Method S1
For RNA-Seq, poly-A RNA was isolated from total RNA using poly-T oligo-attached
magnetic beads. Following purification and fragmentation, the cleaved RNA fragments
were synthesized into first strand cDNA using reverse transcriptase and random primers.
This was followed by the process of second strand cDNA synthesis by DNA polymerase I
and RNase H treatment. Then cDNA fragments went through ends repair, addition of
adenosines to the 3’ ends and ligation of 5’ and 3’ adapters. About 400-500 bp fragments
then were gel purified and amplified by PCR. Following quality control analysis, the
sequencing libraries were run on Illumina HiSeq 2000 sequencer (Illumina). For sRNA
sequencing, small RNA was separated from total RNAs by gel extraction based on
nucleotide length. Following ends repair and purification, the sRNAs were ligated with
adapters. Reverse transcription followed by PCR was used to synthesize and enrich
cDNA fragments with adapters on both ends. After PCR amplification, the ~ 140 bp
fragments were gel purified and collected. Then the sRNA sequencing libraries went
through quality validation and were subjected to high-throughput sequencing using
Illumina HiSeq 2000 sequencer according to the manufacturer’s instruction (Illumina).