Molecular pathology of acute spinal cord injury in middle-aged mice
Single-cell RNA-seq · mouse · 12 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
- 12 samples: 3 × Aged_3dpi vs 3 × Aged_Uninj vs 2 × Spatial_Young_3dpi vs 2 × Spatial_Aged_3dpiGroups 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
- Molecular pathology of acute spinal cord injury in middle-aged miceJournal of neuroinflammation · 2025
Read the full summary ↓
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.
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.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE298545_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1269809 and SRA study SRP588819. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 10 samples.
How we read this: 4 replicated groups read from 12 sample titles; they account for 10 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.
- GSM9016858 Aged_3dpi_rep1 Aged_3dpi
- GSM9016859 Young_3dpi_rep1
- GSM9016860 Aged_3dpi_rep2 Aged_3dpi
- GSM9016861 Aged_3dpi_rep3 Aged_3dpi
- GSM9016862 Aged_Uninj_rep1 Aged_Uninj
- GSM9016863 Aged_Uninj_rep2 Aged_Uninj
- GSM9016864 Aged_Uninj_rep4 Aged_Uninj
- GSM9016865 Young_Uninj_rep2
- GSM9016866 Spatial_Young_3dpi_rep1 Spatial_Young_3dpi
- GSM9016867 Spatial_Young_3dpi_rep2 Spatial_Young_3dpi
- GSM9016868 Spatial_Aged_3dpi_rep1 Spatial_Aged_3dpi
- GSM9016869 Spatial_Aged_3dpi_rep2 Spatial_Aged_3dpi
- GSE285895 Simulating Neonatal Microglial Pan-Programmed Cell Death to Unlock Regenerative Potential in Adult Mice Spinal Cord Injury [RNA-seq] 21 samples shares spinal, injury, cord
- GSE271662 RNA-seq of Mouse Spinal Cord after Lateral Compression Spinal Cord Injury followed by Delayed Atorvastatin or Vehicle Treatment [Bulk RNA-seq of mice spinal cords] 16 samples shares spinal, injury, cord
- GSE279731 The contribution of foam cells to angiogenesis and inflammation after spinal cord injury 48 samples shares spinal, injury, cord
- GSE325662 Gene expression profiling of lung tissue from LPS-induced acute lung injury mice treated with Renshen Baidu Powder 9 samples shares injury, acute
- GSE276647 Gene expression profile of microglia following traumatic brain injury and nasal anti-CD3 treatment at acute and chronic timepoints 54 samples shares injury, acute
- GSE291462 Ontogeny of the spinal cord dorsal horn 37 samples shares spinal, cord
- GSE290810 ALS/FTD-linked TBK1 deficiency in microglia induces an aged-like microglial signature and drives social recognition deficits [FACS_SpinalCord_Microglia & LPS_Brain_SpinalCord] 35 samples shares spinal, cord
- GSE275982 Clonally expanded targetable natural killer-like T cells seed the aged spinal cord to disrupt wound healing [scGEX and TCR] 24 samples shares spinal, cord
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.