title: Single Treated Rep 1
design: Total RNA was isolated using RNeasy Plant Mini Kit (Qiagen).  The purity of RNA was measured using Nanodrop 2000 (Thermo Scientific), and the integrity of RNA was determined by agarose gel electrophoresis. Samples of 1-2 g mRNA were used for library construction and sequencing. Briefly, mRNA was enriched from total RNA using oligo (dT) beads, randomly fragmented and cDNA was synthesized using random hexamers. After cDNA synthesis and library construction (terminal repair, A-tailing, ligation of sequencing adapters, size selection and PCR enrichment). Library concentration was quantified and then diluted to 1 ng/l. The libraries were sequenced on the Illumina HiSeq platform (PE150). Raw reads are filtered to get rid of reads containing adapter or with low quality to get the clean reads for analysis. The Hisat2 v2.0.4 algorithm was used to map the filtered sequenced reads to the reference genome.