Chromatin was prepared from sonicated nuclei and specific protein-DNA complexes were isolated by immunoprecipitation. Libraries for Illumina sequencing were prepared using the Ovation Ultralow System V2 (NuGEN) for Ser5-P samples, the TruSeq ChIP Sample Prep kit (Illumina) for the H2A.Z and input chromatin samples, and the ChIP Seq Sample Preparation Kit (Illumina) for the Pol II samples.