Total RNA was isolated using the standard Trizol (Invitrogen) protocol. Two rounds of PolyA RNA purification were performed for each sample, using the PolyA(Purist)TM-MAG kit (Ambion). The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bioanalyzer. Strand-specific libraries for 76 bp paired-end sequencing were prepared according to a modified UTP-method (Parkhomchuk et al. 2009), as detailed in (Levin et al. 2010).