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Cellular heterogeneity and therapeutic response profiling of human IDH-wildtype glioma stem cell cultures

GSE303069 Homo sapiens (human) Single-cell RNA-seq 18 samples Submitted 2026/01/28 Platform GPL18573
At a glance

Single-cell RNA-seq · human · 18 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)
Topic
GlioblastomaThis series is part of our curated briefing on it.
Samples
18 samples: 6 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
Cellular heterogeneity and therapeutic response profiling of human IDH + glioma stem cell culturesScientific reports · 2025
Summary (written by the submitters)
Glioblastoma stem cell cultures (GSCs) are initiated from glioblastoma (GBM) surgical resection tissue, and can capture and propagate key GBM molecular and cellular features. We have deeply characterized four IDH-wildtype GSCs from unrelated adults as cellular models of a majority of adult primary GBMs. These GSC cultures could be continuously propagated in defined, serum-free media and 5% oxygen without requiring specialized growth substrates.
Read the full summary ↓
They had well-defined genomic and mtDNA variants and gene and protein expression profiles. All four had highly reproducible dose response curves to the GBM standard-of-care therapies of ionizing radiation (IR) and temozolomide (TMZ). Expressed lentiviral barcodes, mtDNA variants and single cell gene expression profiling were used to define cellular heterogeneity, and to track individual cell trajectories and their gene expression programs over 40 days after IR treatment. These well-characterized GSC cultures can support many high throughput in vitro assay formats, as well as xenograft, organoid and other GBM disease modeling approaches. Their use should help to better understand GBM biology, and to identify new and more effective GBM therapies and treatment regimens.
Published in
Cellular heterogeneity and therapeutic response profiling of human IDH + glioma stem cell cultures
Chambwe N, Kennedy SR, Kohrn BF et al. · Scientific reports 2025 · PMID 41423517 · doi:10.1038/s41598-025-33082-8
This dataset
Open GSE303069 in finder → Find more human RNA-seq datasets → Glioblastoma landscape →
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 GSE303069_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 PRJNA1036631 and SRA study SRP514601. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41423517) ↗
Study design
6 conditions, mostly in duplicate
GSC-0131_1_RNA1_Lib ×2 GSC-0131_2_RNA1_Lib ×2 GSC-0131_3_RNA1_Lib ×2 GSC-0827_1_RNA1_Lib ×2 GSC-0827_2_RNA1_Lib ×2 GSC-0827_3_RNA1_Lib ×2 GBM4_1_RNA1_Lib ×1 GBM4_2_RNA1_Lib ×1 +4 more

Supports a between-group comparison across 12 samples.

How we read this: 6 replicated groups read from 18 sample titles; they account for 12 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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