RNA was isolated from three separate biological replicates of either wild-type or zur::TN mutant U112. RNA quality was confirmed with the Agilent Bioanalyzer at the Biomolecular Research Facility at the University of Virginia (UVA). Total RNA was submitted to HudsonAlpha (Huntsville, AL), where ribosomal reduction was performed to concentrate for mRNA. Directional cDNA libraries were then generated, and samples were sequenced in multiplex (50 paired-end reads) with the Illumina HiSeq v4 platform.
Data analysis was performed by the UVA Bioinformatics Core. Briefly, gene reads were first aligned with reference genomes and read counts were quantified with EDGE-pro software. The Deseq2 Bioconductor package was then used to normalize the read counts and estimate dispersion for each gene. These data were then fitted to a negative binomial model, which was used for differential-expression analysis. Genes were considered differentially expressed between groups when the adjusted P value was <0.05.
Data analysis was performed by the UVA Bioinformatics Core. Briefly, gene reads were first aligned with reference genomes and read counts were quantified with EDGE-pro software. The Deseq2 Bioconductor package was then used to normalize the read counts and estimate dispersion for each gene. These data were then fitted to a negative binomial model, which was used for differential-expression analysis. Genes were considered differentially expressed between groups when the adjusted P value was <0.05.