RB50-A
The bacterial cultures were grown to mid-logarithmic phase at 37°C with agitation in 250-ml vented screw-cap flasks containing 50 ml Stainer-Scholte liquid medium with appropriate antibiotics.   Total RNA was extracted from bacterial culture containing ~2 × 1E+9 cells. The bacterial culture pellets after high-speed pulse centrifugation at 4ºC were flash-frozen in dry ice-ethanol slurry and kept at -80°C until RNA extraction. RNA was extracted using the RiboPure™-Bacteria Kit (Ambion). All RNA samples were assessed for quality by agarose gel electrophoresis and integrity determined using the Bioanalyzer 2100 instrument (Agilent).   Ribosomal RNA (rRNA) depletion was performed twice on 8-10 µg of isolated total RNA by using magnetic beads (MICROBExpress, Ambion) according to the manufacturer's protocol.   Libraries for Illumina sequencing were made with TruSeq RNA sample preparation kit version 2.0 rev. A (Illumina) according to manufacturer's high sample protocol. The initial poly A selection step was bypassed and enriched mRNA (350-500 ng) was mixed with 2xEPF buffer prior to cDNA priming/library fragmentation and the protocol was carried out without further changes from that point.  All cDNA libraries were uniquely indexed and were generated from two biological replicates per group.