Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody. 28 ug of sonicated chromatin was used for the Grhl3 IPs. Sequencing libraries were generated for the Grhl3 and Input samples using Illumina Tru-Seq ChIP-Seq kit, multiplexed to be sequenced in a single lane, according to the Illumina protocol for ChIP-Seq library preparation, with some modification. After adaptor ligation, PCR amplification was performed prior to size selection of the library [Schmidt D, Methods, 2009]. Clustering and 50-cycle single end sequencing were performed on the Illumina Hi-Seq 2000 Genome Analyzer.