A-9-30-1-2-non-infested
The RNA-Seq paired end sequencing libraries were prepared from the QC passed RNA samples using lllumina TruSeq Stranded mRNA sample Prep kit. The 1st strand cDNA was then synthesized to second strand using second strand mix. The dscDNA was then purified and used to prepare PE Illumina libraries, which were loaded onto NextSeq 500 for cluster generation and paired end sequencing. The sequenced raw data were processed to obtain high quality clean reads using Trimmomatic v0.35 to remove undesired sequences. These high quality (OV>20), paired-end reads were used for reference based read mapping. The reads were mapped on the reference genome of Triticum aestivum using TopHat v2.1.1 with default parameters. The transcriptome assembled from individual RNA-Seq samples was merged into a master transcriptome using the cuff merge utility in Cufflinks. The gtf of the master transcriptome was used for differential gene expression analysis.