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Regional Molecular Diversity in Chronic Spinal Cord Injury

GSE319931 Mus musculus (mouse) RNA-seq (gene expression) 16 samples Submitted 2026/03/18 Platform GPL21103
At a glance

RNA-seq (gene expression) · mouse · 16 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
16 samples: 4 × uninjured spinal cord vs 4 × SCI 3 mm Above vs 4 × SCI Epicente vs 4 × SCI 3 mm BelowGroups 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
Regional Molecular Diversity in Chronic Spinal Cord InjuryCellular and molecular neurobiology · 2026
Summary (written by the submitters)
The development of next generation cellular and acellular therapies for regenerative repair of the injured spinal cord will benefit from a greater understanding of microenvironment heterogeneity. To address this need, we used genome wide RNA sequencing to illuminate gene expression changes in the spinal cord injury (SCI) epicenter, and in regions above and below, 30 days after contusion-compression (8 g Fejota clip) of the lumbar spinal cord (L1/L3) in adult female C57BL7J mice.
Read the full summary ↓
Across injury zones, there were more upregulated versus downregulated genes, with the most dynamic changes occurring in the epicenter, followed by the below and above regions. The expression of 52.9% of genes was uniquely changed in epicenter, 6.6% in the below region, and 2.8% in the above region, while 18.3% of differentially expressed genes (DEGs) overlapped across regions. Ingenuity Pathway analysis of epicenter DEGs showed 49 unique pathways, including Type II Diabetes Mellitus, P2Y Purinergic Receptor, Amyotrophic Lateral Sclerosis, JAK family kinases, and pathways related to GABA and Glutamate function. Thyroid Hormone Metabolism II, Serotonin degradation, and Myc-Mediated Apoptosis were enriched in the zone above the epicenter, while the Chondroitin sulfate degradation, the Superpathway of Geranylgeranylipidphosphate and Zymosterol Biosynthesis, and Regulation of Cellular Mechanics by Calpain Proteases were enriched below. There were 100 pathways shared across regions emphasizing fundamental roles for Apoptosis, Cytoskeletal organization, Chemokines, Complement, Prothrombin Activation pathways, Type I Diabetes Mellitus Signaling, and RXR signaling. These findings provide a rich resource of candidate mechanisms for additional validation and the design of targeted therapies to improve recovery after spinal cord injury.
Published in
Regional Molecular Diversity in Chronic Spinal Cord Injury
Choi CI, Kim HN, Yoon H et al. · Cellular and molecular neurobiology 2026 · PMID 41721943 · doi:10.1007/s10571-026-01694-x
This dataset
Open GSE319931 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 GSE319931_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 PRJNA1425543 and SRA study SRP678088. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41721943) ↗
Study design
4 × uninjured spinal cord vs 4 × SCI 3 mm Above vs 4 × SCI Epicente vs 4 × SCI 3 mm Below

Supports a between-group comparison across 16 samples.

How we read this: 4 replicated groups read from 16 sample titles; they account for 16 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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