Extended Data Fig. 6: Characterization of SHH MB single-cell programs.

a, Expression scores for individual programs identified by unsupervised NMF analysis in each sample. Cells are ordered as in Fig. 3a (n = 1,135). Metaprograms SHH-A, SHH-B, and SHH-C were identified by hierarchical clustering of individual programs. b, Heat maps show pairwise correlation (left), PCA (centre), and expression scores for NMF-derived metaprograms (right) for 493 cells from SHH MB sample SJ577. The ordering of cells (rows) is maintained between the heat maps. A two-dimensional representation of the same cells using t-SNE is shown on the far right (coloured by expression scores for each metaprogram). This analysis shows that the same programs and cell populations that are identified by the NMF analysis are also supported by PCA and t-SNE clustering. Furthermore, no additional programs and cell populations are identified (starting from PC3, components are less informative). c, Pairwise correlations between the expression profiles of 303 single-cells (rows, columns) from two SHH PDX samples (RCMB18 and RCMB24) (left). Expression scores for each of the NMF-derived metaprograms SHH-A, SHH-B, and SHH-C (columns) (right). Cells are ordered as in the left panel (rows). d, Heat maps show the relative expression of the 60 genes representing the metaprograms SHH-B and SHH-C (rows), across 303 cells for RCMB18 and RCMB24. Cells are sorted by the difference between the two scores. Cells positive for the cell cycle program (SHH-A) are indicated by red bars. Similar cell populations as in the primary samples (undifferentiated GNP-like and differentiated neuron-like cells) are identified in RCMB18. No differentiated cells are identified in RCMB24.