GSE114577
Transcriptomic Analysis of Two Homologous Salmonella Serogroup C1-specific Genes (SC0368 and SC0595)
Purpose:To reveal the function and relationship of the two homologous Salmonella serogroup C1-specific genes (SC0368 and SC0595 in SC). Methods: RNA was isolated from late exponential phase bacteria cultures of wild-type and mutants grown in LB medium. Three biological replicates were carried out per sample. RNA sample was sequenced with Illumina HiSeq 2500 System. DESeq2 method was used to calculate the differentially expressed genes. qRT–PCR were used to validate RNA-seq result. Results: The RNA sequencing yielded more than 28 million reads for 12 samples, and 98.83-99.58% of the high-quality reads were mapped to the reference genome sequence, covering more than 4500 genes in the Salmonella genome. According to the DEGseq analysis software, 76, 78, and 217 genes were considered differentially expressed compared to the wild-type (<2-fold changes, FDR< 0.05) in mutant strains ?0368, ?0595, and ?0368?0595, respectively.  RT–qPCR results of 18 selected genes were highly consistent with the RNAseq results. Conclusions: Combination of biological analyses and RNA-Seq of in-frame deletion mutants, experimental evidence for the possible involvement of SC0368 and SC0595 in regulation of motility, LPS synthesis, growth, virulence, and serotype conversion is provided. Overall design: Three biological repetitions of wild-type, single (?0368 and ?0595) and double (?0368?0595) mutants. Totally for 12 samples were conducted RNA sequncing. Wild-type was used as control.