For each sample, 1 x 10^6 cells were cross-linked with 1% PFA and cell nuclei were prepared using a swelling buffer (25 mM Hepes, pH 7.8, 1 mM MgCl2, 10 mM KCl, 0.1% NP-40, 1 mM DTT). For histone modifications, chromatin was sheared by sonication to mononucleosomal fragments. Total RNA was extracted using Trizol. Prior to library preparation, RNA was digested with DNaseI. Libraries were prepared according to Illumina standard protocols with external barcodes for ChIP-seq. RNA-seq libraries were generated with the Encore RNA-seq kit by Nugen.