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Paternal over- and under-nutrition program fetal and placental development in a sex-specific manner

GSE301011 Mus musculus (mouse) RNA-seq (gene expression) 40 samples Submitted 2025/12/31 Platform GPL19057
At a glance

RNA-seq (gene expression) · mouse · 40 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
40 samples: 40 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.
Summary (written by the submitters)
Under- and over-nutrition are directly linked to poor physiological, metabolic and reproductive health. While the association between paternal diet and offspring well-being is becoming established, the underlying mechanisms are yet to be fully defined. The aim of this study was to establish and compare the impact of over- and under-nutrition on male reproductive fitness and post-fertilisation development, with the additional exploration of the role that specific micronutrient supplementation may play in ameliorating any detrimental effects of poor paternal diet.
Read the full summary ↓
Male C57/BL6J mice were fed either control diet (CD), isocaloric low protein diet (LPD), ‘Western’ diet (WD) or LPD or WD supplemented with methyl-donors and carriers (MD-LPD or MD-WD respectively) for 8 weeks before mating with virgin C57/BL6J females maintained on standard mouse chow. Placental tissue was collected at embryonic day (E)8.5 to assess early placental morphology and metabolism or E17.5 for sex-specific transcriptomic profiling. Post-mating male tissues were harvested for assessment of testicular morphology, gene expression and metabolic profiling and fecal microbiome was analysed. This study found significant increases in adiposity, hepatic cholesterol and FFAs in WD and MDWD fed males, alongside an increase in the abundance of Defferibacteres, Proteobacteria and reduction TM7 abundance in fecal samples compared to CD fed males. Analysis of testicular gene expression revealed 402 (267 down-regulated, 135 upregulated) genes and 285 (187 down-regulated, 98 up-regulated) genes differentically expressed in WD and MD-WD-fed males, respectively, with minimal changes observed in LPD and MD-LPD groups compared to CD-fed males. Placenta from LPD fed fathers had a significant reduction in lactate production at E8.5 and significant sex-specific influences of paternal diet on late gestation fetal and placental growth were observed in both LPD and MD-LPD groups, which had a significantly higher proportion of fetuses with weights below the 10th centile when compared to CD fetuses. We also identified a significant reduction in sexually dimorphic gene expression in response to paternal diet, with 301, 13, 0, 14 and 15 placental genes to be differentially expressed between males and females in the CD, LPD, MD-LPD, WD and MD-WD. We observed that males consuming a high fat/sugar diet (WD and MD-WD), displayed a series of physiological changes in their metabolic health, gut bacterial profiles and testicular morphology and gene expression. While both over- and under-nutritional regimens had no impact on fundamental male fertility, we observed a significant loss in sexual-dimorphism in the late gestation placenta in response to our experimental diets. Such loss of sexual- dimorphism could provide one process through which poor paternal diet programs offspring ill-health in adulthood.
This dataset
Open GSE301011 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 GSE301011_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 PRJNA1283079 and SRA study SRP595701. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
40 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 40 sample titles: 40 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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