3.3.4 Comparisons between tissue type within the same sampling groups
We found that blood and muscle have the lowest number of genes recovered in both tissues compared to the other pairwise tissue comparisons (Supporting Information Tables S3 and S4). We observed differences in gene expression among tissue types (blood, muscle, gills) for each of the sampling methods. Of all the genes that are significantly differentially expressed (adjusted p - value <0.05) among tissue types, only 25-32% are more highly expressed in blood compared to gill and muscle (Supporting Information Tables S3 and S4). Conversely, the proportion of significantly differentially expressed genes in gill and muscle was much more even and within ±10 of 50% (Supporting Information Tables S3 and S4).