Fig. 2: Transformation of LHX6^high CINs toward subpallial trajectories begins at the precursor stage in the Foxg1 cKO MGE lineage.

a Trajectory analyses of the MGE lineage. Streamlines of RNA velocity indicate the forward developmental direction of MGE lineage, and the yellow dashed lines show the direction in which the pallial LHX6^high CIN trajectory transformed towards the subpallial SIN and GP prototypic neuron trajectories in Foxg1 cKO mice. URD branching trees of the MGE lineage; roots are progenitors, tips are SINs, LHX6^high CINs, GP prototypic neurons, and NKX2-1⁺ SPNs. Color: cell identity. b Double immunostaining of anti-NKX2-1 with LHX6 at E16.5, and quantitative analysis of LHX6⁺NKX2-1⁺ neurons among total LHX6⁺ neurons within the yellow-boxed regions (n = 4 mice in each genotype) showing an increased percentage in Foxg1 cKO mice. Data are presented as means ± SEM. Two-tailed unpaired t test; **P  <  0.01, ***P  <  0.001; Control vs. Foxg1 cKO: **P = 0.0012. Source data are provided as a Source Data file. c UMAP plots showing the subclusters of MGE precursors (Cluster 0) in control and Foxg1 cKO mice. d Box plots showing the expression levels of genes specific for pre-CINs and pre-SINs/GP prototypic neurons in two genotypes (in each genotype, GE cells from three mice were pooled together). The boxes indicate the median and quartiles, the whiskers indicate minimum and maximum values. Triangles in the box indicate mean expression values. Source data are provided as a Source Data file. e Pie plots showing a decreased percentage of Pre-CINs and an increased percentage of Pre-SINs/GP prototypic neurons among the Foxg1 cKO MGE precursors compared to that of the control mice.