Fig. 5: FOXG1-driven transcriptional programs direct the fate choice of ID3^high OBINs versus GP arkypallidal neurons and of SP8^high OBINs/PROX1^high CINs versus amygdala neurons.

a, b Scatterplots showing the expression levels of representative genes along the developmental trajectories of the FOXP2^highSP8^low lineage and FOXP2^lowSP8^high lineage in the control mice. Dots: single cells. Vertical axis: normalized gene expression. Horizontal axis: cellular pseudotime of each trajectory. Color: cell identity. c Venn plot showing overlapping genes among the top 500 most dynamic genes of ID3^high OBINs, the top 500 most dynamic genes of GP arkypallidal neurons, and the dLGE/CGE DEGs, and the identification of the three category DEGs of FOXP2^highSP8^low lineage. d Venn plot showing overlapping genes among the top 500 most dynamic genes of SP8^high OBINs/LHX6^high CINs, the top 500 most dynamic genes of amygdala neurons, and the dLGE/CGE DEGs, and the identification of the three category DEGs of FOXP2^lowSP8^high lineage. e Gene programs of connected modules identified by NMF. The connections among the 5 gene modules of different developmental stages in the FOXP2^highSP8^low lineage and the top 10 ranked TFs of each gene module are shown. Dots: NMF modules; Connections indicate the transcription similarity between two modules; Genes among the dLGE/CGE DEGs are bold (refer to Supplementary Data 6). f Gene programs of connected modules identified by NMF. The connections among the 8 gene modules of different developmental stages in the FOXP2^lowSP8^high lineage and the top 10 ranked TFs of each gene module are shown. Genes among the dLGE/CGE DEGs are bold (refer to Supplementary Data 6). g Immunostaining against mCherry and PROX1 at E16.5 in wild type mice (E12.5 IUE) and quantification analysis of the percentage of pallial or subpallial mCherry⁺PROX1⁺ neurons among total mCherry⁺PROX1⁺ neurons that distributed in the entire pallial and subpallial regions in two groups (n = 5 mice in each group). Data are presented as means ± SEM. Two-tailed unpaired t test; **P  <  0.01, ***P  <  0.001, ****P  <  0.0001; Pallium: ****P  <  0.0001, Subpallium: **P  = 0.0011. Source data are provided as a Source Data file. White arrows: pallial mCherry⁺PROX1⁺ neurons, yellow irregular circle: subpallial mCherry⁺PROX1⁺ neurons.