← BioTransfer GEO Dataset Finder
GEO series

Transposable elements are dynamically expressed within medium spiny neurons and associated with molecular and behavioral adaptations to cocaine

GSE296397 Mus musculus (mouse) Single-nucleus RNA-seq 12 samples Submitted 2025/08/27 Platform GPL17021
At a glance

Single-nucleus RNA-seq · mouse · 12 samples

What it is
Single-nucleus RNA-seqGene activity measured in individual nuclei (used when whole cells are hard to isolate, for example from frozen tissue). Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
Mus musculus (mouse)
Samples
12 samples: 4 × Nac tissue, HSV-ZFP189NFD, male, mouse vs 4 × Nac tissue, HSV-ZFP189VPR, male, mouse vs 4 × Nac tissue, HSV-ZFP189WT, male, mouseGroups 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 Elements Are Dynamically Regulated in Medium Spiny Neurons and May Contribute to the Molecular and Behavioral Adaptations to CocaineBiological psychiatry · 2026
Summary (written by the submitters)
A more complete understanding of the molecular mechanisms by which substance use is encoded in the brain could illuminate novel strategies to treat substance use disorders, including cocaine use disorder (CUD). We have previously discovered that Zfp189, which encodes a Krüppel-associated box zinc finger protein (KZFP) transcription factor (TF), differentially accumulates in nucleus accumbens (NAc) Drd1+ and Drd2+ medium spiny neurons (MSNs) over the course of cocaine exposure and is causal in producing MSN functional and behavioral changes to cocaine.
Read the full summary ↓
Here, we aimed to illuminate the brain cell-type specific molecular mechanisms through which this KZFP TF produces chronic cocaine -related brain changes, with emphasis on investigating transposable elements (TEs), since KZFPs like ZFP189 are known regulators of TEs. We discovered that expression of NAc TE transcripts was dramatically increased by cocaine experience, the most sensitive NAc cell-type was MSNs, and TEs in Drd1+ MSNs were considerably more dynamic over the course of cocaine exposure than TEs in Drd2+ MSNs. We demonstrated that synthetic ZFP189VPR is capable of dysregulating NAc TEs. In our snRNAseq data we observed that, relative to ZFP189WT, NAc manipulated with ZFP189VPR impeded cocaine-induced gene expression in NAc cell-types, including both Drd1+ and Drd2+ MSNs. Within either MSN subtype, the consequence of normal ZFP189 function was to enhance immune-related gene expression, and ZFP189VPR impeded these gene expression profiles. We discovered that behavioral and cell morphological adaptations to cocaine are produced by dysregulating TEs with ZFP189VPR in Drd1+ MSNs or stabilizing TEs with ZFP189WT in Drd2+ MSNs, revealing a persistent opponent process balanced across MSN subtypes and weighted by TE stability and consequent gene expression within MSN subtype.
Published in
Transposable Elements Are Dynamically Regulated in Medium Spiny Neurons and May Contribute to the Molecular and Behavioral Adaptations to Cocaine
Silva GM, Kaplan AL, Park CR et al. · Biological psychiatry 2026 · PMID 40716507 · doi:10.1016/j.biopsych.2025.07.014
This dataset
Open GSE296397 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 GSE296397_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1259058 and SRA study SRP583172. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40716507) ↗
Study design
4 × Nac tissue, HSV-ZFP189NFD, male, mouse vs 4 × Nac tissue, HSV-ZFP189VPR, male, mouse vs 4 × Nac tissue, HSV-ZFP189WT, male, mouse

Supports a between-group comparison across 12 samples.

How we read this: 3 replicated groups read from 12 sample titles; they account for 12 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

Search all mouse RNA-seq datasets in GEO →

Share this dataset

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.