Nuclei were extracted from HeLa cells and sonicated using the Covaris instrument. The resulting chromatin was isolated from clarified from sonicated nuclei. The histone-DNA complexes were immunoprecipitated with antibody. Libraries were prepared according to Illumina's instructions accompanying the truseq chip-seq kit from illumina (IP-202-1012). Briefly the ends of DNA are repaired using a combination of T4 DNA polymerase and Klenow DNA polymerase. An 'A' base is then added to the blunt and phosphorylated ends using the Klenow fragment (3' to 5' exo minus), this prepares the fragments for ligation of the adapters which have a 'T' overhang in their 3' end. The illumina specific adapters are then ligated to the DNA fragments and the library is amplified by PCR. The resulting, size selected libraries were sequenced in the Illumina Hiseq 2000.