Cells were permeabilized, biotin end-labeld, and lysed. Genomic DNA was extracted and sonicated to 0.2-2 kb size fragments prior to pull-down of biotin-labeled fragments with streptaviding-coated Dynabeads. Libraries were prepared according to the NEBNext kit. Briefly, DNA was sonicated to ~200 bp. DNA was end-repaired using a combination of T4 DNA polymerase, Klenow DNA polymerase and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo minus) and dATP to yield a protruding 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3' end. After adapter ligation, DNA fragments of ~200 bp (insert plus adaptor) were band isolated from a 2% agarose gel. The purified DNA was PCR amplified with Illumina primers for 18 cycles. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Illumina HiSeq following the manufacturer's protocols.