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A spatial and projection-based transcriptomic atlas of paraventricular hypothalamic cell types (10X Chromium v3)

GSE303185 Mus musculus (mouse) Single-cell RNA-seq 1 samples Submitted 2025/12/16 Platform GPL19057

At a glance

Single-cell RNA-seq · mouse · 1 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: 1 samples
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: A spatial and projection-based transcriptomic atlas of paraventricular hypothalamic cell typesResearch square · 2025

Summary (written by the submitters)

The paraventricular hypothalamus (PVH) controls many behavioral and physiologic processes, including appetite, social behavior, autonomic outflow, and pituitary hormone secretion. However, molecular markers for functionally-specific PVH neuron projections remain largely undefined, and a complete census of PVH cell types has not been established.

Read the full summary ↓

Therefore, we performed extensive single-cell/nucleus RNA sequencing to identify unique neuronal subtypes and multiplexed error-robust fluorescence in situ hybridization (MERFISH) to validate and map them spatially. Our spatial transcriptomic atlas resolved 26 Sim1+ and 29 GABAergic neuron populations from the PVH and surrounding areas, revealing multiple subtypes not described previously and distinct transcriptional programs between neuroendocrine and centrally-projecting neurons. Additionally, projection-based profiling determined neuronal subtypes that project to the parabrachial region (PB) and spinal cord, helping to identify PVH populations that regulate satiety and sympathetic nervous system activity, respectively. Notably, PB-projecting PVH neurons expressing bombesin-like receptor 3 (Brs3) induce satiety, and their silencing causes obesity. Together, this atlas fills a critical gap by contributing high-resolution PVH spatial and circuit-based gene expression profiles, representing a valuable resource for the field of homeostasis.

Published in

A spatial and projection-based transcriptomic atlas of paraventricular hypothalamic cell types

Resch J, Li Y, Butler T et al. · Research square 2025 · PMID 41282229 · doi:10.21203/rs.3.rs-7895391/v1

This dataset

Open GSE303185 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 GSE303185_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 PRJNA1294292 and SRA study SRP602480. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41282229) ↗

Samples in this study

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

Datasets on a similar topic

GSE303083 A spatial and projection-based transcriptomic atlas of paraventricular hypothalamic cell types (10X Chromium v3 multiplexed) 6 samples shares 10x, projection-based, paraventricular, hypothalamic, chromium, spatial, types
GSE303256 A spatial and projection-based transcriptomic atlas of paraventricular hypothalamic cell types 131 samples shares projection-based, paraventricular, hypothalamic, spatial, types
GSE303081 A spatial and projection-based transcriptomic atlas of paraventricular hypothalamic cell types (Smart-Seq2) 81 samples shares projection-based, paraventricular, hypothalamic, spatial, types
GSE303080 A spatial and projection-based transcriptomic atlas of paraventricular hypothalamic cell types (Drop-Seq) 29 samples shares projection-based, paraventricular, hypothalamic, spatial, types
GSE303082 A spatial and projection-based transcriptomic atlas of paraventricular hypothalamic cell types (DroNc-Seq) 14 samples shares projection-based, paraventricular, hypothalamic, spatial, types
GSE246768 Single nuclear RNA sequencing and 10X spatial transcriptomic profiling of murine tumors initiated by transplantation of engineered prostate organoids [snRNA-seq] 1 samples shares 10x, spatial
GSE253859 Injury-Induced CLU-Positive Cardiomyocytes Drive Metabolic Reprogramming of Macrophage Function in Heart Regeneration [10X_chromium] 6 samples shares 10x, chromium
GSE318722 10X Genomics Multiome Assay (GEX + ATAC) of hypothalamic preoptic area in prenatally androgenized and control prepubertal female mice. 16 samples shares 10x, hypothalamic

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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.