Extended Data Fig. 9: Characterization of scATAC–seq atlas and developmental trajectories of accessible elements through cortical development.

Related to Fig. 4. a, scATAC–seq data per time point. UMAP visualization of the single cells coloured by their predicted identity from integration with scRNA-seq datasets (left). Gene accessibility of selected markers for main cell types present in each time point (middle). Maximum prediction score for each cell based on labels transferred from scRNA-seq data (right). b, URD chromatin accessibility trajectories during cortical development. Cells are coloured according to their age of collection. c, ATAC trees highlighting the accessibility of marker genes characteristic of the different cortical cell types, including apical and intermediate progenitors, astrocytes, callosal and corticofugal neurons. d, RNA-based tree generated from only the E13.5, E15.5 and E18.5 time points, corresponding to the scATAC–seq data. Trees are coloured by cell type (left) and time of collection (right). e, Chromatin accessibility and gene expression cascades for layers 2&3 CPN and SCPN. Same genes are plotted for both modalities, in the same order. f, Chromatin accessibility and gene expression across pseudotime for illustrative genes from the SCPN cascade, CPN markers, or general neuronal markers plotted on the SCPN cascade. In many cases accessibility rises before gene expression.