Fig. 1: A comprehensive single-cell atlas of precursor cells across cortical development.

a Schematic overview of the experimental workflow. Forebrain samples were collected from Sox2eGFP mice at 11 developmental timepoints, dissociated into single cells followed by sorting of the GFP + ve /−ve cells and performing single-cell RNA-seq using the 10x Genomics Chromium platform. b Left: two-dimensional Uniform manifold approximation and progression (UMAP) plot with Leiden clustering of 102,504 individual cells identifying 28 transcriptionally and biologically distinct cell types (see Supplementary Fig. 3a and Methods). Each dot represents a single cell and colours correspond to the distinct clusters/cell types. Shown on the right is a dot plot showing the relative fraction (dot size) of the 28 cell types at each developmental timepoint normalized by library size. c UMAP plot of the cells as in (b) but coloured by timepoint. Each dot represents a single cell and the colours correspond to the different timepoints. d, UMAP plot showing the coarse annotation of cells into 4 categories (Neuronal, Glial, Immune and Vascular/other) based on logistic regression from Zeisel et al. 2018. The RNA-velocity field is overlaid on the UMAP. Colours represent the 4 categories of cell annotation and the arrows correspond to the direction of the RNA-velocity flow field (see Methods). RG Radial glia, TAPs Transient amplifying progenitors, aNSCs Active neural stem cells, APCs Astrocyte progenitor cells, EmNBs Embryonic neuroblasts, GE NBs Ganglionic eminence neuroblasts, OPCs Oligoprogenitor cells, PreM-ODCs Immature pre-myelinating oligodendrocytes, INs Interneurons, ImStNeurons Immature striatal neurons, VLMC Vascular leptomeningeal cells, Myeloid-DSCs Myeloid-derived suppressor cells.