title: HEG4 small RNA replicate3: Comparative transcriptome analysis among closely related rice strains
design: Total RNA (30 μg) was isolated from GEG4 seedlings and resolved on 15% denaturing PAGE gels. RNA molecules ranging from 18-30 nt were excised from the gel, recovered by soaking overnight in 0.3 M NaCl followed by ethanol precipitation. Small RNA libraries were constructed as described (Truseq Small RNA Sample Prep Kit; Illumina) and sequenced (Illumina Hiseq 2500 at UCR core facility). After removing the adaptor sequences, 94.2 million reads of small RNAs in the range of 18-30 nt were used for analysis. Bowtie (Langmead et al., 2008) was used to map small RNA reads with perfect matches to mPing and flanking 100 bp sequences or to the Nipponbare reference genome (MSU7). To calculate the number of reads per million, small RNAs was normalized to the mapped small RNA library size. Mapped reads were visualized using the Integrated Genomics viewer (IGV v 2.3.74)