For ChIP-Seq, lysates were cleared from sonicated nuclei and used for immunoprecipitation. For RNA-Seq, RNA was extracted according to TRIzol protocol (invitrogen). For ChIPSeq, cells were cross-linked in 1% formaldehyde and processed according to Mousavi et al. 2012. Purified DNA was processed according to manufacturer's protocol. For polyA RNA-Seq, Illumina protocol was followed. For ribosomal depletion, ribo-zero was used (epicenter).