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Figure 5 (A) Venn diagrams illustrating intersection by common LL gene ID of genes enriched in mia-positive cartilage cells and and1-positive epidermis cells by both indicated annotations. (B) 3' UTR lengths from Ens95 and V4.2 for reference genes identified as cartilage or epidermis-specific uniquely by V4.2. Data are not normally distributed (Shapiro-Wilks test), comparison by Wilcoxon matched-pairs signed-rank test, p-values are shown. (C) Volcano plots showing cartilage- or epidermis-specific genes identified selectively by V4.2 with corresponding values from bulk RNA-seq comparison of pdgfrbpos and pdgfrbneg cells. Red indicates log2 fold change >1 (pdgfrbpos/pdgfrbneg), padj <0.05. (D, E) tSNE plots of the mia-positive cartilage cluster showing expression levels of sox9a and fzd9b using scRNA-seq data quantified using (D) Ens95 and (E) V4.2. Legends indicate log-transformed and normalized expression levels per cell. (F) UCSC browser image of sox9a and fzd9b loci showing 3' UTR annotations from V4.2 and Ens95. Both loci are located on the negative strand. Mapped read depth from kdrlpos cells on the genome, or assigned to each annotation are indicated, as are 3P-seq features, all of which reside in the same orientation as the genes themselves.