Significant differentially expressed genes in the brains of harbor seals with a Phocine herpesvirus-1 infection in the brain.

To determine differentially expressed genes (DEGs) between animals infected with PhV-1 and those with an unknown cause of death (UCD), counts per transcript were analyzed using the R version 3.2.2 with software packages Bioconductor 3.1 and DESeq2-1.8.2. For each gene, DESeq2 fits a log generalized linear model with a negative binomial distribution and normalizes genes counts (23). Transcripts were significantly different if they had at least an adjusted p-value ≤ 0.05. Importantly, since in this study we are comparing two diseases with no true control samples, a positive log fold change was considered up-regulated in UCD samples, while if the log fold change was negative it was considered up-regulated in PhV-1 infected samples.