GEO series

Study of 5mC-DNA, m6A-RNA and RNA-expression in HeLa, ES and EB [m6A in ES and EB and RNAseq in EB]

GSE218292 Mus musculus (mouse) DNA methylation 58 samples Submitted 2025/01/10 Platform GPL19057

At a glance

DNA methylation · mouse · 58 samples

What it is: DNA methylationChemical marks on DNA that help switch genes on or off.
Organism: Mus musculus (mouse)
Samples: 58 samples: 46 distinct titles, 9 of them repeatedGroups 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: Fine-tuning of gene expression through the Mettl3-Mettl14-Dnmt1 axis controls ESC differentiationCell · 2025

Summary (written by the submitters)

The epigenetic marking of DNA, histones, and RNA is central for regulating gene expression in development and disease. On DNA, well-characterized 5-methylcytosine (5mC) controls the chromatin state. On mRNA, the most prevalent internal mark, N6-methyladenosine (m6A), installed by METTL3-METTL14 methyltransferases, regulates RNA metabolism.

Read the full summary ↓

Recent evidences link RNA modifications with epigenetics, notably by connecting m6A to histone marks. The crosstalk between m6A and DNA methylation, however, remains poorly understood. Here we reveal a direct mechanistic link between m6A and DNA methylation. Our findings indicate a proximal co-occurrence of m6A and 5mC marks at gene body and this contributes to enhanced gene expression. We show that the m6A writer METTL3 regulates intragenic methylation and gene expression. Mechanistically, we evidence a direct binding of METTL3-METTL14 to the 5mC methyltransferase DNMT1 and reveal that chromatin-tethered METTL14 recruits DNMT1 to chromatin. We demonstrate that gene-body 5mC and mRNA-stability-enhancing effect of coding-sequence m6A contribute to increased gene expression. We further substantiate our findings in embryonic stem cells by showing that METTL3 regulates gene-body methylation and expression of key differentiation markers. Altogether, our work establishes a key layer of gene expression regulation, involving a direct mechanistic crosstalk between DNA methylation and RNA methylation machinery.

Published in

Fine-tuning of gene expression through the Mettl3-Mettl14-Dnmt1 axis controls ESC differentiation

Quarto G, Li Greci A, Bizet M et al. · Cell 2025 · PMID 39826545 · doi:10.1016/j.cell.2024.12.009

This dataset

Open GSE218292 in finder → Find more mouse methylation 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 GSE218292_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 beta-value tables or raw IDAT files among the supplementary files.

Also filed as BioProject PRJNA903111 and SRA study SRP408575. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39826545) ↗

Study design

46 distinct titles, 9 of them repeated

ES-INP-0h ×3 ES-INP-24h ×3 ES-INP-3h ×3 ES-m6A-0h-2 ×2 ES-m6A-0h-3 ×2 ES-m6A-24h-2 ×2 ES-m6A-24h-3 ×2 ES-m6A-3h-2 ×2 +1 more

How we read this: Read from 58 sample titles: 46 distinct titles with little repetition. 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

GSM6738735 EBd8-WT-1-m6A
GSM6738736 EBd8-WT-2-m6A
GSM6738737 EBd8-WT-3-m6A
GSM6738738 EBd8-WT-1-INPUT
GSM6738739 EBd8-WT-2-INPUT
GSM6738740 EBd8-WT-3-INPUT
GSM6738741 EBd8-METTL3KO-1-RNA
GSM6738742 EBd8-METTL3KO-2-RNA
GSM6738743 EBd8-METTL3KO-3-RNA
GSM6738744 ES-WT-1-RNA
GSM6738745 ES-WT-2-RNA
GSM6738746 ES-WT-3-RNA
GSM8410820 EBd8-WT-1.1-m6A
GSM8410821 EBd8-WT-1.2-m6A
GSM8410822 EBd8-WT-1-INPUT (2)
GSM8410823 EBd8-WT-2.1-m6A
GSM8410824 EBd8-WT-2.2-m6A
GSM8410825 EBd8-WT-2-INPUT (2)
GSM8410826 EBd8-WT-3.1-m6A
GSM8410827 EBd8-WT-3.2-m6A
GSM8410828 EBd8-WT-3-INPUT (2)
GSM8410829 ES-WT-1-INPUT
GSM8410830 ES-WT-1-m6A
GSM8410831 ES-WT-2-INPUT
GSM8410832 ES-WT-2-m6A
GSM8410833 ES-WT-3,1-m6A
GSM8410834 ES-WT-3,2-m6A
GSM8410835 ES-WT-3-INPUT
GSM8410836 ES-WTclon5-1-INP
GSM8410837 ES-WTclon5-1-m6A
GSM8410838 ES-WTclon5-2-INP
GSM8410839 ES-WTclon5-2-m6A
GSM8410840 ES-WTclon5-3-INP
GSM8410841 ES-WTclon5-3-m6A
GSM8410842 ES-INP-0h-1
GSM8410843 ES-INP-0h-2
GSM8410844 ES-INP-0h-3
GSM8410845 ES-INP-24h-1
GSM8410846 ES-INP-24h-2
GSM8410847 ES-INP-24h-3

+ 18 more — browse all 58 samples with per-sample file links →

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GSE272789 Study of 5mC-DNA, m6A-RNA and RNA-expression in HeLa, ES and EB [RNAseq in Mettl14KO and rescued in E14TG2a ES/EB] 18 samples shares 5mc-dna, m6a-rna, rna-expression, hela
GSE272782 Study of 5mC-DNA, m6A-RNA and RNA-expression in HeLa, ES and EB [ActinoD in E14TG2a ES] 24 samples shares 5mc-dna, m6a-rna, rna-expression, hela
GSE272791 Study of 5mC-DNA, m6A-RNA and RNA-expression in HeLa, ES and EB [SLAM seq in J1 ES] 15 samples shares 5mc-dna, m6a-rna, rna-expression, hela
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GSE246051 Iron chelation therapy elicits innate immune control of metastatic ovarian cancer 9 samples shares hela
GSE288553 Phosphine-Nitrogen-Phosphine chelated CoCl2 (Co68) is a novel therapeutic agent for pancreatic cancer [ATAC-seq] 4 samples shares hela
GSE281843 Copper chelation redirects neutrophil function to enhance anti-GD2 antibody therapy in neuroblastoma [scRNA-seq] 4 samples shares hela

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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.