Nuclei were treated with MNase. The reaction was quenched by addition of EDTA to 10 mM and the soluble fraction was extracted. Then the sample was treated wtih proteinase K and was extracted with phenol and chloroform to remove proteins. The DNA was isolated by precipitation with ethanol. DNA was end-repaired using End-It DNA End-Repair Kit (Epicenter) and 3' ends were adenylated by treating the samples with Klenow (exo-) (NEB) in the presence of dATP. The samples were then ligated to Illumina TruSeq adapters. The ligated products were run on agarose gel and were purified using Qiagen MinElute columns. The ligated products were then PCR-amplified using KAPA master mix. The amplified products were run on agarose gel and were purified using Qiagen MinElute columns.