RNA purification of immunoprecipitated RNA was performed using the RNeasy Plus Micro kit (Qiagen) following the manufacturer's protocol. RNA quality was checked on a Bioanalyzer instrument (Agilent Technologies) using a RNA 6000 Pico Chip and only RNA samples with RNA integrity number (RIN) values higher than 9 were used for library preparation and sequencing. Library preparation and RNA sequencing experiments were performed by the Genomic Unit of the Centre for Genomic Regulation (CRG, Barcelona, Spain). Library preparation for all samples was performed using the SMARTer Ultra Low RNAkit and samples were then sequenced paired-end using an Illumina HiSeq 2500 platform to a mean of approximately 60 million mapped reads per sample.