Cells were fixed with 3% formaldehyde followed by treatment with lysozyme, SDS, and Triton X-100. DNA was digested with HpaII. DNA ends were labeled with biotin and ligated. The sample was de-crosslinked at 65 °C in the presence of Proteinase K followed by phenol-chloroform extraction and ethanol precipitation. RNA was removed by RNase A treatment and DNA was further purified with AMpure XP beads. Downstream steps included sonication, biotin pull down, end repair, A-tailing, ligation of Illumina Y adapters, and PCR amplification.