Figure Legends
Figure 1. Bar plot of transcript length versus number of
non-expressed/non-detected genes for each RNA-Seq library technique.Data based on the 14 blood samples processed and sequenced using both
library types. The plot only depicts genes that have been annotated with
a known gene length.
Figure 2. Sample-to-sample distance heatmap . Sample-to-sample
distance heatmaps for the comparison between different sampling
techniques, different tissue harvesting time, and different mRNA-Seq
libraries. The rows and columns are arranged based on hierarchical
clustering, so that samples with similar expression profiles are
positioned near to each other. The color scale represents the distance
between samples. A value of distance 0 indicates that two samples have
identical gene expression. The smaller the distance is, the higher is
the correlation between two samples. Treatment groups (called
“condition ”) compared are indicated in different colors next to
each heatmap. Condition 1 = fish captured by dip netting, condition 2 =
fish captured by electrofishing processed immediately, condition 3 =
fish captured by electrofishing processed 5 minutes after euthanasia.A. QuantSeq dip netting versus electrofishing for all tissues
combined, B. QuantSeq electrofishing with immediate sampling
versus electrofishing with delayed sampling for all tissues combined,C. NEB dip netting versus electrofishing only for blood
samples, D. NEB electrofishing with immediate sampling versus
electrofishing with delayed sampling only for blood samples, E.NEB versus QuantSeq comparisons for dip netting versus electrofishing
only for blood samples, F. NEB versus QuantSeq comparisons for
electrofishing with immediate sampling versus electrofishing with
delayed sampling only for blood samples.
Figure 3. PCA plots showing PC1 and PC2 for samples that are
differentially expressed among sampling techniques, tissue harvesting
time, and library preparation methods. Treatment groups compared are
indicated in different colored symbols next to each PCA plot.A. QuantSeq dip netting versus electrofishing for all tissues
combined, B. QuantSeq electrofishing with immediate sampling
versus electrofishing with delayed sampling for all tissues combined,C. NEB dip netting versus electrofishing only for blood
samples, D. NEB electrofishing with immediate sampling versus
electrofishing with delayed sampling only for blood samples.
Figure 4. PCA plots showing PC1 and PC2 for samples that are
differentially expressed among sampling techniques, tissue harvesting
time, and library preparation methods. Treatment groups compared are
indicated in different colored symbols next to each PCA plot.A. NEB versus QuantSeq comparisons for dip netting versus
electrofishing only for blood samples, B. NEB versus QuantSeq
comparisons for electrofishing with immediate sampling versus
electrofishing with delayed sampling only for blood samples.
Figure 5. Violin and box plots comparing gene expression versus
gene length for NEB and QuantSeq library types. Each individual plot
compares the number of genes with significantly different base mean
expression for NEB versus QuantSeq, calculated as logbasemean NEB -
logbasemean QuantSeq. Genes with equal expression fall on the zero line
of the y-axis; genes with higher expression for the whole mRNA
transcriptome versus QuantSeq have positive numeric values above 0,
while genes with higher expression for QuantSeq vs whole mRNA
transcriptome have negative numeric values below 0. The plot only
depicts genes that have been annotated with a known gene length.