RNA-Sequencing of Salmonella species inoculated in onion bulb tissue. RNA-Sequencing of Salmonella species inoculated in onion bulb tissue

This study aimed to compare differentially expressed transcripts in Salmonella recovered from the inoculated onion bulbs using transcriptome profiling (RNA-seq). The Salmonella strains of Salmonella enterica subsp. enterica ser. Newport, isolated from clinical cases affected by the onion-linked outbreak in 2020 (CDC, 2020), was used for the onion bulb inoculation. Transcriptomic analysis of Salmonella was performed 1 day (24 hours) and 7 days post-inoculation to identify Differentially Expressed Genes (DEGs) . 925 and 736 genes were upregulated within 24 hours and seven days after inoculation, while the number of downregulated genes in the same timeframe was 690 and 826, respectively (FDR0). Overall design: Onion bulbs inoculated with Salmonella enterica were flash-frozen in liquid nitrogen from three independent bulbs at 1 and 7 days after injection. The samples were used for total RNA extractions. For the Day 1 set of inoculated samples (ONtreatedlD1_1, ONtreatedlD1_2, ONtreatedlD1_3) and Day 7 inoculated samples (ONtreatedlD7_1, ONtreatedlD7_2, ONtreatedlD7_3) were compared to cultured Salmoenall strains (SalContrl_1,SalContrl_2, SalContrl_3).