Figure Legends
Figure 1: 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. 3’ Tag-Seq dip netting versus electrofishing for all tissues
combined, B. 3’ Tag-Seq 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 3’ Tag-Seq comparisons for dip netting versus electrofishing
only for blood samples, F. NEB versus 3’ Tag-Seq comparisons
for electrofishing with immediate sampling versus electrofishing with
delayed sampling only for blood samples.
Figure 2: PCA plots showing PC1 and PC2 for samples that are
differentially expressed among sampling techniques, tissue harvesting
time, and library preparation methods. Treatment groups (called
“condition ”) compared are indicated in different colored
symbols next to each PCA plot. Condition 1 = fish captured by net,
condition 2 = fish captured by electrofishing processed immediately,
condition 3 = fish captured by electrofishing processed 5 minutes after
euthanasia. A. 3’ Tag-Seq dip netting versus electrofishing for
all tissues combined, B. 3’ Tag-Seq 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 3’ Tag-Seq comparisons for dip netting
versus electrofishing only for blood samples, F. NEB versus 3’
Tag-Seq comparisons for electrofishing with immediate sampling versus
electrofishing with delayed sampling only for blood samples.
Figure 3. Violin and box plots comparing gene expression versus
gene length for the whole mRNA-Seq (NEB) and 3’ Tag-Seq library
methods. Each individual plot compares the number of genes with
significantly different base mean expression for NEB versus 3’ Tag-Seq,
calculated as logbasemean NEB - logbasemean 3’ Tag-Seq. Genes with equal
expression fall on the zero line of the y-axis; genes with higher
expression for the whole mRNA transcriptome versus 3’ Tag-Seq have
positive numeric values above 0, while genes with higher expression for
3’ Tag-Seq vs whole mRNA transcriptome have negative numeric values
below 0.