Cells in 10-cm2 dishes were fixed in 1% formaldehyde for 10 min, and fixation was quenched with addition of glycine to 125 mM for an additional 5 min. Cells were harvested by scraping from plates and washed twice in 1× PBS before storage at −80°C. ChIP was performed as described in the Young laboratory protocol (Lee et al. 2006b (link)), except that extracts were sonicated twice for 9 min each round (30 sec of sonication with intermediate incubation of 30 sec per round) using a Bioruptor (Diagenode). All ChIPs were performed using 500 μg of extract and 2 μg of antibody per sample. Thirty microliters of Protein G Dynabeads (Invitrogen, 100.02D) was used per ChIP. Controls with IgG and no antibody controls were routinely performed, and all antibodies were tested by titration to be functioning within the linear range of the protocol. Following elution, ChIP DNA was analyzed by standard qPCR methods on a 7900HT Fast-Real-Time PCR (ABI). Primer sequences are available on request. For sequencing, 10 ng of ChIP DNA was used to make sequencing libraries using standard Illumina library single-end construction procedures. Sequencing was performed on either Illumina GAIIx (36 base pairs [bp], single-end reads) or Hi-Seq (100 bp, paired-end or single-end reads) platforms.