RNA-Sequencing of onion bulbs inoculated with Salmonella
The goal of this study was to compare differentially expressed transcripts in onion bulbs induced when inoculated with Salmonella using transcriptome profiling (RNA-seq) .Transcriptomic analysis of onion bulb tissue (Variety Don Victor) in response to Salmonella was performed 24 hours and 7 days post-inoculation to identify Differentially Expressed Genes (DEGs) in onion. Within 24 hours of inoculation, 4259 genes were upregulated while 3393 genes were downregulated. After 7 days, 8213 and 6417 genes were up and down-regulated, respectively, as shown below. (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 RNA extractions. For the Day 1 set of samples, uninoculated samples (ONControlD1_1, ONControlD1_2, ONControlD1_3) were compared to inoculated samples (ONtreatedlD1_1, ONtreatedlD1_2, ONtreatedlD1_3). For Day 7, samples (ONControlD7_1, ONControlD7_2, ONControlD7_3) were compared to inoculated samples (ONtreatedlD7_1, ONtreatedlD7_2, ONtreatedlD7_3).