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Comparison of otic vesicle gene expression from E10.5 mouse and inner ear organoid cultures at 12 days-in-vitro with (BSFL) and without (BFL) TGFβ inhibition

GSE285576 Mus musculus (mouse) RNA-seq (gene expression) 11 samples Submitted 2025/04/11 Platform GPL17021
At a glance

RNA-seq (gene expression) · mouse · 11 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
11 samples: 4 × D12 inner ear organoid culture, otic vesicle, no TGFβ inhibition, BFL vs 4 × E10.5 otic vesice, vs 3 × D12 inner ear organoid culture, otic vesicle, TGFβ inhibition on D3, BSFLGroups 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
Retinoic acid signaling guides the efficiency of inner ear organoid-genesis and governs sensory-nonsensory fate specificationbioRxiv : the preprint server for biology · 2025
Summary (written by the submitters)
The early development of inner ear organoids—from germ layer to otocyst formation—is a highly controlled process with timed chemical cues that recapitulate major signals in vivo. We sought to elucidate additional morphogens that might guide this multi-stage process, improve efficiency, and influence cell fate decisions. Using a whole-transcriptomic approach with bulk RNASeq, we identified major differences in native otic vesicles (OVs) from E10.5 mice and stem cell-derived OVs from cultures at 12 days-in-vitro.
Read the full summary ↓
Stem cell-derived samples included those treated with TGFβ inhibitors at early stages of differentiation--to suppress mesendodermal fates--and those without TGFβ inhibition, since other investigators identified this early inhibitory step as critical for organoid-genesis though dispensible for OV production. Differential gene expression between native and derived OVs identified factors related to anterior-posterior patterning as disregulated in the cell cultures, implicating aberrant retinoic acid (RA) signaling in the organoid culture paradigm.
Published in
Retinoic acid signaling guides the efficiency of inner ear organoid-genesis and governs sensory-nonsensory fate specification
Duncan RK, Liu L, Moyer M et al. · bioRxiv : the preprint server for biology 2025 · PMID 40166165 · doi:10.1101/2025.03.21.644434
This dataset
Open GSE285576 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 GSE285576_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 PRJNA1204914 and SRA study SRP554718. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40166165) ↗
Study design
4 × D12 inner ear organoid culture, otic vesicle, no TGFβ inhibition, BFL vs 4 × E10.5 otic vesice, vs 3 × D12 inner ear organoid culture, otic vesicle, TGFβ inhibition on D3, BSFL

Supports a between-group comparison across 11 samples.

How we read this: 3 replicated groups read from 11 sample titles; they account for 11 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
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