Dataset used

Throughout this manual, we use the single-nucleus RNA-seq dataset from Blanco-Carmona et al. (2025):

A cycling, progenitor-like cell population at the base of atypical teratoid rhabdoid tumor subtype differentiation trajectories

Blanco-Carmona E, Paassen I, He J, DeMartino J, Büllesbach A, Anderson N, et al.

Neuro-Oncology. 2025. DOI: 10.1093/neuonc/noaf179 | PMID: 40726147

This dataset contains single-nucleus transcriptomic data from Atypical Teratoid Rhabdoid Tumors (ATRTs), highly aggressive pediatric central nervous system tumors defined by SMARCB1 inactivation. The study identified three distinct molecular subtypes with unique differentiation trajectories.

The sample is automatically loaded via _common.R and is available as the sample object in all code examples.

Sample preparation

The Seurat object was prepared following the methodology described in the publication.