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Spaceflight induces systemic effects on extracellular matrix and immune system in different age-stages

GSE295428 Mus musculus (mouse) Single-cell RNA-seq 229 samples Submitted 2025/12/18 Platform GPL24247
At a glance

Single-cell RNA-seq · mouse · 229 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
229 samples: 58 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
MiRNAs shape mouse age-independent tissue adaptation to spaceflight via ECM and developmental pathwaysNature communications · 2026
Summary (written by the submitters)
Spaceflights significantly impacts astronaut health, causing muscle atrophy, bone loss, cardiovascular deconditioning and immune system dysregulation, especially during long missions. To explore molecular changes, we generated a single-cell RNA sequencing dataset, of 216 samples from 28 mouse organs and tissues under spaceflight and control conditions.
Read the full summary ↓
Since spaceflight effects closely resemble aspects of aging, we included two age groups (3 and 8 months) to assess age-related influences. Our data revealed that spaceflight drives age-independent systemic changes, primarily affecting tissue remodeling and alterations in cytoskeleton, membrane and extracellular matrix (ECM), particularly in endothelial cells. In contrast, aging has a weaker impact, mainly altering immune regulation in an age-dependent manner. These findings suggest that cytoskeletal and ECM changes may contribute to immune Dysregulation.
Published in
MiRNAs shape mouse age-independent tissue adaptation to spaceflight via ECM and developmental pathways
Grandke F, Rishik S, Wagner V et al. · Nature communications 2026 · PMID 41644562 · doi:10.1038/s41467-026-68737-1
This dataset
Open GSE295428 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 GSE295428_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 PRJNA1253974 and SRA study SRP580401. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41644562) ↗
Study design
58 conditions, mostly with about 4 replicates each
Aorta, HC, Mouse ×4 Aorta, LAR, Mouse ×4 BAT, HC, Mouse ×4 BAT, LAR, Mouse ×4 Blood, HC, Mouse ×4 Blood, LAR, Mouse ×4 Bone, HC, Mouse ×4 Bone, LAR, Mouse ×4 +50 more

Supports a between-group comparison across 229 samples.

How we read this: 58 replicated groups read from 229 sample titles; they account for 229 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

+ 189 more — browse all 229 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

Share this dataset

Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.