GEO series

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

GSE283832 Homo sapiens (human) Spatial transcriptomics 7 samples Submitted 2025/07/24 Platform GPL33762

At a glance

Spatial transcriptomics · human · 7 samples

What it is: Spatial transcriptomicsGene activity measured with its position in a tissue section.
Organism: Homo sapiens (human)
Samples: 7 samples: 7 samples, each with a distinct title — no replicated groupsGroups 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.
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 GSE283832 in finder → Find more human datasets →

Download · which file do I need?

Direct links to NCBI, 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.

All supplementary files ↗

3 · The original raw files

Whole study · RAW.tar

Everything the authors deposited as one archive (GSE283832_RAW.tar), including the raw array or instrument files. Can be large; the picker in step 2 takes just the samples you need.

Whole study · RAW.tar ↓

What the files usually look like: Spatial studies usually ship Space Ranger style folders (count matrix plus tissue images). Look for them among the supplementary files.

Also filed as BioProject PRJNA1195873. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40726147) ↗

Study design

7 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 7 sample titles: 7 distinct titles with little repetition. 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

GSM8672828 ATRT-05 (ATRT-SHH)
GSM8672829 ATRT-15-RV4 (ATRT-TYR)
GSM8672830 ATRT-173 (ATRT-SHH)
GSM8672831 ATRT-207 (ATRT-MYC)
GSM8672832 ATRT-243 (ATRT-MYC)
GSM8672833 ATRT-256 (ATRT-SHH)
GSM8672834 ATRT-340 (ATRT-TYR)

Datasets on a similar topic

GSE283843 A cycling, progenitor-like cell population at the root of atypical teratoid rhabdoid tumor subtype differentiation trajectories 56 samples shares progenitor-like, trajectories, population, atypical, teratoid, rhabdoid, cycling, subtype
GSE283833 A cycling, progenitor-like cell population at the root of atypical teratoid rhabdoid tumor subtype differentiation trajectories [bulk RNA-Seq] 16 samples shares progenitor-like, trajectories, population, atypical, teratoid, rhabdoid, cycling, subtype
GSE282972 An in vitro pharmacogenomic approach reveals subtype-specific therapeutic vulnerabilities in atypical teratoid/rhabdoid tumors (AT/RT) [RNASeq] 13 samples shares atypical, teratoid, rhabdoid, subtype
GSE230742 Investigation of genetic dependencies in atypical teratoid rhabdoid tumors (ATRTs) [I] 21 samples shares atypical, teratoid, rhabdoid
GSE276501 Atypical Teratoid Rhabdoid Tumours Are Susceptible to Panobinostat-Mediated Differentiation Therapy 18 samples shares atypical, teratoid, rhabdoid
GSE213249 Inhibiting EZH2 Targets Atypical Teratoid Rhabdoid Tumor by Triggering Viral Mimicry via Both RNA and DNA Sensing Pathways [RNA-Seq] 12 samples shares atypical, teratoid, rhabdoid
GSE296682 Single-cell transcriptomics of bronchoalveolar lavage reveals divergent macrophage subpopulations and trajectories in interstitial lung disease 9 samples shares trajectories, population
GSE246521 Chronic Lymphocytic Leukemia in African Ancestry Population is Characterized by Increased Genomic Instability 350 samples shares population

Search all human datasets in GEO →

Share this dataset

Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.