Fig. 1

A–C Differential expression of autism risk factor transcripts among foetal cortical cardinal cell classes. A t-SNE plot showing the cardinal cell classes identified in the dataset. B Violin plot illustrating the expression pattern of marker genes among the six cardinal cell classes. C Heatmap illustrating the expression pattern of significantly differentially expressed autism risk factor transcripts across cardinal cell classes (Wilcox test, adjust p < 0.05, log (fold change) > 0.3). Top: monogenic autism risk factor transcripts; Bottom: 16p11.2 transcripts. D, E Unsupervised clustering within the cardinal classes and similarity comparison between cell clusters. D Unsupervised clustering subdividing the cardinal classes into 21 different cell clusters. OPC, astrocytes, and microglia were not further clustered. E Heatmap illustrating the expression pattern of differentially expressed autism risk factor transcripts across 21 cell clusters (Wilcox test, adjust p < 0.05, log (fold change) > 0.3) for differentially expressed monogenic autism risk factor transcripts (top panel) and differentially expressed 16p11.2 transcripts (bottom panel)