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Figure 3 (A) Schematic outline for generating a new zebrafish transcriptome annotation. See Results and Materials and methods sections for details. (B) Pie charts showing the proportion of reference genes with same, longer or shorter 3' UTR in the V4.3 annotation compared to relative 3' UTR length between Ens95 and RefSeq. (C, E) Venn diagrams showing intersection of reference genes with commonly annotated NCBI ID that are significantly enriched in (C) kdrlpos- or (E) pdgfrbpos-cells in each indicated annotation. (D, F) Volcano plots of reference genes with common NCBI ID identified as (D) kdrlpos- or (F) pdgfrbpos-enriched only by Ens95 in comparison to RefSeq. Indicated values are from the same genes quantified using V4.3. Red dots indicate log2 fold change >1 and adjp <0.05. (G) 3' UTR lengths and (H) log10 average expression (n = 3) using RefSeq and V4.3 for reference genes in the indicated dataset. (G, H) Data are not normally distributed, Wilcoxon matched-pairs signed-rank test, p values are indicated. Error bars denote mean and standard deviation. (I) Log10 average expression (n = 3) and (J) 3' UTR lengths across all annotations for reference genes uniquely identified as enriched in indicated transgene-positive cell type using V4.3 (log2 fold change >1, padj <0.05). Data are not normally distributed. Friedman test to assess variance (p<0.0001 in all cases). Dunn's multiple comparison test was used for pairwise comparisons, p values are indicated. Error bars denote mean and standard deviation.