Fig. 3: Lineage-specific gene expression converges in uncommitted progenitors.

a Experimental design for cortical in vitro differentiation assays. b, c Immunohistochemistry (b) and quantifications (c) showing BCL11B, SATB2, SOX5 or POU3F2 expression in TUJ1⁺ neurons derived from E9.5 cortical cells after in vitro differentiation (n = 5 biological independent experiments). d Violin plots show correlations between the transcriptomes of E9.5 cells, uncommitted E11.5 cells (grey) or cells committed to deep-layer (cyan; red line; P-value < 1e-300) or upper-layer (green; blue line; P-value < 1e-300) differentiation trajectories. These correlations are based on 46 E9.5 cells 51 uncommitted E11.5 cells, 25 cells committed to deep-layer differentiation and 21 cells committed to upper-layer differentiation. e tSNE-NN maps coloured by WGCNA gene set enrichment scores for deep-layer-trajectory gene set 1 (red line) and upper-layer-trajectory gene set 1 (blue line). f tSNE-NN map coloured by Orc1 (from deep-layer-trajectory gene set 1; pink 20–100 RPKM, red >100 RPKM) and Cdca2 (from upper-layer-trajectory gene set 1; light-blue 60–100 RPKM, blue >100 RPKM) expression, with co-expressing cells coloured in green. g GO-term fold enrichments and P-values for genes in WGCNA deep-layer-trajectory gene set 1 (red) and upper-layer-trajectory gene set 1 (blue). Violin plots are inset by rings corresponding to the individual data points, a filled dot at the group mean and a vertical line showing standard error. Scale bar in (b) represents 10 µm. Statistics based on two-tailed t tests; ***P < 1e-300. P-values for the GO-term analysis are derived from a Binominal test. Source data are provided as a Source Data file.