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Cocaine-Induced Gene Regulation in D1 and D2 Neuronal Ensembles of the Nucleus Accumbens Revealed by Single-Cell RNA Sequencing

GSE297372 Mus musculus (mouse) Single-cell RNA-seq 16 samples Submitted 2025/06/16 Platform GPL24247

At a glance

Single-cell RNA-seq · mouse · 16 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism: Mus musculus (mouse)
Samples: 16 samples: 8 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: Cocaine-induced gene regulation in D1 and D2 neuronal ensembles of the nucleus accumbensCommunications biology · 2025

Summary (written by the submitters)

Cocaine use disorder is characterized by persistent drug-seeking behavior and a high risk of relapse, driven in part by lasting molecular and circuit adaptations in the nucleus accumbens. To explore the transcriptomic changes underlying these alterations, we employed fluorescence-activated nucleus sorting coupled with single-nucleus RNA sequencing to analyze D1 and D2 medium spiny neurons in this brain region of male mice subjected to acute cocaine exposure or to prolonged withdrawal from repeated cocaine exposure without or with an acute cocaine rechallenge.

Read the full summary ↓

This approach allowed us to precisely delineate and contrast transcriptionally distinct neuronal subpopulations─or ensembles─across various treatment conditions. We identified significant heterogeneity within both D1 and D2 MSNs, revealing distinct clusters with unique transcriptional profiles. Notably, we identified a discrete D1 MSN population characterized by the upregulation of immediate early genes, as well as another group of D1 MSNs linked to prolonged withdrawal, uncovering novel regulators of withdrawal-related transcriptome dynamics. Our findings provide a high-resolution transcriptomic map of D1 and D2 MSNs, illustrating the dynamic changes induced by cocaine exposure and withdrawal. These insights into the molecular mechanisms underlying cocaine use disorder highlight potential targets for therapeutic intervention aimed at preventing relapse.

Published in

Cocaine-induced gene regulation in D1 and D2 neuronal ensembles of the nucleus accumbens

Mews P, Mason AV, Kirchner EG et al. · Communications biology 2025 · PMID 40506501 · doi:10.1038/s42003-025-08327-x

This dataset

Open GSE297372 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 GSE297372_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 PRJNA1263587 and SRA study SRP585829. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40506501) ↗

Study design

8 conditions, mostly in duplicate

D2 sorted cells, Saline-Saline, ×2 D2 sorted cells, Saline-Cocaine, ×2 D2 sorted cells, Cocaine-Saline, ×2 D2 sorted cells, Cocaine-Cocaine, ×2 D1 sorted cells, Saline-Saline, ×2 D1 sorted cells, Saline-Cocaine, ×2 D1 sorted cells, Cocaine-Saline, ×2 D1 sorted cells, Cocaine-Cocaine, ×2

Supports a between-group comparison across 16 samples.

How we read this: 8 replicated groups read from 16 sample titles; they account for 16 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

GSM8989586 D2 sorted cells, Saline-Saline, Replicate 1 D2 sorted cells, Saline…
GSM8989587 D2 sorted cells, Saline-Saline, Replicate 2 D2 sorted cells, Saline…
GSM8989588 D2 sorted cells, Saline-Cocaine, Replicate 1 D2 sorted cells, Saline…
GSM8989589 D2 sorted cells, Saline-Cocaine, Replicate 2 D2 sorted cells, Saline…
GSM8989590 D2 sorted cells, Cocaine-Saline, Replicate 1 D2 sorted cells, Cocain…
GSM8989591 D2 sorted cells, Cocaine-Saline, Replicate 2 D2 sorted cells, Cocain…
GSM8989592 D2 sorted cells, Cocaine-Cocaine, Replicate 1 D2 sorted cells, Cocain…
GSM8989593 D2 sorted cells, Cocaine-Cocaine, Replicate 2 D2 sorted cells, Cocain…
GSM8989594 D1 sorted cells, Saline-Saline, Replicate 1 D1 sorted cells, Saline…
GSM8989595 D1 sorted cells, Saline-Saline, Replicate 2 D1 sorted cells, Saline…
GSM8989596 D1 sorted cells, Saline-Cocaine, Replicate 1 D1 sorted cells, Saline…
GSM8989597 D1 sorted cells, Saline-Cocaine, Replicate 2 D1 sorted cells, Saline…
GSM8989598 D1 sorted cells, Cocaine-Saline, Replicate 1 D1 sorted cells, Cocain…
GSM8989599 D1 sorted cells, Cocaine-Saline, Replicate 2 D1 sorted cells, Cocain…
GSM8989600 D1 sorted cells, Cocaine-Cocaine, Replicate 1 D1 sorted cells, Cocain…
GSM8989601 D1 sorted cells, Cocaine-Cocaine, Replicate 2 D1 sorted cells, Cocain…

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