ES cells were crosslinked with formaldehyde and subsequently sonicated. Sonicated cell extracts were used for ChIP assays. ChIP-enriched DNA was end-repaired using the End-It DNA End-Repair kit (Epicentre), followed by addition of a single A nucleotide, and ligation of PE adapters (Illumina) or custom indexed adapters. PCR was performed using Phusion High Fidelity PCR master mix.