Fixed brains and imaginal discs were dissected from 10 third instar larvae, and sonicated chromatin incubated with anti ChIP was performed with 1:100 dilutions of anti-Cg [custom made], anti-Ph (a kind gift from Donna Arndt-Jovin) antibodies and 1:200 dilutions of anti-H3K27me3 (Millipore, 17-622) antibodies. Input ChIP DNA (30 ng) is blunt-ended and phosphorylated. A single 'A' nucleotide is added to the 3' ends of the fragments in preparation for ligation to an adapter that has a single-base 'T' overhang. The ligation products are purified and accurately size-selected by agarose gel electrophoresis. Size-selected DNA is purified and PCR-amplified to enrich for fragments that have adapters on both ends. The final purified product is then quantitated before cluster generation. http://ethanomics.wordpress.com/chip-seq-library-construction-using-the-illumina-truseq-adapters/.