Transcriptome analysis of RGA1 mutant (d1-1) meristem by RNA-seq

We applied RNA-seq to 3-month-old rice (Oryza sativa) shoot apical meristem to investigate the effect of RGA1(d1-1) mutation on the meristem initiation using transcriptome of d1 as compared to wild type plant. Two biological replicates of rice shoot apical meristem were dissected out from leaf sheath and then collected from three-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.