ChIP assays were performed as previously described (Lee et al., 2006) . Briefly, 5x10^7 cells were crosslinked with 1% paraformaldehyde (Electron microscropy science #15710) at room temperature for 10 min and sonicated to generate chromatin fragments of 200-600bp. The sheared chromatin was immunoprecipated with a specific antibody. Total RNA was extracted with Trizol (Invitrogen #15596), treated with DNAase I (NEB #M0303) for 20 min at room temperature and purified with RNeasy Mini kit (Qiagen #74106). ChIP libraries were prepared with the TruSeq DNA Sample Kit (Illumina #FC-121-2001) according to Illumina's instructions. 2 µg of total RNA was depleted of ribosomal RNA with the Ribo Zero kit (Epicentre #MRZG12324) and libraries were made with the TruSeq RNA sample Pre Kit (Illumina #RS-122-2001).
GEO Accession
GSM1171629