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Sex-dependent amelioration of laser-induced choroidal neovascularization by Short-Chain Fatty Acid treatment in a mouse model

GSE299691 Mus musculus (mouse) RNA-seq (gene expression) 43 samples Submitted 2025/07/01 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 43 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Mus musculus (mouse)
Samples
43 samples: 12 conditions, mostly in triplicateGroups 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
Sex differences on laser-induced choroidal neovascularization and short-chain fatty acid treatment in a mouse modelJournal of neuroinflammation · 2025
Summary (written by the submitters)
Age-related macular degeneration (AMD) is a leading cause of blindness worldwide, with a clinical presentation that varies between sexes. In late-stage AMD, choroidal neovascularization (CNV) triggers retinal inflammation and degeneration, processes that are exacerbated by an overactive response of retinal microglial cells. Short-chain fatty acids (SCFAs) have emerged as potential treatments for AMD due to their anti-inflammatory properties.
Read the full summary ↓
In this study, we investigate the effects of SCFA treatment in a laser-induced CNV mouse model, focusing on sex-dependent differences in disease progression and microglial response. Our findings demonstrate distinct sex-specific patterns in the development of CNV and associated pathological hallmarks. SCFA treatment resulted in a slight increase in density of Iba1+ microglial cells in females at 3 days post-laser (3dpl), while it prevented a massive increase in males at 7 dpl, with both sexes showing enhanced microglial ramification. The dynamics of microglial density were linked to protective effects on CNV, leakage size, and inflammation, which occurred earlier in females and later in males. In vitro assays revealed that SCFAs reduced microglial phagocytosis of retinal debris, suggesting a potential mechanism for their anti-inflammatory action. This study underscores the importance of considering sex-specific responses in the development of AMD treatments, such as SCFAs, and highlights the need for personalized therapeutic strategies.
Published in
Sex differences on laser-induced choroidal neovascularization and short-chain fatty acid treatment in a mouse model
Yan C, Figueiredo CA, Pompös IM et al. · Journal of neuroinflammation 2025 · PMID 40684170 · doi:10.1186/s12974-025-03508-1
This dataset
Open GSE299691 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 GSE299691_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1276071 and SRA study SRP591771. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40684170) ↗
Study design
12 conditions, mostly in triplicate
female SCFA-treated, 3 dpi, sample ×5 male SCFA-treated, 7 dpi, sample ×5 female SCFA-treated, 7 dpi, sample ×4 female control, 3 dpi, sample ×3 female control, 7 dpi, sample ×3 female control, 14 dpi, sample ×3 female SCFA-treated, 14 dpi, sample ×3 male control, 3 dpi, sample ×3 +6 more

Supports a case/control comparison: 24 samples read as cases, 19 as controls.

How we read this: 12 replicated groups read from 43 sample titles; they account for 41 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

+ 3 more — browse all 43 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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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.