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Single-nucleus transcriptomic analysis of the amygdala of mice in acute and chronic neuropathic pain

GSE254360 Mus musculus (mouse) Single-nucleus RNA-seq 15 samples Submitted 2025/06/13 Platform GPL24247
At a glance

Single-nucleus RNA-seq · mouse · 15 samples

What it is
Single-nucleus RNA-seqGene activity measured in individual nuclei (used when whole cells are hard to isolate, for example from frozen tissue).
Organism
Mus musculus (mouse)
Samples
15 samples: 5 conditions, mostly in triplicateGroups 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
A nociceptive amygdala-striatal pathway for chronic pain aversionbioRxiv : the preprint server for biology · 2024
Summary (written by the submitters)
Single-nucleus RNA sequencing was used to profile transcriptional differences in mice in uninjured or neuropathic chronic pain conditions and in response to multiple sensory stimuli to identify cell subtype-specific changes in the transcriptome due to pain
Published in
A nociceptive amygdala-striatal pathway for chronic pain aversion
Wojick JA, Paranjapye A, Chiu JK et al. · bioRxiv : the preprint server for biology 2024 · PMID 38405972 · doi:10.1101/2024.02.12.579947
This dataset
Open GSE254360 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 GSE254360_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 PRJNA1070025 and SRA study SRP486294. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38405972) ↗
Study design
5 conditions, mostly in triplicate
Uninjured light touch biol ×3 SNI light touch biol ×3 Uninjured hot water drop biol ×3 Uninjured no stim biol ×3 SNI no stim biol ×3

Supports a between-group comparison across 15 samples.

How we read this: 5 replicated groups read from 15 sample titles; they account for 15 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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