Table 1.

Experimental design and comparisons

Comparison	Cell strains and experimental conditions	Differentially expressed genes are:
A	axenic AX2 cells incubated on E. coli for 2 hours axenic AX2 cells incubated in medium for 2 hours	upregulated, if the log2 ratio of RNA expression values in nominator vs. denominator: ≥ 1
B	AX2 cells growing exponentially on E. coli AX2 cells growing exponentially in medium
C	axenic AX2 cells incubated on E. coli for 2 hours AX2 cells growing exponentially on E. coli	downregulated, if the log2 ratio of RNA expression values in nominator vs. denominator: ≤ -1
D	V12M2 cells growing exponentially on E. coli AX2 cells growing exponentially on E. coli