Nuclei were isolated, mononucleosomes were subsequently obtained from CCE mESCs and CCE EBs. Cells were lysed in hypotonic TMSD buffer to isolate nuclei, which were then digested with micrococcal nuclease. The resulting mononucleosomes were immunoprecipitated with Protein AG beads (Pierce) bound to either anti-Brd4 (Abcam) or anti-acetyl-H4 (Millipore). Washed beads from ChIP were then treated with RNase A followed by Proteinase K. Samples were cleaned up using DNA Clean & Concentrator-5 (Zymogen) The ChIP library was prepared using the multiplexed ChIP-Seq sample preparation protocol available on the University of Pennsylvania Functional Genomics Core website (http://fgc.genomics.upenn.edu/) anti-Brd4 (Abcam 128874 and anti-acetyl-H4 (Millipore 06-866)