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.