A direct comparison of the signal intensity values of these genes indicated that the difference between log and stationary phases was specifically due to differential gene expression and not array spatial bias, as indicated in Figure 2. When the

average gDNA intensity values for these 454 genes were plotted (stationary phase versus late-log phase), the R2 value was 0.83 (Figure 2A). However, the R2 value for the same genes comparing the Cy3 selleck chemical fluorescence values instead (labeled cDNA amplified from RNA) was extremely low (R2 = 0.049, Figure 2B). Figure 2 Fluorescent signal values of B. melitensis transcript or gDNA from differentially expressed genes at stationary and late-log phases of growth. Average Cy5 (gDNA) or Cy3 (transcript) signal values

for B. melitensis grown in F12K MG 132 tissue culture medium to late-log and stationary phases (4 arrays each) were plotted in Excel. Each dot represents the signal value for an individual spot on the array, determined to be significantly differentially expressed between late-log and stationary phases. (A) Comparison of genomic DNA levels of significant genes at stationary and late-log phases of growth. Stationary phase gDNA signal values are on the ordinate, and late-log phase signal values are on the abscissa. The R-squared value (0.8341) VX-770 supplier is displayed in the upper right-hand quadrant of the graph. (B). Comparison of transcript levels of significant genes at stationary and late-log phases of growth. Stationary phase transcript signal values are on the

ordinate, and late-log phase signal values are on the abscissa. Note the very low R-squared value (0.049), displayed in the upper right-hand quadrant of the graph. Stat refers to stationary phase, Y-27632 2HCl log refers to mid-log phase, and gDNA refers to genomic DNA. To confirm the microarray results, we randomly chose 18 differentially expressed genes (one from each COGs functional category) and performed qRT-PCR. Based on qRT-PCR results, transcript levels of 15 of these genes (83%) were altered greater than 2.0-fold and in the same direction as was determined by microarray analysis. Two other genes (BMEI0402 and BMEI0642) were determined to be differentially expressed and in the same direction of microarray analysis, but the fold change was lower than 2. No significant difference in the expression level of BMEI0344 was observed by qRT-PCR (Figure 3). Figure 3 Validation of DNA microarray results by quantitative RT-PCR. Eighteen randomly selected ORFs that were differentially expressed based on microarray analysis between late-log and stationary growth phase were validated by quantitative RT-PCR. Seventeen of 18 ORFs tested showed fold-changes in the same direction by both methodologies and 15 of them were also altered greater than 2-fold.