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Transcriptome analysis of gene expression of strains JNB5-1 and SK68

ABSTRACT: RNAseq analysis was performed to evaluate gene expression differences between strains JNB5-1 and SK68. S. marcescens JNB5-1 and SK68 cells were grown in LB medium for 4 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 32420858 reads matched to the referenced genome in the sample of JNB5-1, and 32993470 reads in the sample of SK68. The significantly differentially expressed genes (DEGs) were determined between strains JNB5-1 and SK68 with the standards of p-value≤ 0.05, fold change |log2Ratio|≥1. Transcriptome data showed that expression of 210 genes were significantly up-regulated while 106 genes were significantly down-regulated by at least 2-fold when comparing the rcsB mutant strain SK68 to its parent strain JNB5-1. Based on the annotation of KEGG_B_class, the up-regulated and down-regulated genes were classified into 18 and 17 major cellular processes, respectively. The transcriptome data indicated that RcsB may regulates a variety of cellular processes in S. marcescens, including prodigiosin synthesis, and cell motility.

ORGANISM(S): Serratia marcescens

PROVIDER: GSE149400 | GEO | 2020/04/28

REPOSITORIES: GEO

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