GEO series

Genomic Convergence in Hibernating Mammals Elucidates the Genetics of Metabolic Regulation in the Hypothalamus [snRNAseq]

GSE295856 Mus musculus (mouse) Single-nucleus RNA-seq 13 samples Submitted 2025/08/04 Platform GPL24247

At a glance

Single-nucleus RNA-seq · mouse · 13 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: Mus musculus (mouse)
Samples: 13 samples: 3 × snRNA-seq for fed, fasted, or refed mouse hypothalamus Fed vs 3 × snRNA-seq for fed, fasted, or refed mouse hypothalamus Fasted vs 3 × snRNA-seq for fed, fasted, or refed mouse hypothalamus RefedGroups 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: Genomic convergence in hibernating mammals elucidates the genetics of metabolic regulation in the hypothalamusScience (New York, N.Y.) · 2025

Summary (written by the submitters)

Extreme metabolic adaptations can elucidate genetic programs governing mammalian metabolism. Here we used convergent evolutionary changes in hibernating lineages to define conserved cis-regulatory elements (CREs) and metabolic programs. We characterized mouse hypothalamus gene expression and chromatin dynamics across fed, fasted, and refed states, then used comparative genomics of hibernating versus non-hibernating lineages to identify cis-elements with convergent changes in hibernators.

Read the full summary ↓

Multi-omics approaches pinpointed CREs, hub genes, regulatory programs, and cell types underlying lineage divergence. Hibernators accumulated loss-of-function effects for CREs regulating hypothalamic responses, and the refeeding period after fasting served as a key phase for molecular processes with convergent evolutionary changes. This work provides a genetic framework for harnessing hibernator adaptations to understand human metabolic control. Convergent signals define cis-regulatory mechanisms behind food scarcity responses and hibernator-homeotherm divergence.

Published in

Genomic convergence in hibernating mammals elucidates the genetics of metabolic regulation in the hypothalamus

Ferris E, Gonzalez Murcia JD, Rodriguez AC et al. · Science (New York, N.Y.) 2025 · PMID 40743333 · doi:10.1126/science.adp4025

This dataset

Open GSE295856 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 GSE295856_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 PRJNA1238491 and SRA study SRP571763. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40743333) ↗

Study design

3 × snRNA-seq for fed, fasted, or refed mouse hypothalamus Fed vs 3 × snRNA-seq for fed, fasted, or refed mouse hypothalamus Fasted vs 3 × snRNA-seq for fed, fasted, or refed mouse hypothalamus Refed

Supports a between-group comparison across 9 samples.

How we read this: 3 replicated groups read from 13 sample titles; they account for 9 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

GSM8958813 snRNA-seq for fed, fasted, or refed mouse hypothalamus Fed 1 snRNA-seq for fed, fast…
GSM8958814 snRNA-seq for fed, fasted, or refed mouse hypothalamus Fasted 1 snRNA-seq for fed, fast…
GSM8958815 snRNA-seq for fed, fasted, or refed mouse hypothalamus Refed 1 snRNA-seq for fed, fast…
GSM8958816 snRNA-seq for fed, fasted, or refed mouse hypothalamus Fed 2 snRNA-seq for fed, fast…
GSM8958817 snRNA-seq for fed, fasted, or refed mouse hypothalamus Fed 2.1
GSM8958818 snRNA-seq for fed, fasted, or refed mouse hypothalamus Fasted 2 snRNA-seq for fed, fast…
GSM8958819 snRNA-seq for fed, fasted, or refed mouse hypothalamus Fasted 2.1
GSM8958820 snRNA-seq for fed, fasted, or refed mouse hypothalamus Fasted 3 snRNA-seq for fed, fast…
GSM8958821 snRNA-seq for fed, fasted, or refed mouse hypothalamus Fasted 3.1
GSM8958822 snRNA-seq for fed, fasted, or refed mouse hypothalamus Refed 2 snRNA-seq for fed, fast…
GSM8958823 snRNA-seq for fed, fasted, or refed mouse hypothalamus Refed 2.1
GSM8958824 snRNA-seq for fed, fasted, or refed mouse hypothalamus Fed 3 snRNA-seq for fed, fast…
GSM8958825 snRNA-seq for fed, fasted, or refed mouse hypothalamus Refed 3 snRNA-seq for fed, fast…

Datasets on a similar topic

GSE294478 Genomic Convergence in Hibernating Mammals Elucidates the Genetics of Metabolic Regulation in the Hypothalamus [bulk RNA-seq] 30 samples shares hypothalamus, convergence, hibernating, elucidates, genetics, mammals
GSE295855 Genomic Convergence in Hibernating Mammals Elucidates the Genetics of Metabolic Regulation in the Hypothalamus [bulk ATACseq] 32 samples shares hypothalamus, convergence, hibernating, elucidates, genetics, mammals
GSE295866 Genomic Convergence in Hibernating Mammals Elucidates the Genetics of Metabolic Regulation in the Hypothalamus [snATACseq] 20 samples shares hypothalamus, convergence, hibernating, elucidates, genetics, mammals
GSE294476 Genomic Convergence in Hibernating Mammals Elucidates the Genetics of Metabolic Regulation in the Hypothalamus [ChIP-seq_mm] 6 samples shares hypothalamus, convergence, hibernating, elucidates, genetics, mammals
GSE282067 Regulatory T-cells in the hypothalamus control immune activation and improve metabolic impairments upon high-calorie environments 67 samples shares hypothalamus
GSE74672 Single-cell RNA-seq of mouse hypothalamus 2881 samples shares hypothalamus
GSE322787 A skin-hypothalamus axis couples heat stress and metabolic dysfunction 3 samples shares hypothalamus
GSE292341 Single cell RNA sequencing of hippocampus and hypothalamus in AD mice with fructose-induced MetS and DHA and NR supplementation 48 samples shares hypothalamus

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