Transcriptome analysis of RGA1 mutant (d1) by RNA-seq. Oryza sativa

We applied RNA-seq to 60-day-old rice (Oryza sativa) flag leaf tissue to investigate the effect of RGA1 mutation on the transcriptome in d1 as compared to wild type plant. Overall design: Two biological replicates of rice leaf blades, sampled flag leaf at the region of maximum width, were collected from two-month-old WT and d1 plants grown as described above and immediately frozen in liquid nitrogen. Total RNA was extracted from each sample using the NucleoSpin RNA Plant kit. After examination of the quality (Bioanalyzer, Agilent) and quantity (NanoDrop 2000, ThermoFisher) of each RNA sample, aliquots of total RNA were submitted to the Genomics Core Facility at Penn State University for cDNA library preparation and next generation sequencing on a Hiseq 2500 (Illumina). Approximately 40 million 150 bp single-end sequencing reads were obtained for each library.