Extended Data Fig. 2: Molecular signatures and interneuron heterogeneity in the developing cerebral cortex.

Related to Fig. 1. a, Selective expression (normalized) of marker genes per cell type in the combined scRNA-seq dataset. Cell types are grouped on the basis of their identity and shared marker genes. b, Gene signatures for all cell types identified in the combined time points. Top 20 differentially expressed genes for each cell type are presented. Cells were down-sampled to a maximum of 500 cells per cell type. c, Expression of canonical marker genes for selected cell types in the UMAP visualization of the combined scRNA-seq time course. d, Different subtypes of interneuron integrate into the developing cortex through time. Left, clustering of interneurons collected at all time points, visualized via UMAP. Middle, interneuron UMAP plots show the expression of the inhibitory markers Dlx2 and Gad2, as well as a marker of dorsally-derived cell types (Emx1), not expressed by interneurons. Right, proportion of cells corresponding to each cluster in each time point. e, Expression of genes characteristic of interneurons of different embryonic origins. Medial ganglionic eminence (MGE)-derived interneurons express Npy, Sst, Lhx6 and Nxph1. Interneurons originating in the CGE (caudal ganglionic eminence) are positive for Htr3a, Prox1, Cxcl14 and Sp8. A second population of Htr3a⁺ interneurons express Meis2, Etv1 and Sp8, putatively from the pallial–subpallial (P–SP) boundary.