FIGURE 6.

Cell type-specific gene expression comparison between scRNA-Seq and snRNA-Seq. (A) Violin plots to left in upper (scRNA-Seq) and lower (snRNA-Seq) panels show the distribution of the number of genes per cell (upper panel) or nuclei (lower panel) along the vertical axis. In general, transcriptome profiles from cells exhibited a greater number of genes per cell than transcriptome profiles from nuclei. This trend continued as expected when looking at cell type-specific gene expression in marginal, intermediate, and basal cells in the panels to the right in both scRNA-Seq (upper panel) and snRNA-Seq (lower panel). (B) Cell type-specific expression of differentially expressed genes (DEGs) was lower in the scRNA-Seq data compared to the snRNA-Seq data in marginal, intermediate, and basal cells. nGene refers to number of differentially expression genes. (C) Gene counts for WGCNA cell type-specific modules did not demonstrate a consistent relationship between scRNA-Seq and snRNA-Seq datasets. (D) Gene counts for SCENIC cell type-specific regulons in general demonstrated a higher gene count per cell type in scRNA-Seq compared to snRNA-Seq. nGene (# of genes).