Comparative transcriptome of S. aureus strains. Staphylococcus aureus subsp. aureus USA300

We report the transcriptome profiles (RNA seq) of three different co-isolates of S.aureus that have been identified and isolated in both laboratory and infective scenarios. The transcriptome profiles were generated by deep sequencing and transcript levels assessed. For this the raw reads underwent quality-trimming (using the FastX suite), polyA-clipping, size filtering, mapping to the reference genome, coverage calculation, gene wise expression quantification followed by differential gene expression analysis (all done by the tool "READemption" (Förstner et al., unpublished) using "segemehl" (Hoffmann et al., 2009) and "DESeq" (Anders et al., 2010). RT-PCR as well as phenotypical assays were further used to validate the data. Differential gene expression between the isolates was observed in 4% (116 of 2774 genes). This had a significant impact on the physiology of each strain. Overall design: RNA profiles of 3 different subpopulations of S.aureus generated by deep sequencing