The ChIP-seq has been carried out as previously described (Jolma et al., 2013;  Tuupanen et al., 2012; Yan et al., 2013). Briefly, 2 million cells were crosslinked with 1%  formadehyde for 15 min at RT. The reaction was quenched by adding 125 mM of  Glycine and incubating for 5 min at RT. Cells were lysed in RIPA buffer (10 mM TrisHCl  pH 8.0, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium  deoxycholate) supplemented with protease inhibitor (Roche). And chromatin was  sonicated into short fragments (300-700 bp). The fragmented chromatin was incubated  with antibodies to pull down the specific DNA bound TFs or histones. After  intensive wash, DNA was purified and prepared as sequencing library using illumina  Truseq LT kit. Several samples with different indexes were pooled together for 50 or 100  cycles of single read sequencing with illumina Hiseq 2500.
GEO Accession
GSM3263074