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).