← BioTransfer GEO Dataset Finder
GEO series

Metabolic reprogramming of the neovascular niche promotes regenerative angiogenesis in proliferative retinopathy

GSE216676 Mus musculus (mouse) Single-cell RNA-seq 14 samples Submitted 2025/04/01 Platform GPL19057
At a glance

Single-cell RNA-seq · mouse · 14 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
14 samples: 6 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
Metabolic reprogramming of the neovascular niche promotes regenerative angiogenesis in proliferative retinopathyNature communications · 2025
Summary (written by the submitters)
Healthy blood vessels supply neurons to preserve metabolic function. In blinding proliferative retinopathies (PRs), pathological neovascular tufts often emerge in lieu of needed physiological revascularization. Here we show that metabolic shifts in the neovascular niche define angiogenic fate. Fatty acid oxidation (FAO) metabolites accumulated in human and murine retinopathy samples.
Read the full summary ↓
Neovascular tufts with a distinct single-cell transcriptional signature highly expressed FAO enzymes. The deletion of Sirt3, an FAO regulator, shifted the neovascular niche metabolism from FAO to glycolysis and suppressed tuft formation. This metabolic transition increased Vegf expression in astrocytes and reprogrammed pathological neovessels to a physiological phenotype, hastening vascular regeneration of the ischemic retina and improving vision. Hence, strategies to change the metabolic environment of vessels could promote a regenerative phenotype in vascular diseases.
Published in
Metabolic reprogramming of the neovascular niche promotes regenerative angiogenesis in proliferative retinopathy
Cagnone G, Pundir S, Betus C et al. · Nature communications 2025 · PMID 40562775 · doi:10.1038/s41467-025-60061-4
This dataset
Open GSE216676 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 GSE216676_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 PRJNA894955 and SRA study SRP404835. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40562775) ↗
Study design
6 conditions, mostly in duplicate
OIR.P17.CD31.WT.S129_Joyal ×3 OIR.P17.CD31.Sirt3KO.S129_Joyal ×3 NORM.P17.CD31.WT.S129_Joyal ×2 OIR.P14.CD31.WT.S129_Joyal ×2 OIR.P14.CD31.Sirt3KO.S129_Joyal ×2 NORM.P14.CD31.WT.S129_Joyal ×2

Supports a between-group comparison across 14 samples.

How we read this: 6 replicated groups read from 14 sample titles; they account for 14 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
Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

Share this dataset

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.