title: Transcriptome of Hemigraphis alternata
design: RNA was isolated from different tissues such as root stem petiole and leaves of control (in vivo) and treated (in vitro) plants of Hemigraphis alternata using RNAeasy plant mini kit combined with CTAB method according to manufacturers protocol. The pooled RNA samples were then subjected to library preparation using Illumina TruSeq Stranded mRNA SamplePreparation Kit as per its described protocol. The oligo-dT based enriched mRNA was fragmented and converted into first-strand cDNA, followed by second-strand generation, Atailing, adapter ligation and finally ended by limited number of PCR amplification of the adaptor ligated libraries. Library quantification and qualification was performed on Bioanalyzer 2100 (Agilent Technologies) using DNA High Sensitivity Assay Kit. After obtaining the Qubit concentration for the libraries and the mean peak size from Bioanalyser profile, libraries were loaded into Illumina platform for cluster generation and sequencing. The pair-end libraries were prepared using Illumina TruSeq Stranded mRNA Sample Preparation Kit. The libraries were sequenced using 2x150 PE chemistry on Illumina platform. Trimmomatic (ver.0.36) was used for the filtration of raw data. De novo assembly of high quality reads was accomplished using Trinity software at default parameter (kmer 25).