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Unveiling the Temporal Dynamics of Mesenchymal Condensations in Tracheal Development through Non-Canonical Wnt Signaling and Notum

GSE260707 Mus musculus (mouse) RNA-seq (gene expression) 22 samples Submitted 2025/02/28 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 22 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
22 samples: 6 conditions, mostly in triplicateGroups 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
Wnt5a and Notum influence the temporal dynamics of cartilaginous mesenchymal condensations in developing tracheaFrontiers in cell and developmental biology · 2025
Summary (written by the submitters)
The trachea is essential for proper airflow to the lungs for gas exchange. Frequent congenital tracheal malformations affect the cartilage, causing the collapse of the central airway during the respiratory cycle. We have shown that Notum, a Wnt ligand de-acylase that attenuates the canonical branch of the Wnt signaling pathway, is necessary for cartilaginous mesenchymal condensations.
Read the full summary ↓
In Notum deficient tracheas, chondrogenesis is delayed, and the trachea is stenotic. It is unknown if Notum attenuates non-canonical Wnt signaling. Notably, after mesenchymal deletion of the non-canonical Wnt5a ligand, we observed premature tracheal chondrogenesis. We hypothesize that Notum and Wnt5a are required to mediate the timely formation of mesenchymal condensations, giving rise to the tracheal cartilage. Ex vivo culture of tracheal tissue shows that chemical inhibition of the Wnt non-canonical pathway promotes earlier condensations, while Notum inhibition presents delayed condensations. Furthermore, non-canonical Wnt induction prevents the formation of cartilaginous mesenchymal condensations. On the other hand, cell-cell interactions among chondroblasts increased in the absence of mesenchymal Wnt5a. By performing an unbiased analysis of the gene expression in Wnt5a and Notum deficient tracheas, we detected that mRNA of genes essential for chondrogenesis and extracellular matrix formation are upregulated by E11.5 in Wnt5a mutants. The expression profile supports the premature and delayed chondrogenesis observed in Wnt5a and Notum deficient tracheas. We conclude that Notum and Wnt5a are necessary for proper tracheal cartilage patterning by coordinating timely chondrogenesis. Thus, these studies shed light on molecular mechanisms underlying congenital anomalies of the trachea.
Published in
Wnt5a and Notum influence the temporal dynamics of cartilaginous mesenchymal condensations in developing trachea
Bottasso-Arias N, Mohanakrishnan M, Trovillion S et al. · Frontiers in cell and developmental biology 2025 · PMID 40271154 · doi:10.3389/fcell.2025.1523833
This dataset
Open GSE260707 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 GSE260707_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 PRJNA1082737 and SRA study SRP492855. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40271154) ↗
Study design
6 conditions, mostly in triplicate
E11.5 trachea, Control Wnt5af/f, ×5 E11.5 trachea, Mutant Dermo1Cre; Wnt5af/f, ×4 E13.5 trachea cartilage Notum mutant ×4 E13.5 trachea epithelium control ×3 E13.5 trachea muscle control ×3 E13.5 trachea cartilage control ×3

Supports a case/control comparison: 8 samples read as cases, 14 as controls.

How we read this: 6 replicated groups read from 22 sample titles; they account for 22 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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