Cells were fixed by incubation in 11% formaldehyde solution for 15 minutes at room temperature. Fixation was stopped by the addition of a 2.5 M glycine solution. Cells were washed in a 0.5% Igepal-PBS solution prior to snap-freezing. Active Motif (Carlsbad, CA) performed chromatin isolation, immunoprecipitation reactions, library generation and sequencing. ER ChIP reactions were conducted using 30 μg MCF7 breast cancer cell line chromatin and 4 μg of ER alpha antibody (sc-543, Santa Cruz Biotechnology, Dallas, TX). The ChIP reactions also contained a drosophila chromatin spike in for the normalization of the sequencing data. Libraries were prepared from each ER ChIP reaction, as well as an input/control DNA sample, and single-end sequencing data were generated on the Illumina platform