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Protective effects of red filtered light during IVF: transcriptomic analysis of murine embryos and embryo-derived EVs

GSE266335 Mus musculus (mouse) Non-coding RNA profiling 28 samples Submitted 2024/10/28 Platform GPL16417
At a glance

Non-coding RNA profiling · mouse · 28 samples

What it is
Non-coding RNA profilingLevels of RNAs that do not code for proteins, such as miRNA or lncRNA.
Organism
Mus musculus (mouse)
Samples
28 samples: 28 samples, each with a distinct title — no replicated groupsGroups 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
Effects of light exposure during IVF: transcriptomic analysis of murine embryos and embryo-derived EVsFrontiers in immunology · 2025
Summary (written by the submitters)
Background: Light exposure of embryos during assisted reproduction affects embryo quality and implantation capacity in a wavelength dependent manner. We investigated the molecular mechanism of these light-induced changes through the comparative analysis of gene expression and regulatory miRNA profile of murine embryos cultured in dark environment and those exposed to white- or red filtered light.
Read the full summary ↓
miRNA sequencing was used to assess the role of embryo-derived extracellular vesicles in the endometrium-embryo dialogue. Methods: In vitro cultured mouse embryos (3.5 dpc) were exposed to white or red filtered light. After 24 hours mRNA and miRNA content of the embryos as well as the miRNA content of embryo-derived extracellular vesicles were isolated and RNA-sequencing was performed. Differential expression analysis and functional enrichment analysis were used for evaluating the transcriptome results.Results: Light exposure caused transcriptomic changes in the embryos. White light upregulated apoptotic pathways, while red filtered light gave rise to the activation of regeneration pathways, including DNA repair mechanisms. Embryo-derived extracellular vesicles enclosed wavelength dependently unique miRNA cargos the target genes of which play a role in embryo implantation. In conclusion: white light upregulates apoptotic pathways, at both the transcriptome and regulatory miRNAs levels. Red filtration partially counterbalances these negative effects by shifting the cellular processes towards regeneration, including DNA repair mechanisms. Extracellular vesicles of light exposed embryos play a role in blastocyst-decidua communication through the horizontal transfer of regulatory miRNAs. Our data prove that light exposure during in vitro fertilization modifies cell function that might affect the outcome of implantation.
Published in
Effects of light exposure during IVF: transcriptomic analysis of murine embryos and embryo-derived EVs
Nagy B, Bognár Z, Csabai TJ et al. · Frontiers in immunology 2025 · PMID 40051636 · doi:10.3389/fimmu.2025.1429252
This dataset
Open GSE266335 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 GSE266335_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 ↗

Also filed as BioProject PRJNA1106783 and SRA study SRP505140. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40051636) ↗
Study design
28 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 28 sample titles: 28 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
Datasets on a similar topic

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