GEO series
A spatial and projection-based transcriptomic atlas of paraventricular hypothalamic cell types (Drop-Seq)
GSE303080
Mus musculus (mouse)
Single-cell RNA-seq
29 samples
Submitted 2025/12/16
Platform GPL19057
At a glance
Single-cell RNA-seq · mouse · 29 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. 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
- 29 samples: 25 distinct titles, 4 of them repeatedGroups 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
- 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
Resch J, Li Y, Butler T et al.
· Research square 2025
· PMID 41282229
· doi:10.21203/rs.3.rs-7895391/v1
This dataset
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.
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 GSE303080_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1293951 and SRA study SRP602316. Searching any of these in the dataset finder brings you back here.
Study design
25 distinct titles, 4 of them repeated
PVH cells, female, sample 3, drop 1, RT-rxn B… ×2
PVH cells, male, sample 3, drop 1, RT-rxn A, … ×2
PVH cells, female, sample 7, drop 1, RT-rxn A… ×2
PVH cells, female, sample 7, drop 1, RT-rxn B… ×2
How we read this: Read from 29 sample titles: 25 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
- GSM9117326 PVH cells, female, sample 1, drop-run 1, RT-rxn A, lib. 1
- GSM9117327 PVH cells, female, sample 1, drop-run 2, RT-rxn A, lib. 1
- GSM9117328 PVH cells, male, sample 1, drop-run 1, RT-rxn A, lib. 1
- GSM9117329 PVH cells, male, sample 1, drop 2, RT-rxn A, lib. 1
- GSM9117330 PVH cells, male, sample 1, drop 3, RT-rxn A, lib. 1
- GSM9117331 PVH cells, female, sample 2, drop 1, RT-rxn A, lib. 1
- GSM9117332 PVH cells, female, sample 2, drop 2, RT-rxn A, lib. 1
- GSM9117333 PVH cells, male, sample 2, drop 1, RT-rxn A, lib. 1
- GSM9117334 PVH cells, male, sample 2, drop 2, RT-rxn A, lib. 1
- GSM9117335 PVH cells, male, sample 2, drop 3, RT-rxn A, lib. 1
- GSM9117336 PVH cells, female, sample 3, drop 1, RT-rxn A, lib. 1
- GSM9117337 PVH cells, female, sample 3, drop 1, RT-rxn B, lib. 1
- GSM9117338 PVH cells, female, sample 3, drop 1, RT-rxn B, lib. 2
- GSM9117339 PVH cells, male, sample 3, drop 1, RT-rxn A, lib. 1
- GSM9117340 PVH cells, male, sample 3, drop 1, RT-rxn A, lib. 2
- GSM9117341 PVH cells, male, sample 3, drop 1, RT-rxn B, lib. 1
- GSM9117342 PVH cells, male, sample 3, drop 2, RT-rxn A, lib. 1
- GSM9117343 PVH cells, female, sample 4, drop 1, RT-rxn A, lib. 1
- GSM9117344 PVH cells, male, sample 4, drop 1, RT-rxn B, lib. 1
- GSM9117345 PVH cells, male, sample 4, drop 2, RT-rxn A, lib. 1
- GSM9117346 PVH cells, female, sample 5, drop 1, RT-rxn A, lib. 1
- GSM9117347 PVH cells, female, sample 5, drop 1, RT-rxn B, lib. 1
- GSM9117348 PVH cells, female, sample 5, drop 2, RT-rxn A, lib. 1
- GSM9117349 PVH cells, female, sample 6, drop 1, RT-rxn A, lib. 1
- GSM9117350 PVH cells, female, sample 6, drop 2, RT-rxn A, lib. 1
- GSM9117351 PVH cells, female, sample 7, drop 1, RT-rxn A, lib. 1
- GSM9117352 PVH cells, female, sample 7, drop 1, RT-rxn A, lib. 2
- GSM9117353 PVH cells, female, sample 7, drop 1, RT-rxn B, lib. 1
- GSM9117354 PVH cells, female, sample 7, drop 1, RT-rxn B, lib. 2
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