Figure 3

Hierarchical clustering of transcriptome profiles after experimental infection with E. coli. Tissues of udder quarters of five healthy untreated cows (c24h-1 to 5) were used to generate three replicates of expression profiles as controls for three separate comparisons. A: Replicate 1 (c₁24h-1 to 5) was compared to patterns of infected udder quarters 6 h after inoculation with E. coli 1303 (i6h-6 to 10). B: Replicate 2 (c₂24h-1 to 5) was compared to patterns of infected udder quarters 24 h after inoculation (i24h-1 to 5). C: Replicate 3 (c₃24h-1 to 5) was compared to patterns of noninfected quarters of infected cows 24 h after infection (n24h-1 to 5). Samples for n24h-1, 2, 3 and 5 were pooled from one mock inoculated and one untreated udder quarter, while n24h-4 was derived from tissue of a single untreated quarter. The degree of similarity of their expression patterns is shown as a heatmap of the distance matrix (red: more similar, blue: less similar). The trees depict the pair wise relations with branch lengths proportional to the degree of similarity.