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Hypoxia impedes differentiation of cranial neural crest cells into derivatives relevant for palatogenesis

GSE273808 Mus musculus (mouse) RNA-seq (gene expression) 28 samples Submitted 2025/07/24 Platform GPL13112
At a glance

RNA-seq (gene expression) · mouse · 28 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
28 samples: 8 conditions, mostly with about 4 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
Hypoxia impedes differentiation of cranial neural crest cells into derivatives relevant for craniofacial developmentOpen biology · 2025
Summary (written by the submitters)
Orofacial clefts (OFC) are clefts of the lip and/or palate. They are the second-most prevalent congenital malformation. OFC result from failures in fusion processes of facial structures during embryonic development. Craniofacial structures are derived from ectodermal epithelial cells and cranial neural crest cells (CNCCs). In fact, the ectomesenchymal CNCCs are the source of most midface structures.
Read the full summary ↓
They proliferate heavily during development and differentiate into a variety of tissues such as bone, cartilage and smooth muscle. Risk factors for OFC are multifactorial and include genetic components but also environmental factors. One environmental factor is hypoxia that can be caused by several reasons during pregnancy, such as tobacco smoking, medication or living at high altitudes. Knowledge about the molecular mechanisms of how hypoxia evokes OFC is at large. We here show that hypoxia has only modest effects on proliferating CNCCs, but dramatically influences their differentiation potential. We detected massive perturbations of differentiation in all of our tested differentiation paradigms, i.e. chondrocytes, osteoblasts and smooth muscle cells. The transcriptional induction of the majority of regulated genes during each of these processes was grossly impaired by hypoxic conditions, as evidenced by genome-wide transcriptomic analyses. Bioinformatic analyses pointed to a central role of cytoskeletal organization and amino acid metabolism being compromised during all three differentiation processes. We could identify several OFC risk genes amongst the genes with constrained induction during hypoxia. Our analyses reveal a drastic influence of hypoxia on the differentiation potential of CNCCs as a possible source for the occurrence of OFC.
Published in
Hypoxia impedes differentiation of cranial neural crest cells into derivatives relevant for craniofacial development
Schmid T, Rodrian G, Bachmann E et al. · Open biology 2025 · PMID 40695323 · doi:10.1098/rsob.250129
This dataset
Open GSE273808 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 GSE273808_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 PRJNA1143393 and SRA study SRP523850. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40695323) ↗
Study design
8 conditions, mostly with about 4 replicates each
Normoxia, proliferating, ×4 Normoxia, chondrocyte differentiated, ×4 Normoxia, osteoblast differentiated, ×4 Normoxia, smooth muscle cell differentiated, ×4 Hypoxia, proliferating, ×3 Hypoxia, chondrocyte differentiated, ×3 Hypoxia, osteoblast differentiated, ×3 Hypoxia, smooth muscle cell differentiated, ×3

Supports a between-group comparison across 28 samples.

How we read this: 8 replicated groups read from 28 sample titles; they account for 28 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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