title: RNA-seq of E.nitida leaf
design: Library construction was processed at Novogene. mRNA was enriched from total RNA using oligo(dT) beads. The mRNA was then fragmented randomly in fragmentation buffer, followed by cDNA synthesis using random hexamers and reverse transcriptase. After first-strand synthesis, a custom second-strand synthesis buffer (Illumina) wass added, with dNTPs, RNase H and Escherichia coli polymerase I to generate the second strand by nick-translation and AMPure XP beads was used to purify the cDNA. The final cDNA library was ready after a round of purification, terminal repair, A-tailing, ligation of sequencing adapters, size selection and PCR enrichment.Raw reads were filtered to remove reads containing adapters or reads of low quality- as defined by: Discard reads with adaptor contamination. Discard reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%). Discard reads when low quality nucleotides (base quality less than 20) constitute more than 50 percent of the read. Clean reads are de novo assembled by Trinity (version r20140413p1) to assemble the transcriptome