TABLE 3.

Northern blot analysis of transcript levels for selected differentially expressed genes in RNA-seq comparative analysis of RNA repair mutants and WT S. Typhimurium 14028s under MMC-induced stress

Strains and gene	Fold change by:
	RNA-seq	Northern blotting (mean ± SD)a
ΔrtcR+MMC vs WT+MMC
valb	0.003	0.6 ± 0.06
gltUVWc	0.1	0.7 ± 0.1
yafQ	0.03	0.09 ± 0.01
dinJ	0.03	0.05 ± 0.02
rtcA	0.009	NQd
rtcB	0.004	NQ
rsr	0.003	NQ
rhoL	0.3	0.6 ± 0.2
Δrsr+MMC vs WT+MMC:rhoL	0.3	0.4 ± 0.1
ΔrtcB+MMC vs WT+MMC
gltUVWc	0.2	0.7 ± 0.1
argX	4	1 ± 0.0

^a Transcript levels in each strain were normalized to the lpp transcript level, which was unchanged between strains, for calculation of the fold change between mutant and WT strains.

^b The Northern blot probe annealed to transcripts from valV and valW (tRNA-Val), but only valV showed a significant change in transcript levels in the comparative RNA-seq analysis of ΔrtcR+MMC versus WT+MMC.

^c The Northern blot probe annealed to transcripts from gltU, gltV, and gltW (tRNA-Glu); the indicated RNA-seq fold change is the average of the gltU, -V, and -W fold change values.

^d NQ, not quantifiable the transcript level in the mutant strain was too low to detect in quantitation, so the fold change could not be calculated.