Three micrograms of RNA from each sample were used to prepare an mRNA-Seq library with a TruSeq RNA Sample Prep Kit (Illumina), following the manufacturer's instructions. Unique index codes were used to assign sequences to individual samples. Briefly, poly(A)+ RNA was purified and fragmented using divalent cations under elevated temperature conditions. RNA fragments were converted to cDNA using random primers, followed by second-strand cDNA synthesis and end repair. Illumina PE adaptors were attached to the cDNA ends. Fragments with an insert length of ∼300 bp were extracted from a 2% low-range ultra-agarose sizing gel. Adaptor-tagged cDNA fragments were enriched by 10-cycle PCR following the manufacturer's protocol. Library quality and insert length were checked using a High Sensitivity DNA Bioanalyzer Chip (Agilent) to ensure the proper insert size of 300–500 bp was attained (Supplementary Figure S2). The libraries were diluted to 10 pM, and equal amounts of 8 distinctively indexed libraries were mixed and subjected to 100 cycles of paired-end (2 × 100 bp) sequencing on one lane of an Illumina Hiseq 2000 system. A total of three lanes were used to sequence the entire sample set.