3.3.3 3’ Tag-Seq versus whole mRNA-Seq
We compared the gene expression of the same 14 blood samples for which the library for RNA-Seq was built using both 3’ Tag-Seq and whole mRNA-Seq (NEB). We found 15328 out of 26316 genes (58%) showing different expression, with higher expression observed as a 2-log-fold change from the mean gene expression in one or the other library method (Supporting Information Table S3). Differentially expressed genes between 3’ Tag-Seq vs. NEB were found to be 45%, 41% and 44% respectively for dip netting, electrofishing sampled immediately, and electrofishing sampled after 5 min (Supporting Information Table S3). The proportion of identical genes with differential expression favoring one of the two library methods is highly similar, although there is a slight trend toward a greater number of genes with high expression for NEB relative to 3’ Tag-Seq with increased transcript length (Figure 3).