Figure 2.

Integrated snRNA-seq and snATAC-seq indicates a stem-like signature in the RE tumor population

(A) Diffusion map visualization of tumor cells in OD and AS tumors, based on publicly available⁴ astro-like, oligo-like, and stemness program markers. Right: scaled and centered enrichment scores for NMF metaprograms. Cells are ordered along diffusion components 1 (DC_1) and 2 (DC_2); gradient cells were excluded for clarity.

(B) Scaled and centered pathway activity scores (normalized weighted mean from snRNA-seq) for OD and AS tumors.

(C) Scaled and centered regulon activity scores (normalized weighted mean from snRNA-seq) for OD and AS tumors.

(D and E) UMAP embedding of OD (D) and AS (E) snATAC-seq data (OD n = 4, AS n = 5) colored by labels transferred from snRNA-seq datasets. UMAP1, x axis; UMAP2, y axis.

(F) Bar plot showing proportion of cell types in snATAC-seq data.

(G) Pearson correlation of highly variable peaks from snATAC-seq data in OD and AS tumors.

(H and I) Heatmap showing the top significantly enriched transcription factor motifs in OD (H) and AS tumors (I). Scores are scaled and centered for clarity.