Validation of DGE data by qPCR and serum cytokine analysis. (A) qPCR validation of DGE data. Relative quantification was carried out to measure changes in target gene expression in lung samples relative to an endogenous reference sample. Results are expressed as the target/reference ratio of each sample normalized by the target/reference ratio of the calibrator; HPRT1 was used as a reference gene. The Y axis indicates the fold change of transcript abundance in H-PRRSV infected pigs compared to the C. For the C sample, the fold change of transcript abundance relative to the C sample equals one. qPCR-B: the RNA samples from independent extractions from biological replicates; qPCR-P: the RNA samples from pooled samples that were used for deep sequencing. Error bars represent SE. (B-C) the correlation between change in protein concentration from serum and transcript abundance from lungs. The levels of cytokines (TNFα and IFNγ) in serum were analyzed using ELISA. The levels at 96 and 168 hours were compared with the C to determine relative changes. The Y axis represents the relative fold change.