Table 2.

Comparison between microarray and quantitative real time PCR assays

Days post infection	3	7	14	21	28	42
R2	0.85	0.48	0.91	0.83	0.94	0.87

Seven regulated transcripts with a FDR < 0.05 were randomly selected at 14 dpi. Each primer pair was run with each RNA sample at 3, 7, 14, 21, 28 and 42 dpi. The square of the sample correlation coefficient (R²) between the fold changes observed in the qPCR assays and microarray data sets is shown (Additional file 3). Beta-actin transcript levels were used for data normalisation and RNA levels in mock infected ileum tissues were used for normalisation (see in Materials and methods).