Cells were harvested with trypsin and ChIP was performed as previously described (Sailaja et al., Methods in molecular biology, 2012). Library construction was carried out as published (Blecher-Gonen et al., 2013, Nat Prot). Paired end libraries were constructed using standard Illumina protocols, with some modifications. Agencourt AMPure XP (Beckman Coulter) at 0.8x ratio were used to size select out adapter dimers. The Illumina Phusion enzyme was replaced by Kapa HiFi HotStart ready mix (Kapa Biosystems). An Invitrogen SizeSelect R-gel system (Life Technologies) was used to size select following PCR amplification.