Table 1.

Validation of RNA-seq data by qRT-PCR

Target	CodY protein	Copies of transcript relative to sigA*	Expression by qRT-PCR,† %	Expression by RNA-seq,† %
amhX	WT	1.3	0.0	0.0
	F71Y	3.0	1.4	0.9
	R61K	7.2	4.9	5.0
	R61H	45.2	36.2	36.4
	Null	122.6	100.0	100.0
ilvB	WT	14.0	0.0	0.0
	F71Y	124.9	23.3	25.5
	R61K	191.5	37.3	44.0
	R61H	342.7	69.1	74.1
	Null	489.7	100.0	100.0
yoyD	WT	43.8	0.0	0.0
	F71Y	239.0	46.2	61.6
	R61K	382.8	80.2	74.2
	R61H	489.7	105.5	101.5
	Null	466.5	100.0	100.0

^*Transcript abundances were measured by qRT-PCR using RNAs purified from cells grown in chemically defined glucose-ammonium medium with ILV and 13 other amino acids. Transcript abundances are relative to sigA. SEMs were ≤30%.

^†After subtracting the transcript abundances in the WT strain from those determined for the mutant strains, the increased abundance in each point mutant strain was related to the abundance in the codY null mutant strain, which was normalized to 100%.