Cells were crosslinked in 1% formaldehyde for 5 minutes at room temperature, with constant agitation, followed by quenching with 125mM Glycine for 5 minutes at room temperature. Nuclei were isolated and chromatin was sheared using Branson sonifier until the majority of DNA was in the range of 200-700 base pairs. Chromatin was incubated with antibody overnight at 4°C, with constant agitation. Immunoprecipitation of antibody-protein complexes was completed using Protein A or Protein G Dynabeads (Invitrogen) for 2-3 hour at 4°C, with constant agitation. ChIPs were completed using previously reported methods (Mikkelsen et al., 2010). For the bioChIP Streptavidin-coupled Dynabeads (Invitrogen) were incubated with the chromatin for 2-3 hours at 4°C. The SDS concentration in the Low Salt Buffer was raised to 2% and reverse crosslinking was performed on beads overnight at 65°C. Immunoprecipitated DNA was end repaired using the End-It DNA End-Repair Kit (Epicentre), extended using a Klenow fragment (3’-5’ exo)(NEB), and ligated to sequencing adapter oligos (Illumina). Each library was then PCR-amplified using PFU Ultra II Hotstart Master Mix (Agilent), and a size range of 300-600 was selected for sequencing on the Illumina HiSeq 2000.