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Derepression of transposable elements in mouse prefrontal cortex disrupts social behavior

GSE294558 Mus musculus (mouse) RNA-seq (gene expression) 74 samples Submitted 2025/12/15 Platform GPL17021
At a glance

RNA-seq (gene expression) · mouse · 74 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
74 samples: 8 conditions, mostly with about 9 replicates eachGroups 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
Derepression of transposable elements in the mouse prefrontal cortex disrupts social behaviorProceedings of the National Academy of Sciences of the United States of America · 2025
Summary (written by the submitters)
The neurobiological origins of social behaviors are poorly understood. Previous studies have linked the function of a single Krüppel-associated box zinc finger protein (KZFP), ZFP189, in the mouse prefrontal cortex (PFC), with the regulation of transposable elements (TEs), immune genes, and social behaviors. Here, we expand the scope of inquiry to explore the relationship between collective PFC KZFP function and social behaviors by altering the function of the cognate KZFP interacting protein TRIM28 within the PFC of male and female mice.
Read the full summary ↓
We reprogrammed natural TRIM28WT by replacing the endogenous, transcriptionally repressive domain with a synthetic, enhanced transcriptional activation domain VP64-p65-Rta (TRIM28VPR), or by excising the transcriptional regulatory domain (TRIM28NFD). Upon intra-PFC viral-mediated delivery of TRIM28 variants, we observed that inversion of TRIM28 transcriptional control via HSV-TRIM28VPR selectively produced deficits in social behaviors, without affecting non-social behaviors. RNA-sequencing of manipulated PFC revealed that HSV-TRIM28VPR drove transcriptional escape of all classes of TEs, particularly those located within intronic and enhancer regions proximal to downregulated immune genes. HSV-TRIM28VPR-mediated social deficits were reversible by intra-PFC repletion of interferon cytokines. These data point to PFC KZFP-TRIM28 interactions as necessary to stabilize genomic TEs to enable cis-regulation of key immune gene expression, which enhances organismal capacity for complex, pro-social behaviors.
Published in
Derepression of transposable elements in the mouse prefrontal cortex disrupts social behavior
Kim RK, Smith C, Truby NL et al. · Proceedings of the National Academy of Sciences of the United States of America 2025 · PMID 41405865 · doi:10.1073/pnas.2510663122
This dataset
Open GSE294558 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 GSE294558_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 PRJNA1250497 and SRA study SRP578448. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41405865) ↗
Study design
8 conditions, mostly with about 9 replicates each
PFC tissue, HSV-TRIM28VPR, female, mouse ×10 PFC tissue, HSV-TRIM28WT, female, mouse ×10 PFC tissue, HSV-TRIM28WT, male, mouse ×10 PFC tissue, HSV-GFP, female, mouse ×9 PFC tissue, HSV-GFP, male, mouse ×9 PFC tissue, HSV-TRIM28NFD, male, mouse ×9 PFC tissue, HSV-TRIM28VPR, male, mouse ×9 PFC tissue, HSV-TRIM28NFD, female, mouse ×8

Supports a between-group comparison across 74 samples.

How we read this: 8 replicated groups read from 74 sample titles; they account for 74 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

+ 34 more — browse all 74 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.