Fig. 2: Early progenitors can be divided into nine progenitor subtypes.

a, Transition from primarily neuroepithelial to radial glia progenitor identity. Immunostaining of early first trimester samples (including CS14, shown here) show strong staining for all progenitors (SOX2, red), as well as tight junctions (ZO-1, cyan), but limited staining for radial glia (NES, green). By CS22, NES staining increases substantially, ZO-1 decreases and SOX2 expression is maintained. Scale bars, 50 μM. b, scRNA-seq identifies nine progenitor subpopulations. Left: a UMAP plot depicts subclustered progenitor cells; middle: the velocity trajectory across progenitor subtypes. Right: feature plots show high expression of VIM and SOX2 marking all progenitor populations. c, NTRK3 marks progenitor populations before becoming a neuronally enriched marker. Progenitor cluster 3 is specifically and uniquely labeled by NTRK3, as shown in the violin plot. Immunostaining for NTRK3 (cyan) shows early labeling of SOX2 (red) positive progenitors at CS16 (white arrows), but expression shifts to more closely coincide with newborn neurons marked by DCX (green) by CS18 (white arrows). Scale bars, 50 μM. d, DLK1 marks a subset of early progenitors. DLK1 (cyan) is the top marker for progenitor cluster 8 and is exclusively expressed in early first trimester, as shown in the violin plot on the left. Immunostaining for DLK1 at CS16 shows colocalization with low SOX2 (red) expressing cells at the boundary of the cortical edge. This staining disappears from the cortex entirely by CS18 when DCX (green) staining emerges. For all panels, each sample was immunostained once.