The antibodies used were anti-ER (sc-543) from Santa Cruz Biotechnologies, RNA Pol II (ab5131) and FoxA1 (ab5089) from Abcam. At least four 15 cm dishes of cells were used per chromatin immunoprecipitation (ChIP) and samples were processed according to standard ChIP procedures. The ER ChIP samples were performed as described in Schmidt, 2009, Methods. The immunoprecipitated DNA was subsequently amplified as previously described for Illumina sequencing Schmidt, 2009, Methods.