Fig. 8

Ganglioglioma spatial transcriptomics shown for two samples from tumor 1 and tumor 4. A, B Spatial feature plots of final clusters for tumor 1 (A) and tumor 4 (B). Note ‘U’ in the final cluster name is used to denote union of multiple Space Ranger-generated graph-based (kNN) clusters. C GO term enrichment for select tumor 1 clusters. D, E Cell type proportions per spot as determined by cell2location with snRNA-seq as reference for tumor 1 (D) and tumor 4 (E). OPC = oligodendrocyte precursor cell. VLMC = vascular leptomeningeal cell. F Tumor 1 cell2location-calculated neuroectoderm neural precursor cell-like cell abundance per spot. G Analogous to F but for tumor 4. H–J Inverse correlation of neuroectoderm neural precursor-like cell proportion and that of vascular (H), microglial (I), and lymphoid (J) cells, shown for tumor 1 spot cell proportions calculated by cell2location with snRNA-seq clusters as reference. Points and curves are colored according to the cell type whose proportion is being compared to the proportion of neuroectoderm neural precursor-like cells. Curves (outlined in black to enhance visibility) represent non-linear (exponential) least-squares fit for each reference cell type. (K) Overall (left) and cell type-specific (right) expression of neuroectoderm neural precursor celllike cell markers as well as important transcription factors and ligand-receptor pairs based on snRNA/CITE-seq analysis. L Feature plots of log1p (base 2) [RNA] for examples of top spatially-variable features from tumor 1, as determined by mark-variogram method in Seurat