SRA

Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare transcriptome profiling of control of P. aeruginosa PAS71 (RNA-seq) to transcriptome profiling of LVX-treated P. aeruginosa PAS71 and to evaluate protocols for optimal high-throughput data analysis. Methods:LB medium (50 mL) was inoculated with exponential growth phase P. aeruginosa PAS71 at a concentration of 1.0E8 CFU/mL. Levofloxacin was then added at a concentration of either 0 (control) or 0.125 µg/mL, respectively, in triplicate. All six experiment groups were incubated in a water bath shaker at 37 ºC with a shaking rate of 180 rpm for 5 h. Cells were then sampled and centrifuged from the three control groups and three LVX treatment groups, respectively. The cell precipitates were separately snap-frozen at -80ºC. Total RNA was isolated from cells using Trizol (Life Technologies, USA) according to the manufacturer's protocol. Results: The transcriptome sequencing data of control and LVX-treated groups were compared and analyzed in the form of the following: control vs LVX. The details of the differentially expressed genes among the two groups showed that the amount of differential expressed genes between control group and LVX-treated group was high (total 5581, up-regulated 241, down-regulated 16). Overall design: The mRNA profiles of P. aeruginosa PAS71 (control) and LVX-treated P. aeruginosa PAS71 were generated by deep sequencing, in triplicate, using Illumina Higseq 2000.