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In Vitro Fertilization induces reproductive changes in male mouse offspring and has multigenerational effects [RNA-seq II]

GSE290562 Mus musculus (mouse) RNA-seq (gene expression) 22 samples Submitted 2025/03/31 Platform GPL32159
At a glance

RNA-seq (gene expression) · mouse · 22 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
22 samples: 6 × RNA library from Natural F2 male E18.5 Placenta vs 6 × RNA library from IVF F2 male E18.5 Placenta vs 6 × RNA library from IVF F2 female E18.5 Placenta vs 4 × RNA library from Natural F2 female E18.5 PlacentaGroups 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
In vitro fertilization induces reproductive changes in male mouse offspring and has multigenerational effectsJCI insight · 2025
Summary (written by the submitters)
In vitro fertilization (IVF) is a non-coital method of conception used to treat infertility. Although safe, IVF has been associated with adverse outcomes in the fetus, placenta, and adult life, but studies focusing on the male reproductive system are limited. Here, we used a mouse model to assess the morphological and molecular effects of IVF on male offspring.
Read the full summary ↓
We evaluated three developmental stages: 18.5-day fetuses and 12- and 39-week adults. Regardless of age, we observed changes in the testicular-to-body weight ratio, serum testosterone levels, testicular morphology, transcriptome, and DNA methylation. Also, sperm showed changes in morphology and DNA methylation. To assess multigenerational phenotypes, we mated IVF and naturally conceived males with wild-type females. Offspring from IVF males exhibited a decreased fetal weight-to-placental weight ratio regardless of sex. At 12-weeks-of-age, offspring showed higher body weights, differences in glucose, triglycerides, insulin, total cholesterol, HDL and LDL/VLDL levels. Both sexes showed changes in gene expression in liver, testes and ovaries, and decreased global DNA methylation. Collectively, our findings demonstrate that male IVF offspring exhibit abnormal testicular and sperm morphology and molecular alterations and transmit defects multigenerationally. These experiments contribute to our understanding of the long-term impacts of IVF on adult offspring health.
Published in
In vitro fertilization induces reproductive changes in male mouse offspring and has multigenerational effects
Rhon-Calderon EA, Hemphill CN, Savage AJ et al. · JCI insight 2025 · PMID 40036079 · doi:10.1172/jci.insight.188931
This dataset
Open GSE290562 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 GSE290562_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 PRJNA1228628 and SRA study SRP566577. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40036079) ↗
Study design
6 × RNA library from Natural F2 male E18.5 Placenta vs 6 × RNA library from IVF F2 male E18.5 Placenta vs 6 × RNA library from IVF F2 female E18.5 Placenta vs 4 × RNA library from Natural F2 female E18.5 Placenta

Supports a between-group comparison across 22 samples.

How we read this: 4 replicated groups read from 22 sample titles; they account for 22 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

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