Extended Data Fig. 2: Validation of GBM-associated astrocyte analyses in an independent patient cohort.
From: Glioblastoma-instructed astrocytes suppress tumour-specific T cell immunity
(a) Transcript capture in snRNA-seq from frozen GBM tissues. (b) Results of copy number variation (CNV) calling algorithm CONICSmat used for exclusion of malignant GBM cells by chromosome 7 polysomy and chromosome 10 monosomy in validation snRNA-seq studies. (c) Cell type calling by use of canonical markers in validation snRNA-seq studies. Clusters 0 and 2 were selected for analysis of astrocytes. (d) Proportion of each cell type captured in validation snRNA-seq studies. (e) Elbow plot showing Principal Component Analysis (PCA) in GBM snRNA-seq astrocyte data. (f) UMAP of validation snRNA-seq analysis of non-malignant cells (n = 6,502 nuclei; Control = 1,154 nuclei, GBM = 5,348 nuclei). (g) Astrocyte cluster proportions by sample. (h) Cluster distribution of subclustered astrocytes in snRNA-seq. (i) Heatmap of cluster markers from GBM astrocyte snRNA-seq validation studies. (j) TNFSF10 expression in GBM cells analysed by scRNA-seq4. OPC, oligodendrocyte progenitor cell; NPC, neural progenitor cell; AC, astrocyte; MES, mesenchymal. n indicates biologically independent samples.
