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Dnmt1 determines bone length by regulating energy metabolism of growth plate chondrocytes [RNA-seq]

GSE270640 Mus musculus (mouse) RNA-seq (gene expression) 22 samples Submitted 2025/09/15 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 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
Dnmt1 determines bone length by regulating energy metabolism of growth plate chondrocytesNature communications · 2025
Summary (written by the submitters)
Chondrocytes differentiated from mesenchymal stem cells play a role in determining skeletal patterns by ossification. However, it is still unclear how the maintenance DNA methylation in chondrocytes regulates differentiation and skeletal formation. In Musculoskeletal Knowledge Portal, Dnmt1 was significantly associated with “Height”. In fact, long bone of limb specific Dnmt1 deficient mice was significantly shortened due to decreased chondrocyte proliferation and accelerated differentiation.
Read the full summary ↓
Furthermore, integrated analysis of RNA-Seq and MBD-Seq revealed that in Dnmt1ΔPrx1 chondrocytes, reduced DNA methylation resulted in an increase in energy metabolism-related genes in addition to ossification-related genes. Metabolomic analysis confirmed that almost all energy metabolites were increased in Dnmt1ΔPrx1 chondrocytes. These results indicate that Dnmt1 mediated maintenance DNA methylation governs chondrocyte differentiation by regulating energy metabolism through both gene expression and metabolite supply. Taken together, this study suggested that appropriate DNA methylation status in chondrocytes can orchestrate growth plate mineralization and subsequently determine bone length.
Published in
Dnmt1 determines bone length by regulating energy metabolism of growth plate chondrocytes
Yanagihara Y, Takahashi M, Izumi Y et al. · Nature communications 2025 · PMID 41188231 · doi:10.1038/s41467-025-65145-9
This dataset
Open GSE270640 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 GSE270640_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 PRJNA1127613 and SRA study SRP515733. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41188231) ↗
Study design
6 conditions, mostly with about 4 replicates each
Chondrocyte, Control, BMP2, Day3, Biol ×4 Chondrocyte, cKO, BMP2, Day3, Biol ×4 Cartilage, Prx1Dnmt1_vivo_flox ×4 Cartilage, Prx1Dnmt1_vivo_cKO ×4 Chondrocyte, Control, biol ×3 Chondrocyte, cKO, biol ×3

Supports a between-group comparison across 22 samples.

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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