ChIP experiments were performed as described (20 (link)) with minor modifications. Hormone-deprived MM134 cells were treated with 1nM E2 or 0.01% EtOH for 45 minutes. Immunoprecipitation used ERα (HC-20) and rabbit IgG (sc2027) antibodies (Santa Cruz Biotechnologies). DNA from six independent ChIPs was pooled for sequencing at Genome Quebec Innovation Center (McGill University). 50bp DNA sequencing on the Illumina HiSeq 2000 platform allocated >6×107 single-end reads per sample.
Output was mapped to the Human Reference Genome (hg18) by BWA (21 (link)). Peaks were called using MACS v1.4.2 (22 (link)), with a P-value cutoff of 10−5. Features of ER binding sites were mapped by CEAS (23 (link)) and BedTools (24 (link)). MCF-7 consensus ER binding sites represented the overlap of nine published data sets (25 (link)–29 (link)). Data is available in GEO as GSE51022.
Output was mapped to the Human Reference Genome (hg18) by BWA (21 (link)). Peaks were called using MACS v1.4.2 (22 (link)), with a P-value cutoff of 10−5. Features of ER binding sites were mapped by CEAS (23 (link)) and BedTools (24 (link)). MCF-7 consensus ER binding sites represented the overlap of nine published data sets (25 (link)–29 (link)). Data is available in GEO as GSE51022.