Figure 2

Differential expression of genes between and within the lines of mice prior to, and in response to, C. rodentium infection. (a) Summary of transcripts differentially expressed in individual and combined comparisons. The analysis was performed using an Affymetrix whole mouse genome oligonucleotide chip (430 2.0 Array), which contains >45,000 probe sets comprising expression levels of >39,000 transcripts and variants from >34,000 well-characterized mouse genes. The normalization and processing of the results were performed using DNA-Chip Analyzer (dChip) software implementing model-based expression analysis. One percent of the total probe sets presented on the array were more than two-fold differentially expressed between SW and FVB mice prior to infection. In response to C. rodentium inoculation, 11.4% of the probe sets were either induced or repressed in one or both of the lines of mice. There were more differentially expressed genes in response to infection in susceptible FVB mice than in resistant SW mice, especially as disease progressed. Overall, alterations in 12.4% of the probe sets were detected throughout the experiment. (b) Validation of microarray results by qRT-PCR (TaqMan) of selected genes. Transcript levels were normalized to the endogenous control GAPDH, and expressed as fold change compared with untreated control FVB mice, which were set at 1, using the Comparative Ct method. The resultant log2 ratios were matched with corresponding log2 ratios detected in microarray analysis and subjected to Pearson correlation analysis. Significant correlation was observed between the two assays (Pearson correlation coefficient r = 0.87, R² = 0.75, p < 0.0001). Pearson correlations for individual genes ranged from 0.67 to 1. Only two out of 35 examined genes did not confirm the array results, yielding a predictability rate of 94%.