GEO series

Sensory nerve input is not required for digit tip regeneration

GSE325460 Mus musculus (mouse) RNA-seq (gene expression) 29 samples Submitted 2026/04/01 Platform GPL30172

At a glance

RNA-seq (gene expression) · mouse · 29 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: 29 samples: 10 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.

Summary (written by the submitters)

Peripheral nerves are a major component of the post-injury microenvironment and are required for successful appendage regeneration in non-mammalians. However, the role of innervation in mouse digit tip regeneration is unclear. We developed a denervation technique that maintains mechanical loading while significantly reducing innervation to the digit.

Read the full summary ↓

Using this model, we found that denervation does not impair digit tip regeneration. Histological analysis showed the amputation stump proceeds through the expected phases of wound healing, blastema formation, and tissue outgrowth, and that regenerate bone volume is not significantly impaired in denervated digits. Interestingly, despite minimal change in regenerative outcome, bulk RNA sequencing identified significant changes in gene expression over time during regeneration in the absence of innervation. This study is the first to use RNA sequencing to characterize changes in gene expression during digit tip regeneration in the absence of innervation. Overall we show that digit tip regeneration is not dependent on innervation and our results suggest that regeneration may be achieved through activation of redundant signalling pathways.

This dataset

Open GSE325460 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 GSE325460_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 PRJNA1439966 and SRA study SRP685263. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

10 conditions, mostly in triplicate

SHAM, 7DPA, ×3 SHAM, 14DPA, ×3 SNI, 7DPA, ×3 SNI, 14DPA, ×3 SNI, 21DPA, ×3 SNI amputation, 7DPA, ×3 SNI no amputation, 7DPA, ×3 SNI amputation, 14DPA, ×3 +2 more

Supports a between-group comparison across 29 samples.

How we read this: 10 replicated groups read from 29 sample titles; they account for 29 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

GSM9604306 SHAM, 7DPA, Replicate 1 SHAM, 7DPA,
GSM9604307 SHAM, 7DPA, Replicate 2 SHAM, 7DPA,
GSM9604308 SHAM, 7DPA, Replicate 3 SHAM, 7DPA,
GSM9604309 SHAM, 14DPA, Replicate 1 SHAM, 14DPA,
GSM9604310 SHAM, 14DPA, Replicate 2 SHAM, 14DPA,
GSM9604311 SHAM, 14DPA, Replicate 3 SHAM, 14DPA,
GSM9604312 SHAM, 21DPA, Replicate 1 SHAM, 21DPA,
GSM9604313 SHAM, 21DPA, Replicate 2 SHAM, 21DPA,
GSM9604314 SNI, 7DPA, Replicate 1 SNI, 7DPA,
GSM9604315 SNI, 7DPA, Replicate 2 SNI, 7DPA,
GSM9604316 SNI, 7DPA, Replicate 3 SNI, 7DPA,
GSM9604317 SNI, 14DPA, Replicate 1 SNI, 14DPA,
GSM9604318 SNI, 14DPA, Replicate 2 SNI, 14DPA,
GSM9604319 SNI, 14DPA, Replicate 3 SNI, 14DPA,
GSM9604320 SNI, 21DPA, Replicate 1 SNI, 21DPA,
GSM9604321 SNI, 21DPA, Replicate 2 SNI, 21DPA,
GSM9604322 SNI, 21DPA, Replicate 3 SNI, 21DPA,
GSM9604323 SNI amputation, 7DPA, Replicate 1 SNI amputation, 7DPA,
GSM9604324 SNI amputation, 7DPA, Replicate 2 SNI amputation, 7DPA,
GSM9604325 SNI amputation, 7DPA, Replicate 3 SNI amputation, 7DPA,
GSM9604326 SNI no amputation, 7DPA, Replicate 1 SNI no amputation, 7DPA,
GSM9604327 SNI no amputation, 7DPA, Replicate 2 SNI no amputation, 7DPA,
GSM9604328 SNI no amputation, 7DPA, Replicate 3 SNI no amputation, 7DPA,
GSM9604329 SNI amputation, 14DPA, Replicate 1 SNI amputation, 14DPA,
GSM9604330 SNI amputation, 14DPA, Replicate 2 SNI amputation, 14DPA,
GSM9604331 SNI amputation, 14DPA, Replicate 3 SNI amputation, 14DPA,
GSM9604332 SNI no amputation, 14DPA, Replicate 1 SNI no amputation, 14DP…
GSM9604333 SNI no amputation, 14DPA, Replicate 2 SNI no amputation, 14DP…
GSM9604334 SNI no amputation, 14DPA, Replicate 3 SNI no amputation, 14DP…

Datasets on a similar topic

GSE301749 TTBK2-Driven Ciliogenesis Is Required for Intrinsic Neuronal Regeneration after Spinal Cord Injury 15 samples shares regeneration, required
GSE267938 Functional optic tract rewiring via subtype- and target-specific axonal regeneration and presynaptic activity enhancement 256 samples shares regeneration
GSE255004 Sensory Flicker Stimulation of 5xFAD Mice Activates Immune Pathways in a Frequency and Time Dependent Manner 176 samples shares sensory
GSE316925 Transcriptome changes in trigeminal ganglia in the mouse chronic constriction injury of the infraorbital nerve model - role of TRPM3. 136 samples shares nerve
GSE283692 A ketogenic diet and voluntary exercise modify the sciatic nerve and gastrocnemius transcriptome in diet-induced obese mice 96 samples shares nerve
GSE278534 EZHIP-mediated PRC2 inhibition is required to maintain H3K27me3-dependent imprinting post fertilization 76 samples shares required
GSE297143 EZH2 alters aggressive variant prostate cancer subtype evolution, but is not required for neuroendocrine prostate cancer [RNAseq] 54 samples shares required
GSE276182 NF-κB activation in astrocytes critically affects wound regeneration after traumatic brain injury 51 samples shares regeneration

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.