Crosslinked nuclear extracts were subjected to DNA fragmentation by Covaris S220 sonifier, and chromatin-DNA complexes were pulled down using specific antibodies. Libraries were prepared using an Ion Plus Fragment Kit (Lifetechnologies, Part no. 4471252) according to the manufacturer's instructions. Briefly, ChIP DNA was end-repaired using an end repair enzyme, and was purified with two rounds of AMPure XP bead capture to size‐select fragments approximately 100–250 bp in length. After adapter ligation, DNA was PCR amplified with Ion primers for 13 cycles. The purified DNA was checked for quality on Agilent 2100 Bioanalyzer instrument with an Agilent High Sensitivity DNA kit. The library DNA was approximately 170–220 bp in length.  Libraries ware quantified using quantitative real-time PCR with the Ion Library Quantitation Kit (Part no. 4468802). Diluted librarie DNA was subjected to emulsion PCR using Ion OneTouch System and sequenced on the Ion PGM and Ion Proton semiconductor sequencers (Lifetechnologies) according to the manufacturer's protocols.
GEO Accession
GSM1447104