Fig. 3: Single-nucleus ATAC-seq of primary and metastatic ependymal tumors uncovers transcription factors and enhancers associated with the differentiation and EMT of posterior fossa ependymoma.

a Single-nucleus ATAC-seq data of 14,461 cells from six primary and metastatic posterior fossa ependymal tumors. The UMAP representation of the data is colored and annotated by the 11 cell populations identified. b Stacked bar chart showing the proportion of each cell type in each of the six tumors. The UMAP representation is labeled according to the origin (primary/metastasis) of each cell (c), and the presence/absence of chromosomal aberrations as inferred from the single-nucleus ATAC-seq data (d). e Transcription factor (TF) binding motif accessibility score for TFs with differentially accessible binding motifs (Wilcoxon rank-sum test; FDR < 0.01) in at least one of the tumor cell populations and z-score fold-change \(\Delta z\ge 1\). f The UMAP representation is colored by the TF binding motif accessibility score of five representative TFs that are significantly associated with individual tumor cell populations and are discussed in the main text. The JASPER database ID for the corresponding motif is indicated in parenthesis. g Venn diagrams showing the overlap between differentially accessible (DA) enhancers and enhancers associated with differentially expressed genes (DEGs) in tumor-derived cell populations. The number of enhancers in each class and the level of significance for the association are indicated (two-sided Fisher’s exact test; **p value \(\le 0.01\)). Numeric p values for MLCs and ependymal cells are 0.0016 and 0.0075, respectively. MLCs mesenchymal-like tumor cells, NPCs neural progenitor tumor cells, OPCs oligodendrocyte progenitor cells.