GEO series

Paternal under and over nutrition modify semen composition and preimplantation embryo developmental kinetics in mice

GSE241404 Mus musculus (mouse) RNA-seq (gene expression) 25 samples Submitted 2024/07/18 Platform GPL19057

At a glance

RNA-seq (gene expression) · mouse · 25 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: 25 samples: 25 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: Paternal undernutrition and overnutrition modify semen composition and preimplantation embryo developmental kinetics in miceBMC biology · 2024

Summary (written by the submitters)

The importance of parental diet in relation to eventual offspring health is increasing in prominence due to the increased frequency of reproductive age adults consuming poor diets. Whilst maternal health and offspring outcome have been studied in some detail, the paternal impacts are not as well understood. A father’s poor nutritional status has been shown to have negative consequences on fetal growth and development and ultimately impact the long-term adult health of the offspring.

Read the full summary ↓

In this study we examined sperm and seminal plasma mediated mechanisms of preimplantation embryo development alterations in response to sub-optimal paternal diets. Male mice were fed a diet to model either under (low protein diet (LPD)) or over (high fat/sugar (Western) diet (WD)) nutrition, LPD or WD supplemented with methyl-donors or a control diet before mating with age-matched control fed females. Male metabolic health was influenced by WD and MD-WD; with significant changes in serum lipids and hepatic 1-carbon metabolites. Sperm RNA sequencing revealed significant changes to mRNA profiles in all groups when compared to CD (LPD: 32, MD-LPD: 17, WD: 53, MD-WD: 35). In vitro embryo development was revealed all sub-optimal diets with and without methyl-donors increased the rate of embryo development. As embryo development can be directed by sperm and seminal plasma mediated mechanism, we also examined the proteomic profile of the seminal plasma, revealing a significant number of changes in all groups compared to control (LPD: 13, MD-LPD: 27, WD: 24, MD-WD: 19). Male diet also altered uterine gene expression examined via qPCR, specifically alterations in Cd14 and Ptgs1 were observed in response to male WD matings. Our current study shows that paternal nutritional status has the potential to influence male metabolic and reproductive factors, which can ultimately alter embryonic development and the post-mating maternal environment. This study highlights potential direct (sperm mediated) and indirect (semen mediated) pathways in which a father's poor diet could shape the long-term health of his offspring.

Published in

Paternal undernutrition and overnutrition modify semen composition and preimplantation embryo developmental kinetics in mice

Morgan HL, Eid N, Holmes N et al. · BMC biology 2024 · PMID 39278917 · doi:10.1186/s12915-024-01992-0

This dataset

Open GSE241404 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 GSE241404_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 PRJNA1008081 and SRA study SRP456559. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39278917) ↗

Study design

25 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 25 sample titles: 25 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

GSM7728327 Sperm_NPD_Male10 [NPD10]
GSM7728328 Sperm_NPD_Male11 [NPD11]
GSM7728329 Sperm_NPD_Male12 [NPD12]
GSM7728330 Sperm_NPD_Male14 [NPD14]
GSM7728331 Sperm_NPD_Male15 [NPD15]
GSM7728332 Sperm_LPD_Male10 [LPD10]
GSM7728333 Sperm_LPD_Male11 [LPD11]
GSM7728334 Sperm_LPD_Male12 [LPD12]
GSM7728335 Sperm_LPD_Male13 [LPD13]
GSM7728336 Sperm_LPD_Male15 [LPD15]
GSM7728337 Sperm_MDL_Male9 [MDL9]
GSM7728338 Sperm_MDL_Male10 [MDL10]
GSM7728339 Sperm_MDL_Male11 [MDL11]
GSM7728340 Sperm_MDL_Male14 [MDL14]
GSM7728341 Sperm_MDL_Male15 [MDL15]
GSM7728342 Sperm_WD_Male10 [WD10]
GSM7728343 Sperm_WD_Male11 [WD11]
GSM7728344 Sperm_WD_Male12 [WD12]
GSM7728345 Sperm_WD_Male13 [WD13]
GSM7728346 Sperm_WD_Male14 [WD14]
GSM7728347 Sperm_MDWD_Male9 [MDWD9]
GSM7728348 Sperm_MDWD_Male10 [MDWD10]
GSM7728349 Sperm_MDWD_Male12 [MDWD12]
GSM7728350 Sperm_MDWD_Male14 [MDWD14]
GSM7728351 Sperm_MDWD_Male16 [MDWD16]

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