GSE64353
RNA-sequencing based analysis of transcriptomes of Listeria monocytogenes grown on cold smoked salmon and modified BHI broth
In this study, RNA-seq was used to compare the transcriptomes of L. monocytogenes strain H7858 grown on cold smoked salmon (CSS) and in modified brain heart infusion broth (MBHIB, water-phase salt 4.65%, pH 6.1) at 7oC.  RNA-seq was performed on H7858 RNA samples representing four independent biological replicates of growth experiments that involved growth of H7858 on CSS or in MBHIB. Samples for RNA preparation were collected when H7858 was grown to late log phase on these two matrices. Indexed and purified cDNA libraries (8 libraries including 4 replicates for each CSS and MBHIB) were loaded together onto an independent flow cell without any other samples; sequencing was carried out by running Hiseq 2000 (single-end, 100-bp per read). Reads alignment was carried out using the Burrows-Wheeler Aligner (BWA). Differential expression of genes in different strains was statistically assessed using the BaySeq method. Significant differential transcription of 149 genes in H7858 was observed between these two treatments including 88 genes and 61 genes up- and downregulated, respectively, in H7858 grown on CSS compared to in MBHIB. Our results show that genes involved in cobalamin biosynthesis, ethanolamine and 1,2-propanediol utilization, and specific carbohydrate transport systems have significantly higher transcript level in H7858 grown on CSS compared to in MBHIB. PrfA-dependent gene enrichment analysis showed that, genes regulated by PrfA were overrepresented among L. monocytogenes genes with higher transcript level on CSS than in MBHIB. Overall design: Transcriptome profiles of L. monocytogenes grown on cold smoked salmon and in modified BHI broth at 7oC were generated by deep sequencing, in quadruplicate, using Illumina Hiseq 2000 (100 bp per read, single-end).