Fig. 2

Regions controlling cell-type identity can be defined by combining snATAC-seq and scRNA-seq. A Schematic workflow to define cell-type-specific signatures. Digital gene expression is obtained from DropViz. For each gene, the 85th percentile of its expression across all cell types was calculated. To define a gene as a cell-type-identity gene, at least 60% of the cells of a cell type should have expression more than the 85th percentile, while at the same time no other cell type was permitted to have the same gene among its top expressed genes (above the 85th percentile) in more than 40% of the cells. Enrichment analysis with cell-type-identity genes found GO terms corresponding to cell-type characteristics. The cell-type-identity peaks are defined by peaks overlapping with the regulatory regions of cell-type-identity genes (basal region ± 100 kb until nearby genes). Subsequently, the enriched motifs in cell-type-identity peaks are detected. B Examples of identified cell-type-identity genes. The identified cell-type-identity genes for six major cell types show selective expression in the respective cell types when observing scRNA-seq data of the entire population of midbrain cells