Standard methods were used for RNA-seq library construction, EZBead preparation and Next-Gen sequencing using the Life Technologies SOLiD system. Briefly, total RNA (≤ 400 ng per sample) was first ribosome-depleted using Ribominus™ Eukaryote Kit for RNA-Seq (Ambion, CA), and whole transcriptome library was prepared and barcoded per sample using the standard protocol of SOLiD Total RNA-seq Kit (Life Technologies, Carlsbad, CA). Each barcoded library was quantified by quantitative PCR using SOLiD Library Taqman qPCR Module (Life Technologies, Carlsbad, CA), and pooled in equal molarity. EZBead preparation, bead library amplification, and bead enrichment were then conducted using Life Technologies EZ Bead™ E80 System (Life Technologies, Carlsbad, CA). And finally sequencing by ligation was carried out using standard single-read, 5′-3′ strand-specific sequencing procedure on SOLiD4™ Sequencer (50b-read), as well as on SOLiD™ 5500xl Sequencer (75 b read). The average number of mapped reads per sample was 20.8 million.
