← BioTransfer GEO Dataset Finder
GEO series

Transcriptional Profiling of Otic Capsule and Femur in the oim Mouse Model of Osteogenesis Imperfecta

GSE333701 Mus musculus (mouse) RNA-seq (gene expression) 140 samples Submitted 2026/06/24 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 140 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
140 samples: 12 conditions, mostly with about 12 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
Transcriptional profiling of otic capsule and femur in the oim mouse model of osteogenesis imperfectaJBMR plus · 2026
Summary (written by the submitters)
Hearing loss is a common and debilitating complication of the brittle bone disorder osteogenesis imperfecta (OI). Existing treatments that are designed to address age-related hearing loss in the broader population do not meet the needs of OI patients, who exhibit skeletal fragility and begin to lose their hearing when they are young-adults.
Read the full summary ↓
The biologic mechanisms responsible for hearing loss in OI are unknown, hindering the development of preventative therapies. To identify potential mechanisms that drive this condition, we performed transcriptome profiling on femoral and otic capsule specimens obtained from the Col1a2oim mouse model at 12- and 25-weeks of age. We found that the bulk transcriptomes of femora and otic capsules were markedly different, regardless of mouse genotype. Further, bone formation-associated transcripts were reduced at 25-weeks, compared to 12-weeks. Mice homozygous for the oim mutation exhibited increased abundance of transcripts associated with osteoblast activity and type I collagen production compared to wild-type mice in both femoral and otic capsule specimens. The most notable difference between oim and wild-type mouse otic capsules was the depletion of the transcripts that encode mucin and keratin, suggesting dysregulation of epithelial cells, which has been previously linked to hearing loss. Our data offer new insights into the mechanisms that disrupt the middle ear in OI. Analysis of epithelial cells obtained from OI patients and additional models of OI could suggest novel strategies to prevent and/or treat hearing loss.
Published in
Transcriptional profiling of otic capsule and femur in the oim mouse model of osteogenesis imperfecta
Ayturk UM, Rogers M, Seide K et al. · JBMR plus 2026 · PMID 42306554 · doi:10.1093/jbmrpl/ziag088
This dataset
Open GSE333701 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 GSE333701_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 PRJNA1472078 and SRA study SRP704611. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42306554) ↗
Study design
12 conditions, mostly with about 12 replicates each
WT_Ossicle_wk25 ×16 WT_Femur_wk25 ×15 OIM_Femur_wk12 ×12 OIM_Femur_wk25 ×12 OIM_Ossicle_wk12 ×12 OIM_Ossicle_wk25 ×12 HET_Femur_wk12 ×11 HET_Ossicle_wk12 ×11 +4 more

Supports a between-group comparison across 140 samples.

How we read this: 12 replicated groups read from 140 sample titles; they account for 140 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

+ 100 more — browse all 140 samples with per-sample file links →

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.