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Single Cell Transcriptional Characterization of the Developing Organ of Corti Identifies Etv4/5/1 as Regulators of Lateral Cell Identity

GSE292561 Mus musculus (mouse) Single-cell RNA-seq 24 samples Submitted 2026/03/13 Platform GPL19057
At a glance

Single-cell RNA-seq · mouse · 24 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
24 samples: 8 conditions, mostly with about 4 replicates eachGroups 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
Single-Cell Profiling of the Developing Organ of Corti Identifies Etv4/5/1 as Key Regulators of Pillar Cell IdentitybioRxiv : the preprint server for biology · 2026
Summary (written by the submitters)
The mammalian auditory sensory epithelium, the organ of Corti, is comprised of a complex and highly ordered cellular mosaic that includes multiple unique cell types. The small number of each of these cell types and their close association with one another has limited efforts to transcriptionally characterize the development of these cells.
Read the full summary ↓
To provide a better understanding of the development events that regulate cell type specification, we dissociated developing cochlear ducts at time points between embryonic day 11 and 16 and collected duct epithelial cells for single cell RNA-sequencing. From the resulting data we were able to build a developmental trajectory from undifferentiated precursor cells to each of the major cell types in the organ of Corti. Bioinformatic analyses including SCENIC, TradeSeq and CellOracle were then used to identify transcription factors and other genes that may regulate different phases of cell type development. To validate the analysis, the role of one set of candidate transcription factors, Etv4/5/1 was examined by generating triple knock out mice. As predicted from the bioinformatic analysis, results demonstrated key roles for Etvs in the development of inner and outer pillar cells. and accurately identified down-stream Etv targets. This data set will provide significant insights regarding the specification of unique cochlear cell types which will have implications for understanding congenital deficits and potential applications in the development of regenerative strategies.
Published in
Single-Cell Profiling of the Developing Organ of Corti Identifies Etv4/5/1 as Key Regulators of Pillar Cell Identity
Sakamoto S, Kelley MW · bioRxiv : the preprint server for biology 2026 · PMID 41684939 · doi:10.64898/2026.01.19.700450
This dataset
Open GSE292561 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 GSE292561_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 PRJNA1240219 and SRA study SRP572176. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41684939) ↗
Study design
8 conditions, mostly with about 4 replicates each
Cochlear epithelium, E11_WT ×4 Cochlear epithelium, E12_WT ×4 Cochlear epithelium, E16_Fgfr3_KO ×4 Cochlear epithelium, E13 ×3 Cochlear epithelium, E16_Fgfr3_WT ×3 Cochlear epithelium, E14 ×2 Cochlear epithelium, E14se ×2 Cochlear epithelium, E16se ×2

Supports a between-group comparison across 24 samples.

How we read this: 8 replicated groups read from 24 sample titles; they account for 24 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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