Fig. 3

Comparison between snRNA-seq and scRNA-seq datasets following harmonization on reference dataset. A Global UMAP plots and cell type prediction in the scRNA-seq (middle panel) and snRNA-seq (right panel) following harmonization on the reference dataset generated by integrating five published scRNA-seq datasets of cultured human islets [21, 23, 26, 27, 57] (left panel). Y-axis is similar in all three panels. B Venn diagram of detected genes in the reference (pink circle) and in our scRNA-seq dataset (blue circle). C Venn diagram of detected genes in our scRNA-seq (blue circle) and in our snRNA-seq dataset (green circle). D, E Scatter plots of harmonized cell type-specific gene expression in α-cells, β-cells, PP-cells, or δ-cells D between the reference and the scRNA-seq datasets and E between the scRNA-seq and the snRNA-seq datasets. X-axis and Y-axis represent the expression levels in natural log of counts in the indicated datasets. The blue line in each plot represents the regression line, whose fit is indicated by the R² value (the square of the Pearson correlation coefficient). The P and R values are provided for each correlation. F Fractional overlap expressed in percentages (%, Y-axis) of increasing numbers (100, 200, 500, and 1000, X-axis) of top genes within α-cells (yellow bars), β-cells (green bars), PP-cells (blue bars), or δ-cells (red bars) in reference vs. scRNA-seq (upper panel) and in scRNA-seq vs. snRNA-seq (lower panels) datasets following harmonization to the reference. G Pie chart representing proportions of biotypes of genes detected with higher confidence in snRNA-seq compared to scRNA-seq (snRNA-seq enriched genes)