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Microglia in diffuse midline glioma contribute to extracellular matrix remodelling and cancer cell invasion

GSE309866 Mus musculus (mouse) RNA-seq (gene expression) 18 samples Submitted 2026/06/03 Platform GPL30172
At a glance

RNA-seq (gene expression) · mouse · 18 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Mus musculus (mouse)
Samples
18 samples: 6 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
Microglia in diffuse midline glioma contribute to extracellular matrix remodelling and cancer cell invasionCell death & disease · 2026
Summary (written by the submitters)
Background: Diffuse midline glioma, H3K27-altered (DMG) are aggressive and universally fatal paediatric tumours that arise in midline structures of the brain. DMG tumours are characterized by a substantial infiltration of tissue-resident microglia. The aim of this study was to determine whether in response to stimulation by DMG cells, microglia could acquire a reactive state that contributes to the progression of DMG.
Read the full summary ↓
Methods: The microglial transcriptomic response to DMG cells was analysed by RNA-sequencing of microglia exposed to DMG, H3K27M cells and of tumour-associated myeloid cells isolated from DMG tumour biopsies. Meta-analysis of human paediatric glioma cohorts (Kids First, PNOC, and CBTTC) was used to confirm upregulation of expression for selective genes in DMG patients. Immunofluorescence analysis performed on archival DMG biobank tissues was used to confirm the findings at protein level. Invasion assay’s using a panel of DMG, H3K27M cells was used to evaluate the contribution of microglia-derived fibronectin,to promote DMG cell invasion. Results: Microglia are enriched in human DMG, H3K27M tumours. Upon stimulation by DMG, H3K27M cells, microglia contribute to the expression of extracellular matrix (ECM) components. Microglia-derived fibronectin promotes tumour invasiveness, and its inhibition reduces DMG cell migration. Across patient cohorts, DMG, H3K27M tumours exhibit elevated expression of myeloid cell-derived ECM components, with fibronectin expression showing prognostic value. Conclusions: Microglia appear to actively contribute to the diffuse invasive nature of DMG by producing ECM components, particularly fibronectin, which enhances tumour invasiveness. These findings identify microglia as potential therapeutic targets in DMG.
Published in
Microglia in diffuse midline glioma contribute to extracellular matrix remodelling and cancer cell invasion
Keane L, Škandík M, Posada-Pérez M et al. · Cell death & disease 2026 · PMID 42218137 · doi:10.1038/s41419-026-08891-y
This dataset
Open GSE309866 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 GSE309866_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1363912 and SRA study SRP644479. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42218137) ↗
Study design
6 conditions, mostly in triplicate
BV-2 cells, unexposed, 3h, N ×3 BV-2 cells, SF188 exposed, 3h, N ×3 BV-2 cells, SF8628 exposed, 3h, N ×3 BV-2 cells, unexposed, 6h, N ×3 BV-2 cells, SF188 exposed, 6h, N ×3 BV-2 cells, SF8628 exposed, 6h, N ×3

Supports a between-group comparison across 18 samples.

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