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. 2023 Oct 31;13:18696. doi: 10.1038/s41598-023-46142-8

Figure 1.

Figure 1

Experimental procedure for whole-transcriptome analysis of Salmonella enterica persisters induced by exposure to 100-fold MIC of ciprofloxacin or ceftazidime. Three biological replicates were performed for each time point. Overnight cultures were diluted 1:30 in fresh LB and incubated until mid-exponential growth phase (1). Ciprofloxacin or ceftazidime was added to a final concentration 100-fold above the MIC, and the samples were incubated for 48 h (2). 5-mL aliquots were removed at 0, 6, and 48 h after exposure (3) and treated with Bacteria RNAprotect prior to RNA extraction (4). RNA was treated with DNase I, and rRNA was depleted using the RiboZero Magnetic Kit for Gram-negative bacteria (5) before dsDNA synthesis and library preparation (6). RNASeq was performed with Illumina MiSeq platform (7) and the differentially expressed genes were identified with CLC Genomics Workbench 12.0 (8).