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 (FDR<0.05 and Abs (log 2(Y/X) >0). 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).