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Gliomagenesis mimics an injury response orchestrated by neural crest-like cells

GSE278511 Mus musculus (mouse) Single-cell RNA-seq 40 samples Submitted 2025/01/01 Platform GPL17021
At a glance

Single-cell RNA-seq · mouse · 40 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
Mus musculus (mouse)
Samples
40 samples: 5 conditions, mostly with about 6 replicates eachGroups 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
Gliomagenesis mimics an injury response orchestrated by neural crest-like cellsNature · 2025
Summary (written by the submitters)
To explore the early steps in glioma formation, we utilized conditional gene deletion and lineage tracing in tumour mouse models, coupled with serial magnetic resonance imaging to initiate and then closely track tumour formation. We isolated labeled and unlabeled cells at multiple stages -- before the first visible abnormality, at the time of the first visible lesion, and then through the stages of tumour growth -- and subjected each stage to single-cell profiling.
Read the full summary ↓
We identify a malignant cell state with a neural crest-like gene expression signature that is highly abundant in the early stages, but relatively diminished in the late stage of tumour growth. Genomic analysis based on the presence of copy number alterations suggests that these neural crest-like states exist as part of a heterogenous clonal hierarchy that evolves with tumour growth. By exploring the injury response in the wounded normal mouse brain, we identify cells with a similar signature that emerge following injury and then disappear over time, suggesting that activation of an injury response programme occurs during tumourigenesis. Indeed, our experiments reveal a non-malignant injury-like microenvironment that is initiated in the brain following oncogene activation in cerebral precursor cells. Collectively, our findings provide insight into the early stages of gliomagenesis, identifying a unique stem cell-like state and an injury response programme tied to early tumour formation. This will have implications on glioblastoma therapies and raises exciting new possibilities for early disease diagnosis and prevention. Some of the data in this series can also be explored through the following App link: gbm.stem-cells.ca.
Published in
Gliomagenesis mimics an injury response orchestrated by neural crest-like cells
Hamed AA, Hua K, Trinh QM et al. · Nature 2025 · PMID 39743595 · doi:10.1038/s41586-024-08356-2
This dataset
Open GSE278511 in finder → Find more mouse 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 GSE278511_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 PRJNA1118442 and SRA study SRP510949. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39743595) ↗
Study design
5 conditions, mostly with about 6 replicates each
Endpoint ×6 Early_lesion ×5 Preneoplastic ×4 Mid_lesion ×3 Control ×2 Control_1 td -ve ×1 Control_2 GFP -ve ×1 Preneoplastic_rep_1 td -ve ×1 +17 more

Supports a case/control comparison: 11 samples read as cases, 6 as controls.

How we read this: 5 replicated groups read from 40 sample titles; they account for 20 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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