Chromatin was isolated from 2i mouse ES cells (2 male, 2 female; C57BL/6J background) and sonicated to produce 100 to 700 bp frgments. Immunoprecipitation was performed with the following antibodies; anti-H3K27me3 (07-449, Millipore), anti-H3K4me3 (39159, Active Motif) and anti-H3K9me3 (ab8898, Abcam). ChIP-seq libraries were prepared using the Illumina TruSeq ChIP sample prep kit.