Gene expression profiling of drought-sensitive (IR64) and tolerant (N22) rice cultivars

We generated the global transcriptome profile of the two rice genotypes under control and drought conditions. More than 80 million high-quality reads were obtained for each cultivar and different conditions using the Illumina platform. Reference-based assembly was generated for each cultivar and condition. Differentially expressed genes were identified between drought and control condittons for each cultivar. Overall design: We collected 21-day-old seedlings of the drought sensitive (IR64) and tolerant (N22) rice cultivars under drought and control conditions. The RNA-seq libraries were prepared for sequencing using standard Illumina protocols and sequencing was performed on the Illumina HiSeq platform by a commercial sequencing service provider. The raw reads were filtered using NGSQC Toolkit (v2.3.3) at default parameters . Rice genome downloaded from RGAP (v7.0) was indexed using bowtie (v2.3.3.0) and filtered reads were mapped against the rice genome using Tophat (v2.1.1) at default parameters. Reference-based transcriptome assembly was performed using cufflinks (v2.2.1). The FPKM for each transcript was calculated using cufflinks by fragments per kilobase of transcript per million mapped fragments. Transcripts ID identified in at least two of three biological replicates were selected and the missing value for one replicate was imputed by random forest imputation using the missForest R package. Differential gene expression (log2 fold change ± 1 and FDR = 0.05) analysis was performed using edgeR.