Extended Data Fig. 4: Spatial chromatin accessibility mapping of E11 mouse embryo and spatiotemporal analysis (50 µm pixel size).

a, Unsupervised clustering analysis and spatial distribution of each cluster. Overlay with the tissue image reveals that the spatial chromatin accessibility clusters precisely match the anatomic regions. For better visualization, we scaled the size of the pixels. b, UMAP embedding of unsupervised clustering analysis for chromatin accessibility. Cluster identities and colouring of clusters are consistent with (a). c, Spatial mapping of gene scores for selected marker genes in different clusters and the chromatin accessibility at select genes are highly tissue specific. d, Integration of scRNA-seq from E11.5 mouse embryos²⁰ and spatial ATAC-seq data. Unsupervised clustering of the combined data was coloured by different cell types. e, Anatomic annotation of major tissue regions based on the H&E image. f, Spatial mapping of selected cell types identified by label transferring from scRNA-seq to spatial ATAC-seq data. g, Pseudotemporal reconstruction from the developmental process from radial glia to excitatory neurons plotted in space. h, Spatial mapping of gene scores for Notch1. i, dynamics for selected gene score along the pseudo-time shown in (g). j, Pseudo-time heatmap of TF motifs changes from radial glia to excitatory neurons.