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Identification of distinct mesenchymal factors in the developing mouse bladder and urethra (E14.5 and E18.5)

GSE275616 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2025/01/01 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 12 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
12 samples: 3 × Bladder Mesenchyme, E14.5 mus female, vs 3 × Urethral Mesenchyme, E14.5 mus female, vs 3 × Bladder Mesenchyme, E18.5 mus female, vs 3 × Urethral Mesenchyme, E18.5 mus female,Groups 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
Epithelial and mesenchymal compartments of the developing bladder and urethra display spatially distinct gene expression patternsDevelopmental biology · 2025
Summary (written by the submitters)
The lower urinary is derived from the endodermal precursor, the cloaca. Despite common embryological origins, the epithelial linings and surrounding mesenchyme of the bladder and urethra show divergence. The bladder forms from the anterior part of the urogenital sinus, a cloacal derivative formed after septation of the cloaca to give rise to the anorectal and urogenital tracts.
Read the full summary ↓
The urethra elongates posteriorly and shows sex-specific differences as a result of hormonal action. The bladder is a target for regenerative therapies and tissue reconstruction strategies. A significant shortcoming of these strategies has been the inability to recapitulate all layers of bladder epithelial cells, most importantly the apical uroplakin positive layer that forms a tight, impermeable barrier against components in the urine. The urethral epithelium is contiguous with the bladder epithelium but has distinct cellular architecture and lacks a uroplakin expressing apical layer. We hypothesized that comparison of the developing urethra and bladder epithelium will identify early genes that are responsible for urethra and bladder-specific differentiation. In this study, we compared the epithelial compartments of the developing mouse bladder and urethra to identify genes that are differentially expressed in these two compartments. Our study identified transcription factor genes and other tissue-specific markers that are confined to either the urethra or bladder epithelium. Additionally, we describe sex-specific differences in the lower urinary tract epithelium which are more pronounced between the male and female urethral epithelium and less evident in the bladder epithelium between sexes.
Published in
Epithelial and mesenchymal compartments of the developing bladder and urethra display spatially distinct gene expression patterns
Jasmine, Baraiya DH, Kavya TT et al. · Developmental biology 2025 · PMID 39798644 · doi:10.1016/j.ydbio.2025.01.005
This dataset
Open GSE275616 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 GSE275616_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 PRJNA1152254 and SRA study SRP528569. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39798644) ↗
Study design
3 × Bladder Mesenchyme, E14.5 mus female, vs 3 × Urethral Mesenchyme, E14.5 mus female, vs 3 × Bladder Mesenchyme, E18.5 mus female, vs 3 × Urethral Mesenchyme, E18.5 mus female,

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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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