Fig. 4

Direct comparison of scRNAseq and snRNAseq datasets on the level of major cell types. A Dot plot showing the expression of all genes used as cell type markers (Additional file 2: Table S2) in scRNA (red lanes) and snRNA data (blue lanes) split by cell type. The color intensity of the dots represents the expression level of a gene in a cluster and the size of the dots represent the percentage of cells in a cluster expressing the respective gene. B, C UMAPs of integrated scRNAseq and snRNAseq data. Cells are colored by cluster identity B or the initial dataset (i.e. scRNAseq and snRNAseq) C. The cluster annotations are based on a combination of similar clusters. See Additional files 1 and 3: Fig. S9 and Table S3 for the annotation of all clusters prior to cluster merging. D Proportion of cell or nuclei contribution to each cluster by dataset. The total number of cells in each cluster is provided for each cell type at the top of the bar plot. E Alluvial plots depicting changes of cell identities between separately analyzed scRNAseq (left) and snRNAseq (right) data and integrated data. The Y-axes indicate the number of cells (left) and nuclei (right) of the separately analyzed datasets