Fig. 1

scRNA sequencing reveals tumour subpopulations characterized by specific gene expression patterns in SHH and Group 3 MB models. Analysis of scRNA sequencing data from ONS-76 (SHH) cells a and HD-MB03 (Group 3) cells b growing as 3D hydrogel models identified 9 different graph-based clusters for each cell line (t-SNE plot, see also Additional file 1: Table S1 for cluster characteristics). Gene expression of each cell was used to annotate a particular cell cycle phase. Relative proportion of cells in G1, S and G2/M phase for ONS-76 c and HD-MB03 d cells highlights heterogeneity between clusters (see Additional file 2: Fig. S1 for t-SNE plot of cell cycle annotation). e The network graph highlights similar clusters based on their gene expression (Intersection Tables with Jaccard Indices used to create the network graph are shown in Additional file 2: Fig. S2). Note that clusters O4 and H4 are most similar while cluster H7 is mostly unique in its gene expression compared to all other clusters. (The network graph shows cluster similarity based on the Jaccard indices of shared up-and downregulated genes with the number of connections indicating higher Jaccard values [1: 0.15 < Jaccard ≥ 0.1; 2: 0.2 < Jaccard ≥ 0.15; 3: 0.3 < Jaccard ≥ 0.2; 4: Jaccard ≥ 0.3]). f Extract of Top20 KEGG pathways of significantly up-(dark grey) and down-(light grey) regulated genes are listed for each cluster (full overview shown in Additional file 2: Fig. S3). Note the unique presence of ECM and adhesion subpopulations in ONS-76 clusters while metabolic clusters are dominant in HD-MB03