Fig. 3: Perturbation effects of SCZ associated NRXN1 deletions across development.

a UMAPs showing distributions of cell classes (left), time points (top right), and genotypes (bottom right) of SCZ-NRXN1^del donor derived brain organoids. A total of 16 samples were processed – 2 SCZ-NRXN1^del donors and 2 Ctrl donors for 3 weeks (3 wk); 2 SCZ-NRXN1^del donors and 2 Ctrl donors for 2 months (2 mo); 4 SCZ-NRXN1^del donors and 4 Ctrl donors for 3.5 months (3.5 mo). b Ridge plots showing the density of cell abundance across the dimension of pseudotime for 3 wk, 2 mo, and 3.5 mo engineered brain organoids. c, d Dot plots showing significant differential gene expression in deletion vs. control across time points and cell types. The size and color of each dot show the number and significance of overlapping DEGs for each comparison of two cell classes. The significance was measured by \(-{\log }_{10}({FDR\; adjusted\; p\; values})\) of hypergeometric tests (see Methods). e Representative enriched gene sets were shown for GSEA results of DEGs of multiple cell classes using ToppGene. Different categories of Gene Ontology are shown in different colors (blue: molecular function, orange: biological process, and red: pathway). Enrichment scores were defined as \(-{\log }_{10}({FDR\; adjusted\; p\; values})\) to represent the associations between DEG sets and Gene Ontology gene sets.