Illumina HiSeq 2500 sequencing
ChIP-Seq library preparation and sequencing was carried out at the ACRF Cancer Genomics Facility, Centre for Cancer Biology, Adelaide. ChIP-Seq libraries were prepared according to Illumina’s TruSeq Sample Prep Guide Revision A with some minor modifications.  Briefly, DNA was end-repaired, followed by adenylation of the 3’ ends.  Next, Illumina indexing adapters were ligated to the DNA. 18 cycles of PCR was performed to enrich for successfully adapter ligated molecules. Ligation products were purified with a 2% Pippin Prep gel (Sage Science), selecting a size range of 250 – 300 base pairs.  The size distribution and yield of the purified libraries were determined using an Agilent Bioanalyzer High Sensitivity chip and Qubit dsDNA HS assay (Invitrogen), respectively.  Libraries were pooled in equimolar ratios and sequenced in one lane of a HiSeq 2500 short read flowcell (1 x 50bp).