Extended Data Fig. 9: Characterization of axes of variation in glioblastoma and single nuclei RNA-sequencing of 53,853 nuclei from 10 patient tumors.
a, Spearman correlation of cell type gene signature scores to PC1 and PC2 cell embeddings for combined PCA of GSC and tumor cells (n = 65,655 cells from 28 GSC cultures and 14,207 malignant cells from 7 tumors). Only correlations with Spearman correlation coefficient greater than |0.4| shown. Bars colored by gene signature source. b, Projection of GSCs (top row; n = 65,655 cells) and =patient tumor cells (bottom row; n = 14,207 cells) onto GBM cell state map: astrocyte-like (AC; bottom left quadrant), oligodendrocyte precursor cell-like (OPC; upper left quadrant), neural progenitor cell-like (NPC, upper right quadrant) and mesenchymal-like (MES; bottom right quadrant). Cells are colored by density (left panels) and Developmental - Injury Response gradient program scores (right panels). c, Proportion of cells across samples that map to each of the 4 GBM cell states. d, UMAP visualization of 53,853 nuclei from 10 patient tumors colored by transcriptional cluster (left), patient (middle) and cell type (right). e, Pearson correlation between average transcriptional cluster expression (left). Proportion patient cells per transcriptional cluster (middle), as colored in panel B. Box plots detailing expression of cell type marker genes per cluster (right). Box plots represent the median, first and third quartiles of the distribution and whiskers represent either 1.5-times interquartile range or most extreme value. Outliers are removed. f, Proportion of cell types across tumors (as colored in the right panel of Extended Data Fig. 9d). Numbers in brackets represent the total number of nuclei per tumor.
