll_ChIP_exo
design: Carroll_ChIP_exo
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 an antibody against ER (Santa-Cruz, sc-543). For ChIP-seq library preparation, the immunoprecipitated DNA was end-repaired, A-tailed and Illumina TruSeq adapters ligated before 18 cycles of PCR amplification. A 2% agarose gel was used to select 300-500 bp DNA fragments.
attributes.tag: Experimental Factor: cell line
attributes.value: MCF-7
attributes.tag: Experimental Factor: immunoprecipitate
attributes.value: ER
attributes.tag: Experimental Factor: organism
attributes.value: Homo sapiens
attributes.tag: Experimental Factor: protocol
attributes.value: ChIP-seq