Differential gene expression between wild type (Col 0) and mutants (Atplh1, Atplh2, Atplh3)

RNA sequencing of Arabidopsis 10 day old wild type and mutant seedlings (grown on MS media with and without ABA, NaCl for 5 days) using Illumina platform. Differential gene expression between wild type and mutants along with the effect of ABA and NaCl on gene expression was studied. Overall design: Total RNA was extracted from all the samples using TRIzol followed by DNase1 treatment and purification. Sequencing was performed on Illumina HiSeq platform to generate 150bp long reads in paired-end mode. Adapter contamination and low-quality reads were removed using NGS QC Toolkit (v2.3.3). High-quality filtered reads were mapped on Arabidopsis reference genome using HISAT2. Differentially expressed genes were then identified using StringTie and cuffdiff.