Extended Data Fig. 8: Molecular effects of SHH and spatial gene expression patterns in neural organoids.

a. GSEA analysis on GO CC, MF and BP terms, and on KEGG pathways, performed on a rank list of differentially expressed genes between control and induced progenitors. P-values: Benjamini-Hochberg-corrected GSEA test. b. Dotplot of exemplary differentially expressed genes in CTR vs SHH organoids, for human neural tube scRNA-seq data. c. Heatmap of HOX genes and additional anterior-posterior markers showing that control and induced organoids have hindbrain/spinal cord identity, marked by expression peak between HOXB2 and HOXC4. d. Featureplot of log-normalized expression of a set of positional marker genes along the ventral (SHH)-dorsal(MSX1) axis. e. Assignment probabilities of progenitor cells from control and induced organoids to each of the 13 progenitor domains specified by positional markers of the mouse neural tube atlas. P-values (Benjamini-Hochberg-corrected Wilcoxon Mann Whitney) for the comparison between control and SHH-induced organoids are indicated on top for each DV domain. f. Correlation matrices for mouse, human and organoids reconstructed DV gene expression, computed on 1000 highly variable genes filtered for expression in each dataset. g. Left: DV scaled (z-score) expression of SIM1 from organoid reconstructed and mouse/human DV domains. Right: featureplot of log-normalized expression of SIM1 in organoids. h. Featureplot of module score for a gene module comprised of the heat shock transcription factor HSF1′s targets.