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TRIM28-dependent developmental heterogeneity determines cancer susceptibility through distinct epigenetic states [RNA-seq - matched healthy and tumor tissues]

GSE263021 Mus musculus (mouse) RNA-seq (gene expression) 41 samples Submitted 2024/04/02 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 41 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
41 samples: 16 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
TRIM28-dependent developmental heterogeneity determines cancer susceptibility through distinct epigenetic statesNature cancer · 2025
Summary (written by the submitters)
Mutations in cancer risk genes increase susceptibility, but not all carriers develop cancer. Indeed, while DNA mutations are necessary drivers of cancer, only a small subset of mutated cells go on to cause the disease. To date, the mechanisms underlying individual cancer susceptibility remain unclear. Here, we took advantage of a unique mouse model of intrinsic developmental heterogeneity (Trim28+/D9) to investigate whether early-life epigenetic variation influences cancer susceptibility later in life.
Read the full summary ↓
We found that heterozygosity of Trim28 is sufficient to generate two distinct early-life epigenetic states associated with differing cancer susceptibility. These developmentally primed states exhibit differential methylation patterns at typically silenced heterochromatin, detectable as early as 10 days of age. The differentially methylated loci are enriched for genes with known oncogenic potential, frequently mutated in human cancers and correlated with poor prognosis. This study provides genetic evidence that intrinsic developmental heterogeneity can prime individual, lifelong cancer susceptibility.
Published in
TRIM28-dependent developmental heterogeneity determines cancer susceptibility through distinct epigenetic states
Panzeri I, Fagnocchi L, Apostle S et al. · Nature cancer 2025 · PMID 39856421 · doi:10.1038/s43018-024-00900-3
This dataset
Open GSE263021 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 GSE263021_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 PRJNA1095465 and SRA study SRP499338. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39856421) ↗
Study design
16 conditions, mostly in duplicate
intestine_Trim28_heavy_normal ×3 intestine_Trim28_heavy_tumor ×3 prostate_Trim28_light_normal ×3 prostate_Trim28_light_tumor ×3 seminal_vesicle_Trim28_heavy_normal ×3 seminal_vesicle_Trim28_light_normal ×3 seminal_vesicle_Trim28_light_tumor ×3 intestine_Trim28_light_normal ×2 +10 more

Supports a case/control comparison: 20 samples read as cases, 21 as controls.

How we read this: 16 replicated groups read from 41 sample titles; they account for 39 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

+ 1 more — browse all 41 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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