EvgSc (n = 2) and wild-type (n = 2) cultures were used for microarray profiling. RNA was isolated from cells using the Qiagen RNeasy kit (Qiagen, USA) according to the manufacturers' instructions. RNA purity and quality were checked using a Nanodrop spectrophotometer (Thermo Scientific, USA) and Agilent Bioanalyser system respectively. The 260/280 nm absorbance ratio was between 1.8 and 2.1 for all samples and the average RIN score was > 8. Fifty nanograms of input RNA was labelled with Cy3 dye using an Agilent Low-Input Quick Amp kit (Agilent, USA) with random primers according to the manufacturer's protocol. Six hundred nanograms of labelled cDNA was hybridized overnight to Agilent E. coli Gene Expression Microarrays then immediately washed and scanned using an Aglient SureScan microarray scanner in accordance with the recommended procedure.
Array data were normalized using quantile normalization (Bolstad et al., 2003 (link)). Fold change ratios were calculated between all wild-type and EvgSc sample pairs. Differentially expressed genes were identified using the fold change ratios by applying a one sample t-test followed by Benjamini-Hochberg FDR correction (Benjamini and Hochberg, 1995 ). Genes with a false discovery rate (FR) < 1% and an average log2-fold change of > 2 were defined as differentially expressed.
Array data were normalized using quantile normalization (Bolstad et al., 2003 (link)). Fold change ratios were calculated between all wild-type and EvgSc sample pairs. Differentially expressed genes were identified using the fold change ratios by applying a one sample t-test followed by Benjamini-Hochberg FDR correction (Benjamini and Hochberg, 1995 ). Genes with a false discovery rate (FR) < 1% and an average log2-fold change of > 2 were defined as differentially expressed.