GEO series

Single-cell RNA sequencing of the mouse hippocampus after spared nerve injury (SNI) modeling

GSE329706 Mus musculus (mouse) Single-cell RNA-seq 11 samples Submitted 2026/07/15 Platform GPL24247

At a glance

Single-cell RNA-seq · mouse · 11 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism: Mus musculus (mouse)
Samples: 11 samples: 3 × SNI,DAY21,SAMPLE vs 2 × SNI,DAY3,SAMPLE vs 2 × SNI,DAY7,SAMPLE vs 2 × SNI,DAY14,SAMPLEGroups 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.

Summary (written by the submitters)

Chronic pain (CP) affects more than 30% of the global population and is often accompanied by significant cognitive impairments. Although an increasing number of studies have focused on the pathological mechanisms associated with chronic pain-induced cognitive impairments, most have concentrated on the stage after the onset of cognitive impairments.

Read the full summary ↓

Currently, the course by which chronic pain induces cognitive impairment has not been fully reported. Therefore, single-cell RNA sequencing were conducted in this study in order to map the mice hippocampus altas before and after cognitive impairments induced by spared nerve injury (SNI) on days 3, 7, 14, and 21. After quality control screening, 53852 out of 64207 cells from 11 samples were retained for subsequent analysis. The reliability of the sequencing data was verified through analysis of various evaluation indicators and sequencing alignment rates. Preliminary analysis identified 16 major cell types in the hippocampal tissue, and differential expression analysis revealed transcriptomic changes in hippocampal cells following SNI model establishment, with these early transcriptomic changes being more pronounced in neurons.

This dataset

Open GSE329706 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 GSE329706_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 PRJNA1460754 and SRA study SRP696577. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

3 × SNI,DAY21,SAMPLE vs 2 × SNI,DAY3,SAMPLE vs 2 × SNI,DAY7,SAMPLE vs 2 × SNI,DAY14,SAMPLE

Supports a between-group comparison across 9 samples.

How we read this: 4 replicated groups read from 11 sample titles; they account for 9 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

GSM9709530 SNI,DAY3,SAMPLE2 SNI,DAY3,SAMPLE
GSM9709531 SNI,DAY3,SAMPLE3 SNI,DAY3,SAMPLE
GSM9709532 SNI,DAY7,SAMPLE1 SNI,DAY7,SAMPLE
GSM9709533 SNI,DAY7,SAMPLE2 SNI,DAY7,SAMPLE
GSM9709534 SNI,DAY14,SAMPLE1 SNI,DAY14,SAMPLE
GSM9709535 SNI,DAY14,SAMPLE2 SNI,DAY14,SAMPLE
GSM9709536 SNI,DAY21,SAMPLE1 SNI,DAY21,SAMPLE
GSM9709537 SNI,DAY21,SAMPLE2 SNI,DAY21,SAMPLE
GSM9709538 SNI,DAY21,SAMPLE3 SNI,DAY21,SAMPLE
GSM9709539 SHAM,DAY7,SAMPLE1
GSM9709540 SHAM,DAY3,SAMPLE2

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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.