RNA-seq analysis of the P. aeruginosa ΔznuA mutant

RNA isolated from biological triplicates of wild-type PAO1 and ΔznuA strains was pooled and submitted to the Adelaide Microarray Centre (University of Adelaide) for sequencing. Briefly, the Epicentre Bacterial Ribozero Kit (Illumina) was used to reduce the ribosomal RNA content of the total RNA pool, followed by use of the Ultra Directional RNA kit (New England Biolabs) to generate the barcoded libraries. Prepared libraries were then sequenced using the Illumina HiSeq2500 with Version 3 SBS reagents and 2 × 100 bp paired-end chemistry. Reads were aligned to the P. aeruginosa PAO1 genome (GenBank accession number AE004091.2)26 (link) using BOWTIE2 version 2.2.362 (link). Counts for each gene were obtained with the aid of SAMtools (v 0.1.18)63 (link) and BEDtools64 (link) and differential gene expression was examined using DESeq65 (link); the data has been submitted to GEO (accession number GSE60177).