TABLE 2.

RNA-Seq analysis of the total number of genes that were differentially expressed in E2348/69 and its plasmid mutants

Sample 1	Sample 2	No. of genesa
		Increased (LFC ≥ 2)	Decreased (LFC ≤ −2)	Total altered
E2348/69 in LB	E2348/69 in DMEM	201	267	468
E2348/69 in LB	ΔperABC mutant in LB	30	58	88
E2348/69 in DMEM	ΔperABC mutant in DMEM	56	34	90
ΔperABC mutant in LB	ΔperABC mutant in DMEM	345	335	680
JPN15 in LB	ΔperABC mutant in LB	365	367	732
JPN15 in DMEM	ΔperABC mutant in DMEM	59	134	193
E2348/69 in LB	JPN15 in LB	313	322	635
E2348/69 in DMEM	JPN15 in DMEM	79	91	170
JPN15 in LB	JPN15 in DMEM	265	410	675

^aLFC is the log₂ fold change, determined as the normalized read counts of sample 2 divided by those of sample 1.