Staphylococcus_aureus
RNA was processed as previously described (Osmundson et al. 2013) with some variations. Briefly, bacterial rRNA was depleted with RiboZero rRNA removal kit for gram-positive organisms (Epicenter, XX). RNA quality was assessed for each passage by the Agilent Bioanalyser 2100 (Agilent, Santa Clara, CA). Libraries were prepared using TruSeq® Stranded mRNA LT Sample Prep Kit (Illumina), eliminating the step for mRNA amplification. Samples were sequenced on a Miseq Instrument (Illumina) for 51 cycles.