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Identification of distinct mesenchymal factors in the developing bladder and urethra

GSE253103 Mus musculus (mouse) RNA-seq (gene expression) 16 samples Submitted 2025/01/01 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 16 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
16 samples: 4 × E16.5 Bladder mesenchyme, female, biol vs 4 × E16.5 Bladder mesenchyme, male, biol vs 4 × E16.5 Urethra mesenchyme, female biol vs 4 × E16.5 Urethra mesenchyme, male biolGroups 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 form 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 expressing cell layer that forms a tight, impermeable barrier against components in the urine. Epithelial-mesenchymal interactions are critical for organogenesis. Several studies have shown the ability of embryonic bladder mesenchyme to reprogram non-bladder epithelium to resemble bladder tissue at the molecular and cellular level. In this study, we performed bulk RNA-sequencing on the mesenchymal layers of the developing mouse bladder and urethra and identified compartmentalized organ-specific gene expression. Our study identified transcription factor genes and secreted protein genes specific to the bladder or urethra mesenchymal compartments. Additionally, we describe sex-specific differences in the lower urinary tract mesenchyme which are more pronounced between the male and female urethral mesenchyme and less evident in the bladder mesenchyme 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 GSE253103 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 GSE253103_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 PRJNA1064038 and SRA study SRP483487. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39798644) ↗
Study design
4 × E16.5 Bladder mesenchyme, female, biol vs 4 × E16.5 Bladder mesenchyme, male, biol vs 4 × E16.5 Urethra mesenchyme, female biol vs 4 × E16.5 Urethra mesenchyme, male biol

Supports a between-group comparison across 16 samples.

How we read this: 4 replicated groups read from 16 sample titles; they account for 16 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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