Extended Data Fig. 1: Identification of malignant cells and their developmental states from scRNA-seq and scATAC-seq data.
From: Evolving cell states and oncogenic drivers during the progression of IDH-mutant gliomas
a. Genome tracks show aggregated (pseudo-bulk) scATAC-seq data for IDH-mutant gliomas (n=10) over a representative neural locus (ASCL1). b. UMAP visualization of IDH-mutant glioma cells profiled by scRNA-seq and scATAC-seq. The leftmost plots indicate annotated malignant cells, while the others depict expression or promoter and gene body accessibility (red) of cell type-specific genes. c. Genome tracks show aggregated scRNA-seq and scATAC-seq data over representative cell type-specific genes. d. CNAs inferred from scATAC-seq data for malignant cells from IDH-mutant cohorts used in this study (see Methods). CNAs inferred directly from the scATAC-seq data (right) were consistent with CNAs derived by applying inferCNV to imputed gene activity scores (left). e. UMAP visualizations of integrated scRNA-seq and scATAC-seq data from normal fetal and adult brain cells. Cells are colored by annotated cell types (left) and donor types (right). f. Pie charts depict the distributions of cell state annotations nominated by scRNA-seq (left) or scATAC-seq (right). g. Gene programs enriched in OPC-like cells from IDH-mutant oligodendrogliomas (IDH-O) or astrocytomas (IDH-A) by NMF analysis. h. Genome tracks show aggregated scATAC-seq data for each cell state over oligodendrocyte- (APOD) and astrocyte-specific (APOE) genes.
