GSE158829
Transcriptome analysis of gene expression of strains JNB5-1 and SK8-37
RNAseq analysis was performed to evaluate gene expression differences between strains JNB5-1 and SK8-37. S. marcescens JNB5-1 and SK8-37 cells were grown in LB medium for 10 h before harvesting. The collected cells were then treated with RNAprep pure Kit (TIANGEN) to extract total bacterial RNA and delivered to GENEWIZ in dry ice for transcriptome resequencing analysis. For annotation, the genome of S. marcescens WW4 (NC_020211.1) was used as reference. A total of 31206068 reads matched to the referenced genome in the sample of JNB5-1, and 29862970 reads in the sample of SK8-37. The significantly differentially expressed genes (DEGs) were determined between strains JNB5-1 and SK8-37 with the standards of p-value= 0.05, fold change |log2Ratio|=1. Transcriptome data showed that expression of 60 genes were significantly up-regulated while 558 genes were significantly down-regulated by at least 2-fold when comparing the psrA mutant strain SK8-37 to its parent strain JNB5-1. Based on the annotation of KEGG_B_class, the up-regulated and down-regulated genes were classified into 10 and 19 major cellular processes, respectively. The transcriptome data indicated that PsrA may controls a variety of cellular processes in S. marcescens, including prodigiosin synthesis, serrawttin W1 biosynthesis, extracellular polysaccharide production, biofilm formation, cell motility and T6SS-mediated antibacterial activity. Overall design: Gene expression of strains JNB5-1 and SK8-37 were generated by deep sequencing, in triplicate, using Illumina HiSeq X10