GEO series

Spatiomolecular mapping reveals anatomical organization of heterogeneous cell types in the human nucleus accumbens [snRNA-seq]

GSE307587 Homo sapiens (human) Single-nucleus RNA-seq 20 samples Submitted 2025/09/10 Platform GPL24676

At a glance

Single-nucleus RNA-seq · human · 20 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).
Organism: Homo sapiens (human)
Samples: 20 samples: 20 samples, each with a distinct title — no replicated groupsGroups 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: Spatiomolecular mapping reveals anatomical organization of heterogeneous cell types in the human nucleus accumbensbioRxiv : the preprint server for biology · 2025

Summary (written by the submitters)

The nucleus accumbens (NAc) is a key component of the mesolimbic dopamine system that critically regulates many behaviors related to reward and motivation. The NAc is implicated in several neuropsychiatric disorders, including major depressive disorder, schizophrenia, and substance use disorder. Rodent studies have identified spatial organization of heterogeneous medium spiny neuron (MSN) subtypes across the NAc core and shell, but the extent to which this cellular diversity and spatial organization is conserved in the human brain remains unclear.

Read the full summary ↓

Here, we generated a spatiomolecular atlas of NAc cell types and spatial domains by integrating spatial transcriptomics and single-nucleus RNA sequencing data from postmortem NAc tissue from 10 neurotypical adult donors. We identified 20 transcriptionally unique cell populations and 8 spatial domains, including specialized D1 islands composed of distinct dopamine receptor 1 (DRD1) MSN subtypes, which were enriched for OPRM1. In contrast to a discrete core vs. shell division, we observed continuous spatial gradients of gene expression across MSN domains, suggesting a more complex organization of DRD1 and DRD2 MSNs. Cross-species comparisons demonstrated conservation of MSN subtypes and spatial features between human, rodent, and nonhuman primate NAc. Genetic enrichment analysis with stratified linkage disequilibrium score regression revealed specific spatial domains associated with risk for psychiatric and addiction-related traits. To investigate this further, we spatially mapped ligand-receptor interactions involving neuropsychiatric risk genes. Finally, we leveraged existing rodent NAc data to identify drug-responsive transcriptional programs and predict their spatial distribution in the human NAc. Collectively, we provide a spatiomolecular framework for understanding the human NAc and its relevance to neuropsychiatric disease.

Published in

Spatiomolecular mapping reveals anatomical organization of heterogeneous cell types in the human nucleus accumbens

Ravichandran P, Bach SV, Phillips RA 3rd et al. · bioRxiv : the preprint server for biology 2025 · PMID 40964296 · doi:10.1101/2025.09.10.675374

This dataset

Open GSE307587 in finder → Find more human 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 GSE307587_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 PRJNA1322344. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40964296) ↗

Study design

20 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 20 sample titles: 20 distinct titles with little repetition. 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

GSM9227466 Br8325_Nac-PI+
GSM9227467 Br8325_Nac-PI+NeuN+
GSM9227468 Br8492_Nac-PI+
GSM9227469 Br8492_Nac-PI+NeuN+
GSM9227470 Br2720_Nac-PI+
GSM9227471 Br2720_Nac-PI+NeuN+
GSM9227472 Br6423_Nac-PI+
GSM9227473 Br6423_Nac-PI+NeuN+
GSM9227474 Br2743_Nac-PI+
GSM9227475 Br2743_Nac-PI+NeuN+
GSM9227476 Br3942_Nac-PI+
GSM9227477 Br3942_Nac-PI+NeuN+
GSM9227478 Br6432_Nac-PI+
GSM9227479 Br6432_Nac-PI+NeuN+
GSM9227480 Br6471_Nac-PI+
GSM9227481 Br6471_Nac-PI+NeuN+
GSM9227482 Br6522_Nac-PI+
GSM9227483 Br6522_Nac-PI+NeuN+
GSM9227484 Br8667_Nac-PI+
GSM9227485 Br8667_Nac-PI+NeuN+

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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.