Extended Data Fig. 11: Use of developmental atlas to investigate Fezf2-knockout cortex.

Related to Fig. 5. a, Violin plots of number of genes (left), number of mRNA molecules (counts; middle), and percentage of mitochondrial counts (right) per cell in control (Het) and Fezf2 knockout, and UMAP visualizations of merged scRNA-seq datasets at E15.5 (top) and P1 (bottom). UMAP visualizations are coloured by genotype or assigned cell type. b, UMAP visualization of single-cell transcriptomes from the excitatory lineage of control and KO cortices at P1 (as shown in Fig. 5c for E15.5), coloured by genotype (left) and cell type (right). Proportion of cells of each cell type by genotype (bottom). c, Heat map showing the overlapping scores between NMF modules identified in the E15.5 Fezf2 datasets and the original E15.5 wild-type modules. All modules were identified with an overlapping score of 40% or higher. d, Left, scaled module expression of significant modules in all cells (two-sided Wilcoxon Sum Rank test, Bonferroni correction). Right, average expression of the top 30 genes from selected modules, in apical and intermediate progenitors, and excitatory neurons, by genotype. Differential expression between control (Fezf2 Het) and knockout neurons, at the single-cell level (two-sided Wilcoxon rank-sum test, Bonferroni correction). e, Gene Ontology terms enriched in the Fezf2-knockout-specific module. f, Confusion matrix for random forest classifier calculated using 1,000 cells per cluster of the wild-type developmental atlas. The remaining held-out cells were used to test accuracy. g, Classification of control (Fezf2 Het) and Fezf2 knockout excitatory neurons by the classifier presented in f, for P1 (left) or E15.5 (right) datasets. Cells are grouped according to their manually assigned identity on the basis of the expression of marker genes. Box plots to the right show the corresponding classification scores in which the middle line is the median, the lower and upper hinges correspond to the 25% and 75% quantiles, the upper whisker corresponds to the largest value no larger than 1.5 × IQR from the hinge and the lower whisker corresponds to the smallest value at most 1.5 × IQR of the lower hinge. Lines in magenta, cyan and green indicate 1, 0.5 and 0 values, respectively. Total number of cells: Fezf2 Het E15.5 = 6,092, Fezf2 knockout E15.5 = 6,110, Fezf2 Het P1 = 5,101, Fezf2 knockout P1 = 4,235.