Fig. 4: Integrative analysis of snATAC-Seq and scRNA-Seq from embryonic mouse forebrain.

a Workflow depicting integration of embryonic snATAC-Seq (top left) and scRNA-Seq (top right) data. Bottom, UMAP plot showing integrated snATAC-Seq nuclei and scRNA-Seq cells colored by tissue. b–d UMAP visualization of integrated snATAC-Seq/scRNA-Seq data colored by assay (b), Louvain cluster (c), and pseudotime (d). e–j UMAP visualization of integrated scRNA-Seq cells and snATAC-sec nuclei colored by transcript counts or GAS for Nes (e, f), Nkx2-1 (g, h), and Neurod2 (i, j). Gray dots in the background represent cells/nuclei from other assays. k–m Genome browser tracks displaying enhancer predictions regulating Nkx2-1 (k), Neurod2 (l), Ascl1 (m), and Emx1 (n). Gene-Peak interactions are visualized in blue arcs, arc heights indicate the relative interaction scores between gene TSS (red line) and peaks. snATAC-Seq Peaks: displays co-accessible coordinates, H3K27ac ENCODE: Forebrain E12.5 H3K27ac peaks from ENCODE project, VISTA: enhancers from the VISTA Genome Browser project.