Fig. 4: Molecular effects of SHH and spatial gene expression patterns in neural organoids.

a, Sample identity (left), annotated cell types (middle) and SHH module score (right) from two replicates of control and SHH-induced organoids scRNA-seq data (UMAP). b, Featureplot of log-normalized expression of markers for main cell types. c, Heatmap of log-normalized and scaled expression for selected examples of differentially expressed genes. d, Featureplot of module scores for marker genes of ventral (floor plate, FP) to dorsal (roof plate, RP) domains of gene expression of the mouse developing caudal neural tube. e, NovoSpaRc reconstruction of DV identities in organoids single-cell transcriptomic data. The left shows a set of positional marker genes is selected from neural tube sRNA-seq data. The middle shows that control and SHH-induced organoids single-cell transcriptomes are merged, and the right shows cells are probabilistically embedded into a DV geometry and genome-wide gene expression is reconstructed. f, The left shows the scaled gene expression of positional marker genes in mouse (top) and human (bottom) scRNA-seq data. The right shows the same in organoid reconstruction based on mouse (top) or human (bottom) expression data. g, Correlation matrix for mouse (top) and human (bottom) versus organoid reconstructed DV gene expression domains, computed on 1,000 highly variable genes subsequently filtered for expression in each dataset. h, Scaled (z-score) expression of a set of genes involved in axon guidance in progenitor cells of the mouse developing spinal cord and in the organoids spatial reconstruction. i, As h, for the reconstruction based on human scRNA-seq data.