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In vivo intratumoral Heterogeneity in a dish: Scalable Forebrain Organoid Models of Embryonal Brain Tumors for High-Throughput Personalized Drug Discovery (human organoids+cell lines subset 1)

GSE269254 Homo sapiens (human) Single-cell RNA-seq 17 samples Submitted 2025/11/13 Platform GPL30173
At a glance

Single-cell RNA-seq · human · 17 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. 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
17 samples: 5 conditions, mostly in triplicateGroups 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
In vivo intratumoral heterogeneity in a dish: scalable forebrain organoid models of embryonal brain tumors for high-throughput personalized drug discoveryCancer communications (London, England) · 2025
Summary (written by the submitters)
Embryonal brain tumors (EBTs), arising during early brain development, present significant challenges in understanding pathogenesis and developing treatments. This study explores the efficacy of forebrain organoid models in replicating the complexities of the EBT microenvironment. We established an EBT-forebrain-organoid (EBT-FBO) model, incorporating embryonal tumor with multilayered rosettes (ETMR) and atypical teratoid and rhabdoid tumor (ATRT), using a scalable liquid-handling-assisted coaggregation method.
Read the full summary ↓
Comprehensive characterization, including wholemount immunostaining, immunohistochemistry, single-cell RNA sequencing, integration with existing datasets, and automated cell-type-specific drug screening, validated the EBT-FBO model. EBT-FBOs closely mimicked mid-gestational fetal brain environments, with EBTs reflecting intratumoral heterogeneity at both histological and transcriptomic levels. Drug screening on ETMR-FBOs identified promising treatment options, including anthracyclins and Triptolide, which demonstrated anti-tumoral effects with minimal neurotoxicity. Scalable EBT-FBO models that resemble immature neuronal microenvironments similar to ETMR or ATRT mark significant progress towards targeted therapy and personalized precision medicine that requires recapitulation of individual tumor heterogeneities.
Published in
In vivo intratumoral heterogeneity in a dish: scalable forebrain organoid models of embryonal brain tumors for high-throughput personalized drug discovery
Riedel NC, Walter C, de Faria FW et al. · Cancer communications (London, England) 2025 · PMID 41177766 · doi:10.1002/cac2.70074
This dataset
Open GSE269254 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 GSE269254_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 PRJNA1120830 and SRA study SRP512219. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41177766) ↗
Study design
5 conditions, mostly in triplicate
Forebrain-Organoid D ×3 Forebrain-Organoid D100 ×3 FB-Organoid D30 BT-183 ×3 Forebrain-Organoid D60 ×2 BT-183 ×2 SHH ×1 Chla ×1 FB-Organoid D40 SHH ×1 +1 more

Supports a between-group comparison across 13 samples.

How we read this: 5 replicated groups read from 17 sample titles; they account for 13 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
Datasets on a similar topic

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