Small RNA-seq of log-phase Salmonella enterica subspecies enterica serovar Typhimurium (S. Typhimurium) strain SL1344
The mouse virulent Salmonella enterica subspecies enterica serovar Typhimurium (S. Typhimurium) strain SL1344 was grown overnight in MOPS-buffered salts, (MS) medium. Desired strains were grown overnight in MS hiC medium at 37°C with shaking overnight (18-24-h). Overnight cultures were diluted 1:100 into fresh MS hiC (0.4% w v-1 glucose) and fresh MS loC (0.03% w v-1 glucose) medium, and incubated with aeration at 37°C. Growth was monitored spectrophoto-metrically at 600 nm (optical density at 600 nm; OD600).  MS hiC cultures were grown to an OD600 of 0.3-0.4 to generate log-phase cells.     The total RNA from the log-phase was isolated with Trizol® (Life Sciences) per standard manufacture protocol and submitted to Otogenetics (http://www.otogenetics.com/) for commercial RNA-Seq on an Illumina MiSeq genome sequencer using a small RNA protocol. For each culture, Otogenetics provided raw paired-end reads corresponding to ~600 million base pairs. Adapter sequences were removed with cutadapt(http://cutadapt.readthedocs.org/en/latest/index.html) and reads with less than 10bp were cut using trimmomatic (http://www.usadellab.org/cms/index.php?page=trimmomatic). The reads were then mapped against the SL1344 genome using BWA-MEM.