Worm extract was made from adult worms. Frozen worm popcorn was ground up in a mixer mill. Samples were then fixed with 1% formaldehyde for 10 minutes. Chromatin was then sheared by sonication in the Bioruptor, and the soluble fraction was collected and stored at -80°C for future use. Worm extract from adult worms and 5 ?g of affinity purified antibody was used for ChIP. Dynal Protein A or G beads were used to recover the ChIPed DNA. Samples were then treated with RNase A and Proteinase K, and reverse crosslinked at 65°C. ChIPed DNA was purified and then quantified using the Pico Green HS fluorescent assay. Libraries were prepared according to Illumina's instructions for ?Preparing Samples for ChIP Sequencing of DNA?, with some variation. DNA was end-repaired using T4 DNA polymerase, Klenow DNA polymerase and T4 DNA polymerase. A?s were then added to the 3? ends of the fragments using Kelow fragment (3? ? 5? exo minus). Paired-end adapters were then ligated onto the ends of the fragments. DNA library was size selected by gel purification, fragments of 250-500 bp were band isolated from an agarose gel. DNA was PCR amplified for 18 cycles. The Bioanalyzer was used to verify fragment purification and quantify DNA. Prepared sample are sequenced using Illumina GAII or HiSeq2000 at the High Throughput Sequencing Facility of University of North Carolina at Chapel Hill or Cambridge.