GEO series

m6A RNA methylation in the maintenance of X-chromosome inactivation and X to autosome dosage compensation in early embryogenesis [RNA-Seq]

GSE295196 Mus musculus (mouse) DNA methylation 14 samples Submitted 2026/03/04 Platform GPL24247

At a glance

DNA methylation · mouse · 14 samples

What it is: DNA methylationChemical marks on DNA that help switch genes on or off.
Organism: Mus musculus (mouse)
Samples: 14 samples: 6 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: The role of m6A RNA methylation in the maintenance of X chromosome inactivation and X-to-autosome dosage compensation in early embryonic lineagesStem cell reports · 2026

Summary (written by the submitters)

In females, inactivation of one X-chromosome balances the dosage of X-linked genes similar to males. In addition, transcriptional upregulation balances the dosage of genes expressed from the single active-X to the double copy of autosomes in both sexes. However, the factors and mechanisms involved in the maintenance of X-chromosome inactivation (XCI) and X to autosome dosage compensation remain poorly understood.

Read the full summary ↓

In this study, we report the contribution of m6A RNA methylation in maintenance of XCI and X to autosome dosage compensation in early embryonic and extraembryonic lineages. In the study, we find that m6A RNA methylation has a minimal role to play in maintenance of silencing of the inactivated-X chromsoome in TSC, XEN and EpiSC . Moreover, we also show that the X-linked transcripts are less enriched with m6A than the autosomal transcripts suggesting its role in increased X-transcript stability and hence upregulation. In addition, surprisingly we observed that X-linked transcripts without m6A are fully dosage compensated than the transcripts with m6A which undergo partial X to autosome dosage compensation in TSC, XEN and EpiSC. Further, we also found that global depletion of m6A level in TSC, XEN and EpiSC has a minor effect on the X to autosome dosage balance implicating the minor contribution of m6A RNA methylation during early embryogenesis.

Published in

The role of m6A RNA methylation in the maintenance of X chromosome inactivation and X-to-autosome dosage compensation in early embryonic lineages

Naik HC, Baro R, Sarkar A et al. · Stem cell reports 2026 · PMID 41386228 · doi:10.1016/j.stemcr.2025.102740

This dataset

Open GSE295196 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 GSE295196_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 PRJNA1253682 and SRA study SRP580296. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41386228) ↗

Study design

6 conditions, mostly in duplicate

XEN_DMSO ×3 XEN_STM2457 ×3 TSC_DMSO ×2 TSC_STM2457 ×2 EpiSC_DMSO ×2 EpiSC_STM2457 ×2

Supports a between-group comparison across 14 samples.

How we read this: 6 replicated groups read from 14 sample titles; they account for 14 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

GSM8943469 XEN_DMSO_rep_1 XEN_DMSO
GSM8943470 XEN_STM2457_rep_1 XEN_STM2457
GSM8943471 XEN_DMSO_rep_2 XEN_DMSO
GSM8943472 XEN_STM2457_rep_2 XEN_STM2457
GSM8943473 XEN_DMSO_rep_3 XEN_DMSO
GSM8943474 XEN_STM2457_rep_3 XEN_STM2457
GSM8943475 TSC_DMSO_rep_1 TSC_DMSO
GSM8943476 TSC_DMSO_rep_2 TSC_DMSO
GSM8943477 TSC_STM2457_rep_1 TSC_STM2457
GSM8943478 TSC_STM2457_rep_2 TSC_STM2457
GSM8943479 EpiSC_DMSO_rep_1 EpiSC_DMSO
GSM8943480 EpiSC_DMSO_rep_2 EpiSC_DMSO
GSM8943481 EpiSC_STM2457_rep_1 EpiSC_STM2457
GSM8943482 EpiSC_STM2457_rep_2 EpiSC_STM2457

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GSE251883 NFkB Signaling is Required for Xist RNA Localization at the Inactive X and for X-Chromosome Inactivation Maintenance Following T cell Activation 39 samples shares x-chromosome, inactivation, maintenance
GSE251879 NFkB Signaling is Required for Xist RNA Localization at the Inactive X and for X-Chromosome Inactivation Maintenance Following T cell Activation [CUT&RUN] 14 samples shares x-chromosome, inactivation, maintenance
GSE274492 The remodeling of bivalent chromatin is essential for mouse peri-implantation embryogenesis [Valid RNA-Seq] 200 samples shares embryogenesis, rna-seq

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