GEO series

Stem cell specification and niche formation in developing incisor depend on actomyosin forces

GSE299463 Mus musculus (mouse) Single-cell RNA-seq 10 samples Submitted 2025/12/01 Platform GPL24247

At a glance

Single-cell RNA-seq · mouse · 10 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism: Mus musculus (mouse)
Samples: 10 samples: 4 × E11.5 vs 4 × E14.5 vs 2 × E16.5Groups 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: Stem cell specification and niche formation in developing incisor require actomyosin forcesStem cells (Dayton, Ohio) · 2026

Summary (written by the submitters)

The precise timing of stem cell specification and niche formation during murine incisor development is poorly understood, and it is unclear whether these processes occur simultaneously or in a sequential manner. Functional dental epithelial stem cells are marked by the expression of Sox2, a transcription factor that is broadly expressed in the dental epithelium at the dentition onset and restricted to stem cells in fully developed incisor.

Read the full summary ↓

Using genetic lineage tracing in Sox2CreERT2/+; R26RmT/mGand Sox2CreERT2/+; R26RtdT/+embryos along with a single-cell RNA sequencing at different stages of incisor development, we investigated the timing of the stem cell specification and its temporal relationship with niche formation. Our results reveal the presence of a Sox2-expressing stem cell-like population prior to formation of the functional niche. These cells localize to the leading edge of the advancing incisor epithelium where they are maintained in an undifferentiated state. Our data demonstrate presence of actomyosin network and a generation of a contractile tension which helps confine Sox2+ stem cells to the leading edge. This mechanical confinement likely plays an important role in maintaining their stemness until the niche is functionally and structurally established. Partial or complete disruption of the actomyosin network disables the clustering of Sox2-expressing cells, potentially triggering their premature differentiation, and ultimately leads to impaired formation of the functional stem cell niche and abnormal growth of the incisor.

Published in

Stem cell specification and niche formation in developing incisor require actomyosin forces

Mohtadi Hamadani Y, Evers L, Myllymäki SM et al. · Stem cells (Dayton, Ohio) 2026 · PMID 41296682 · doi:10.1093/stmcls/sxaf074

This dataset

Open GSE299463 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 GSE299463_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1274481 and SRA study SRP591126. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41296682) ↗

Study design

4 × E11.5 vs 4 × E14.5 vs 2 × E16.5

Supports a between-group comparison across 10 samples.

How we read this: 3 replicated groups read from 10 sample titles; they account for 10 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

GSM9039523 E11.5_1 E11.5
GSM9039524 E11.5_2 E11.5
GSM9039525 E11.5_3 E11.5
GSM9039526 E11.5_4 E11.5
GSM9039527 E14.5_1 E14.5
GSM9039528 E14.5_2 E14.5
GSM9039529 E14.5_3 E14.5
GSM9039530 E14.5_4 E14.5
GSM9039531 E16.5_1 E16.5
GSM9039532 E16.5_2 E16.5

Datasets on a similar topic

GSE247069 Self-organised pattern formation in the developing dorsal neural tube by a temporal relay of BMP signalling 48 samples shares developing, formation
GSE275908 CXCL12-CXCR4 signaling mediates the formation of a macrophageal niche for mammary gland development and tumorigenesis 30 samples shares formation, niche
GSE291987 Z-DNA formation induces the totipotent-like state and primes Zscan4-dependent chromatin compartmentalization [RNA-Seq] 23 samples shares formation, depend
GSE215759 Mettl3-dependent m6A modification is essential for effector differentiation and memory formation of CD8+ T cells [RNA-seq] 15 samples shares formation, depend
GSE215762 Mettl3-dependent m6A modification is essential for effector differentiation and memory formation of CD8+ T cells 41 samples shares formation, depend
GSE306026 Dosage-dependent role of Gata3 in primitive endoderm and trophectoderm specification in embryonic stem cells 22 samples shares specification, depend
GSE287098 Influenza virus-induced type I interferons disrupt alveolar epithelial repair and tight junction integrity in the developing lung 96 samples shares developing
GSE185862 A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation 95 samples shares formation

Search all mouse RNA-seq datasets in GEO →

Share this dataset

Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.