Cells were fixed with 1% paraformaldehyde for 10 minutes at room temperature. Soluble chromatin was prepared as described by Ciofani et al (Cell,2012, PubMed ID: 23021777), and immunoprecipitated with antibodies. At least 1.5 ng of ChIP or input DNA was used for library preparation according to the Illumina ChIP-seq protocol. After end-repair and indexed adapter ligation, fragments were size-selected using Agencourt AMPure XP beads (Beckman Coulter, Brea, CA, USA) prior to amplification. The size-selected and amplified fragment libraries were verified on a 2100 Bioanalyzer (Agilent) prior to being pooled and sequenced