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EHMT2 represses totipotency- and differentiation-associated genes in pluripotent stem cells through distinct regulatory modes [RNA-seq]

GSE280605 Mus musculus (mouse) RNA-seq (gene expression) 45 samples Submitted 2025/01/15 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 45 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
45 samples: 8 conditions, mostly in triplicateGroups 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
Coordinated repression of totipotency-associated gene loci by histone methyltransferase EHMT2 through binding to LINE-1 regulatory elementsbioRxiv : the preprint server for biology · 2024
Summary (written by the submitters)
Mouse embryonic stem cells (mESCs) and other naïve pluripotent stem cells, under specific conditions, can reverse typical developmental trajectories and de-differentiate into 2-cell-like cells (2CLCs) that resemble the mammalian embryo during zygotic genome activation (ZGA). We implemented a multipurpose allele for acute protein depletion and efficient immunoprecipitation to dissect the molecular functions of EHMT2 in mESCs.
Read the full summary ↓
This approach allowed us to define different types of EHMT2 target genes and distinct modes of chromatin engagement and repression. Most notably, EHMT2 directly represses large clusters of co-regulated gene loci that comprise a significant fraction of the 2CLC-specific transcriptome by initiating H3K9me2 spreading from distal LINE-1 elements. Conversely, the loss of EHMT2 allows the recruitment of the activator DPPA2/4 to promoter-proximal ERVs in 2CLCs, thus facilitating the mESC-to-2CLC transition. Repression of germ layer-associated transcripts by EHMT2 occurs outside of gene clusters in collaboration with ZFP462 and entails binding to non-repeat enhancers. Our data suggests that EHMT2 functions as an attenuator of the bidirectional differentiation potential of mouse naïve pluripotent stem cells and define molecular models for the gene-specific repressive activity of this essential histone methyltransferase.
Published in
Coordinated repression of totipotency-associated gene loci by histone methyltransferase EHMT2 through binding to LINE-1 regulatory elements
Chatterjee K, Uyehara CM, Kasliwal K et al. · bioRxiv : the preprint server for biology 2024 · PMID 39763795 · doi:10.1101/2024.12.18.629181
This dataset
Open GSE280605 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 GSE280605_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 PRJNA1179482 and SRA study SRP541866. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39763795) ↗
Study design
8 conditions, mostly in triplicate
e2Merv_dmso_gfpNeg_72hr_rna ×3 e2Merv_dmso_gfpPos_72hr_rna ×3 e2Merv_dtag_gfpNeg_72hr_rna ×3 e2Merv_dtag_gfpPos_72hr_rna ×3 mESC , WT, DMSO, ×3 mESC , WT, UNC0638, ×3 mESC , Dppa4 KO, DMSO, ×3 mESC , Dppa4 KO, UNC0638, ×3 +21 more

Supports a between-group comparison across 24 samples.

How we read this: 8 replicated groups read from 45 sample titles; they account for 24 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

+ 5 more — browse all 45 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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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.