Extended Data Fig. 9: Deep cell and lineage sampling of micro-dissected regions from cerebral organoids.

(a) Schematic of data projection procedure for single-cells from two regions of a micro-dissected organoid to the whole-organoid scRNA-seq data to assist cell annotation. UMAP embedding of single cells colored by projected annotation from the whole-organoid scRNA-seq data. (b) Expression of selected cell type markers in cells in the two regions of the micro-dissected organoid. (c) Heatmap of cell type and cell state marker genes across all micro-dissected organoid clusters. (d) Hierarchical clustering of the micro-dissected organoid clusters, based on the barcode family composition distances. UMAP embedding of single-cells is colored by the resulting three groups of clusters (CG.1-CG.3). Clusters in each group share similar barcode family compositions. (e) Hierarchical clustering of cluster group 2 (CG.2) based on scar family composition distance, to identify two subgroups of clusters. Clusters in each of the subgroups share similar scar family compositions. (f) Stacked bar plots showing distributions of cell proportions across subgroups of CG.2 clusters with distinct scar family compositions. Each stacked bar shows a different scar family in the same example barcode family 3. (g) UMAP embedding of cells in CG.2 clusters, colored by the two cluster subgroups with distinct scar family compositions, and expression of example genes with differential expression between the two subgroups. (h) Hierarchical clustering of cluster group 3 (CG.3) based on scar family composition distance, to identify three subgroups of clusters. Clusters in each of the subgroups share similar scar family compositions. (i) Stacked bar plots showing distributions of cell proportions across subgroups of CG.3 clusters with distinct scar family compositions. Each stacked bar shows a different scar family in the same example barcode family 4 (left) or barcode family 5 (right). (j) UMAP embedding of cells in CG.3 clusters, colored by the three cluster subgroups with distinct scar family compositions, and expression of example genes with differential expression between the two subgroups.