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A bilaminar stem cell core governs tooth establishment.

GSE272194 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 27 samples Submitted 2025/05/01 Platform GPL24247Platform GPL34290
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 27 samples

What it is
ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism
Mus musculus (mouse)
Samples
27 samples: 8 conditions, mostly in duplicateGroups 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
A spatially organized Cd24a(+)/Pax9(+) stem cell core governs postnatal tooth establishmentScience advances · 2025
Summary (written by the submitters)
Establishment of human teeth relies on coordinated formation of dentin-pulp complex for nurturing and periodontal tissues for anchoring in alveolar bone. The exact cell origin of dentin-pulp complex and periodontal tissues, and the integrative developmental process remain elusive. Here, we identified a bilaminar core of Cd24a+ and Pax9+ stem cells that governs the tooth establishment and persists into adulthood.
Read the full summary ↓
Specifically, Cd24a+ stem cells gave rise to the dentin-pulp complex while Pax9+ stem cells mainly generated periodontal tissues as well as partial dental pulp. DTA-mediated cell ablation of the Cd24a+/Pax9+ stem cells significantly compromised tooth establishment. Moreover, during development, the Cd24a+/Pax9+ bilaminar core concentrated on the apical region, collectively migrated and contributed to the newly formed dental root, potentially guided by PDGF-B derived from the alveolar bone. Integrated multi-omic analysis and spatial mapping further revealed lineage-associated key signaling pathways in Cd24a+/Pax9+ stem cells and the unique organization of different cell compositions. Finally, the CD24+/PAX9+ bilaminar core was also detected in human teeth at different stages, suggesting it a conserved developmental mechanism. Together, our work identified a unique bilaminar core of bona fide dental stem cells governing tooth establishment and might guide the future regenerative therapy to treat pulpitis, pulp necrosis and periodontal diseases.
Published in
A spatially organized Cd24a(+)/Pax9(+) stem cell core governs postnatal tooth establishment
Shan C, Wang W, Lu H et al. · Science advances 2025 · PMID 40479070 · doi:10.1126/sciadv.adu5653
This dataset
Open GSE272194 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 GSE272194_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA1135489 and SRA study SRP519739. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40479070) ↗
Study design
8 conditions, mostly in duplicate
Cd24a-Pax9- anti-H3K4me3 Cut&Tag ×2 Cd24a+Pax9- anti-H3K4me3 Cut&Tag ×2 Cd24a+Pax9+ anti-H3K4me3 Cut&Tag ×2 Cd24a-Pax9+ anti-H3K4me3 Cut&Tag ×2 Cd24a-Pax9- anti-IgG Cut&Tag ×2 Cd24a+Pax9- anti-IgG Cut&Tag ×2 Cd24a+Pax9+anti-IgG Cut&Tag ×2 Cd24a-Pax9+ anti-IgG Cut&Tag ×2 +11 more

Supports a between-group comparison across 16 samples.

How we read this: 8 replicated groups read from 27 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
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