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Suture-specific regulation of coronal and lambdoid suture patency by PTHLH and HHIP activity in mice

GSE294710 Mus musculus (mouse) RNA-seq (gene expression) 15 samples Submitted 2025/09/26 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 15 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
15 samples: 4 × Coronal suture, wild-type, sample vs 4 × Lambdoid suture, wild-type, sample vs 4 × Lambdoid suture, HHIP knockout, sample vs 3 × Coronal suture, HHIP knockout, sampleGroups 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
Differential regulation of coronal and lambdoid suture patency by PTHLH and HHIP activity in miceDevelopment (Cambridge, England) · 2025
Summary (written by the submitters)
Craniofacial development depends on the formation of fibrous joints, or sutures, between skull bones. Premature fusion of sutures, or craniosynostosis, is a common human pathology. Ectopic Hedgehog (HH) signaling is one cause of craniosynostosis. Hhip encodes an inhibitor of HH ligands, and we previously identified coronal suture dysgenesis in embryonic Hhip-/- mice, in which suture mesenchyme was depleted between closely opposed but unfused osteogenic fronts at E18.5.
Read the full summary ↓
Here, we report that the lambdoid suture fuses in Hhip-/- mice by E18.5. RNA-seq analysis of the Hhip-/- coronal and lambdoid sutures show that HH target gene expression, including Pthlh, is upregulated. Paradoxically, expression of Ihh is downregulated. We hypothesized that PTHLH, a negative regulator of Ihh expression, may reduce HH signaling to promote coronal suture patency and prevent fusion of the Hhip-/- coronal suture. We generated Hhip-/-;Pthlh-/- embryos and found that coronal sutures are fusing by E18.5. Our results reveal a previously undescribed role for Pthlh in suture development and demonstrate suture-specific roles for HH inhibitors in maintaining suture patency.
Published in
Differential regulation of coronal and lambdoid suture patency by PTHLH and HHIP activity in mice
Saturne MD, Motch Perrine SM, Li Q et al. · Development (Cambridge, England) 2025 · PMID 41000054 · doi:10.1242/dev.204875
This dataset
Open GSE294710 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 GSE294710_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 PRJNA1251357 and SRA study SRP578962. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41000054) ↗
Study design
4 × Coronal suture, wild-type, sample vs 4 × Lambdoid suture, wild-type, sample vs 4 × Lambdoid suture, HHIP knockout, sample vs 3 × Coronal suture, HHIP knockout, sample

Supports a case/control comparison: 7 samples read as cases, 8 as controls.

How we read this: 4 replicated groups read from 15 sample titles; they account for 15 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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