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A cycling, progenitor-like cell population at the root of atypical teratoid rhabdoid tumor subtype differentiation trajectories [bulk RNA-Seq]

GSE283833 Homo sapiens (human) Single-nucleus RNA-seq 16 samples Submitted 2025/07/24 Platform GPL24676
At a glance

Single-nucleus RNA-seq · human · 16 samples

What it is
Single-nucleus RNA-seqGene activity measured in individual nuclei (used when whole cells are hard to isolate, for example from frozen tissue). Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
Homo sapiens (human)
Samples
16 samples: 8 conditions, mostly in duplicateGroups are read from the sample names, not from the paper. Check the list below.
Data you can get
A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper
A cycling, progenitor-like cell population at the base of atypical teratoid rhabdoid tumor subtype differentiation trajectoriesNeuro-oncology · 2025
Summary (written by the submitters)
Atypical teratoid rhabdoid tumors (ATRTs), characterized by the loss of SMARCB1, are among the most lethal pediatric brain tumors. Three molecular subtypes have been identified, each defined by distinct molecular and clinical features. Still, no subtype-specific treatments are available, highlighting the need to understand their inter and intra-subtype heterogeneity.
Read the full summary ↓
Here, we generated a single-nucleus transcriptome atlas of ATRTs, validated with single-cell ATAC-seq and spatial transcriptomics, to study subtype-specific differentiation trajectories. We identified retained brain progenitor expression profiles within unique subtype-specific differentiation lineages. A shared cycling, progenitor-like cell population, interspersed throughout tumors, was observed across all ATRT patients. Finally, we demonstrate that subtype-specific differentiation trajectories can be induced pharmacologically in ATRT tumoroids directing tumor cells towards a non-proliferative, mature phenotype. Our study reveals that ATRT subtypes exhibit signaling trajectories mirroring normal fetal brain development, potentially enabling the development of maturation therapies tailored towards ATRTs.
Published in
A cycling, progenitor-like cell population at the base of atypical teratoid rhabdoid tumor subtype differentiation trajectories
Blanco-Carmona E, Paassen I, He J et al. · Neuro-oncology 2025 · PMID 40726147 · doi:10.1093/neuonc/noaf179
This dataset
Open GSE283833 in finder → Find more human RNA-seq datasets →
Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE283833_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1195872. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40726147) ↗
Study design
8 conditions, mostly in duplicate
AT-SHH04 tumoroid model treated with DMSO ×2 AT-SHH04 tumoroid model treated with Entinost… ×2 AT-SHH04 tumoroid model treated with RO31-822… ×2 AT-SHH04 tumoroid model treated with Thiostre… ×2 AT-MYC08 tumoroid model treated with DMSO ×2 AT-MYC08 tumoroid model treated with Entinost… ×2 AT-MYC08 tumoroid model treated with RO31-822… ×2 AT-MYC08 tumoroid model treated with Thiostre… ×2

Supports a between-group comparison across 16 samples.

How we read this: 8 replicated groups read from 16 sample titles; they account for 16 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study
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