← BioTransfer GEO Dataset Finder
GEO series

In Vivo and Ex Vivo Utricles treated with ATOH1 under different promoters

GSE240846 Mus musculus (mouse) Single-cell RNA-seq 27 samples Submitted 2024/09/24 Platform GPL24247
At a glance

Single-cell RNA-seq · mouse · 27 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
27 samples: 6 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
Precise genetic control of ATOH1 enhances maturation of regenerated hair cells in the mature mouse utricleNature communications · 2024
Summary (written by the submitters)
Vestibular hair cells are mechanoreceptors critical for detecting head position and motion. In mammals, hair cell loss causes vestibular dysfunction as spontaneous regeneration is nearly absent. Constitutive expression of exogenous ATOH1, a hair cell transcription factor, increases regeneration of hair cells, but these cells fail to mature.
Read the full summary ↓
With the aim of developing an optimized AAV-based ATOH1 gene therapy, we used single-cell RNA-Seq and explored the impact of defined promoters on ATOH1 transgene expression level, timing, effects in distinct cell types, and the maturity of regenerated vestibular hair cells ex vivo and in vivo.
Published in
Precise genetic control of ATOH1 enhances maturation of regenerated hair cells in the mature mouse utricle
Wang T, Yang T, Kedaigle A et al. · Nature communications 2024 · PMID 39448563 · doi:10.1038/s41467-024-53153-0
This dataset
Open GSE240846 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 GSE240846_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 PRJNA1005480 and SRA study SRP455086. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39448563) ↗
Study design
6 conditions, mostly in duplicate
Explant, CMV-ATOH1, day 12, ×3 Explant, GFAP-ATOH1, day 12, ×3 Explant, RLBP1-ATOH1, day 12, ×2 In vivo cristae, GFAP-ATOH1, 4wk, ×2 In vivo cristae, IDPN only, 4wk, ×2 In vivo utricle, IDPN only, 4wk, ×2 Explant, CMV-ATOH1, day 7, ×1 Explant, GFAP-ATOH1, day 7, ×1 +11 more

Supports a between-group comparison across 14 samples.

How we read this: 6 replicated groups read from 27 sample titles; they account for 14 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

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.