rep1
RNA-seq libraries were constructed using the TruSeq RNA Sample Preparation Kit (Illumina) with 2 g of total RNA. Ribosomal RNA was depleted via the Ribo-Zero Magnetic Kit (Epicenter), and mRNA was fragmented into ~200 nt pieces. Double-stranded cDNA was synthesized using the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen) with random hexamer primers (Illumina), incorporating dUTP in place of dTTP. Libraries were size-selected for 200 bp fragments by gel electrophoresis, amplified by PCR, and sequenced on the Illumina HiSeqTEN platform (2  150 bp paired-end reads). Base calling and quality filtering were performed using the Illumina GA Pipeline (version 1.6), and clean reads were selected using a custom Perl script.