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Cartography and mechanism of enhanced transcriptome plasticity by transposable elements

GSE297796 Mus musculus (mouse) RNA-seq (gene expression) 24 samples Submitted 2026/01/06 Platform GPL19057Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 24 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
24 samples: 10 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
Transposable element-gene chimera cartography, origination and role in enhancing transcriptome plasticityNature structural & molecular biology · 2026
Summary (written by the submitters)
Transposable elements (TEs) in our genome are the heritage of ancient parasitic infections. While most of human DNA is comprised of TEs and TE-derived elements, their repetitive nature poses technical challenges and thus little is known about their positional identity and regulatory roles. Here, by integrating long-read and multidimensional transcriptional analyses, we investigated when, where and how TEs become part of a gene.
Read the full summary ↓
We characterized how TE-derived isoform and new genes change across mouse-human variation and are linked to gene regulatory networks controlling cell states during differentiation, organogenesis and health (aging and pathological states). Mechanistically, we identified an RNA degradation-dependent and a splicing-dependent quality control mechanism that operate independently of conventional mechanisms of TE suppression (DNA methylation and heterochromatinization) and prevents TE-exonization and TE-induced cell differentiation. Overall, our findings reveal new mechanisms by which viral-derived elements enhance transcriptome plasticity.
Published in
Transposable element-gene chimera cartography, origination and role in enhancing transcriptome plasticity
Cheon Y, Alvstad EG, Torre D et al. · Nature structural & molecular biology 2026 · PMID 41741738 · doi:10.1038/s41594-026-01757-z
This dataset
Open GSE297796 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 GSE297796_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 PRJNA1266193 and SRA study SRP586851. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41741738) ↗
Study design
10 conditions, mostly in duplicate
mESCs, EtOH and SCR ASO, ×3 mESCs, EtOH and MERVL ASO, ×3 mESCs, cKO (tamoxifen) and SCR ASO, ×3 mESCs, cKO (tamoxifen) and MERVL ASO, ×3 mESCs, EtOH and U1 AMO, ×2 mESCs, EtOH and U6atac AMO, ×2 mESCs, EtOH and SCR AMO, ×2 mESCs, cKO (tamoxifen) and U1 AMO, ×2 +2 more

Supports a between-group comparison across 24 samples.

How we read this: 10 replicated groups read from 24 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
Datasets on a similar topic

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