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Dual Mechanisms of Supporting Cell Regeneration in the Neonatal Mouse Cochlea

GSE291228 Mus musculus (mouse) Single-cell RNA-seq 16 samples Submitted 2026/01/12 Platform GPL24247
At a glance

Single-cell RNA-seq · mouse · 16 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
16 samples: 8 conditions, mostly in duplicateGroups 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
Dual mechanisms of supporting cell regeneration in the neonatal mouse cochleaiScience · 2026
Summary (written by the submitters)
Cochlear supporting cells are critical for proper hearing function and regeneration of hair cells, which are responsible for perceiving sound in the inner ear. In the neonatal mouse cochlea, when supporting cells are ablated, they can regenerate through progenitor cells in the cochlea. Here, we show through single cell RNA sequencing and in vivo fate mapping, that upon supporting cell ablation in the neonatal cochlea, inner phalangeal cells regenerate through two independent mechanisms; one which requires proliferation and the other by which transdifferentiation (i.e.
Read the full summary ↓
regeneration without mitotic division) of cochlear progenitor cells occurs. These dual mechanisms are spatially distinct where transdifferentiation occurs in all three turns of the cochlea, while proliferation-induced regeneration occurs exclusively in the apical and middle turns. Inhibiting proliferation using aphidicolin, slightly decreased the number of regenerated IPhCs in the apex middle turns, but not the base, after damage. We also observed a medial to lateral transition in the compartmentalization of the GER after supporting cell damage, suggesting de-differentiation of these domains. Overall, our study reveals GER cells as supporting cell progenitors that undergo dual mechanisms of regeneration (mitotic and non-mitotic). Additionally, we uncover transcriptomic changes after supporting cell damage in the neonatal mouse cochlea that could be used as gene targets in therapies for hearing loss.
Published in
Dual mechanisms of supporting cell regeneration in the neonatal mouse cochlea
Abitbol JM, Matern MS, Billings SE et al. · iScience 2026 · PMID 41867623 · doi:10.1016/j.isci.2026.115113
This dataset
Open GSE291228 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 GSE291228_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 PRJNA1232607 and SRA study SRP568326. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41867623) ↗
Study design
8 conditions, mostly in duplicate
P4 Ki67CreERT/+;Lgr5DTR/+;Rosa26RtdTomato/+ c… ×2 P4 Ki67CreERT/+;Rosa26RtdTomato/+ cochlea, ×2 P5 Ki67CreERT/+;Lgr5DTR/+;Rosa26RtdTomato/+ c… ×2 P5 Ki67CreERT/+;Rosa26RtdTomato/+ cochlea, ×2 P6 Ki67CreERT/+;Lgr5DTR/+;Rosa26RtdTomato/+ c… ×2 P6 Ki67CreERT/+;Rosa26RtdTomato/+ cochlea, ×2 P7 Ki67CreERT/+;Lgr5DTR/+;Rosa26RtdTomato/+ c… ×2 P7 Ki67CreERT/+;Rosa26RtdTomato/+ cochlea, ×2

Supports a between-group comparison across 16 samples.

How we read this: 8 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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