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Effect of chronic mechanical compression on co-cultures of human induced neurons and murine glia

GSE313799 Homo sapiens (human) RNA-seq (gene expression) 24 samples Submitted 2025/12/18 Platform GPL30202
At a glance

RNA-seq (gene expression) · human · 24 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
Homo sapiens (human)
Samples
24 samples: 6 conditions, mostly with about 4 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
Mechanical compression induces neuronal apoptosis, reduces synaptic activity, and promotes glial neuroinflammation in mice and humansProceedings of the National Academy of Sciences of the United States of America · 2026
Summary (written by the submitters)
Human induced neurons and primary murine glia were subjected to a controlled in vitro model of mechanical compression to determine how solid stress—similar to forces present in glioblastoma—directly alters neuronal and glial transcriptional programs. RNA sequencing was performed after 24 hours of compression, with species-specific alignment enabling independent analysis of neuronal and glial responses.
Read the full summary ↓
Compressed human neurons showed strong activation of hypoxia-responsive metabolic genes, pro-inflammatory signaling pathways, and intrinsic apoptotic programs. Murine glia exhibited parallel induction of hypoxia and apoptotic pathways, accompanied by robust NF-κB/AP-1-driven inflammatory cytokine expression characteristic of astrocytic and microglial activation. These data define the conserved transcriptional responses by which neurons and glia detect and respond to solid stress, providing a resource for understanding mechanotransduction and neuroinflammatory signaling in diseases characterized by mass effect, including glioblastoma.
Published in
Mechanical compression induces neuronal apoptosis, reduces synaptic activity, and promotes glial neuroinflammation in mice and humans
Zarodniuk M, Wenninger A, Najera J et al. · Proceedings of the National Academy of Sciences of the United States of America 2026 · PMID 41481451 · doi:10.1073/pnas.2513172122
This dataset
Open GSE313799 in finder → Find more 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 GSE313799_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 PRJNA1381607 and SRA study SRP655300. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41481451) ↗
Study design
6 conditions, mostly with about 4 replicates each
1019 (iN 3), Control, Biol ×4 1019 (iN 3), Compressed, Biol ×4 I27 (iN 2), Control, Biol ×4 I27 (iN 2), Compressed, Biol ×4 WBO2 (iN 1), Control, Biol ×4 WBO2 (iN 1), Compressed, Biol ×4

Supports a between-group comparison across 24 samples.

How we read this: 6 replicated groups read from 24 sample titles; they account for 24 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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