GEO series

Sub-optimal paternal diet at the time of mating perturbs maternal adaptations in the late gestation mouse

GSE265783 Mus musculus (mouse) RNA-seq (gene expression) 30 samples Submitted 2024/07/18 Platform GPL19057

At a glance

RNA-seq (gene expression) · mouse · 30 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: 30 samples: 5 conditions, mostly with about 6 replicates eachGroups 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: Sub-Optimal Paternal Diet at the Time of Mating Disrupts Maternal Adaptations to Pregnancy in the Late Gestation MouseNutrients · 2024

Summary (written by the submitters)

Pregnancy represents a stage during which maternal physiology and homeostatic regulation undergo dramatic change and adaptation. The fundamental purpose of these adaptations is to ensure the survival of her offspring through adequate nutrient provision and an environment that is tolerant to the semi-allogenic fetus. While poor maternal diet during pregnancy is associated with perturbed maternal adaptations during pregnancy, the influence of paternal diet on maternal well-being is less clearly-defined.

Read the full summary ↓

We fed male mice either a control (CD), low protein diet (LPD), a high fat/sugar Western diet (WD) or the LPD or WD supplemented with methyl donors (MD-LPD and MD-WD respectively) for a minimum of 8 weeks prior to mating. Females were culled at day 17 of gestation for the analysis of maternal metabolic, gut, cardiac and bone health. Paternal diet had minimal influences on maternal metabolic status or gut microbiota diversity. However, analysis of the maternal hepatic transcriptome revealed distinct profiles of differential gene expression in response to the diet of the father. Paternal LPD and MD-LPD resulted in differential expression of genes associated with lipid metabolism, transcription, ubiquitin conjugation and immunity in dams, while paternal WD and MD-WD modified the expression of genes associated with ubiquitin conjugation and cardiac morphology. Finally, we observed changes in maternal femur length, volume of trabecular bone, trabecular connectivity, volume of the cortical medullar cavity and thickness of the cortical bone in response to the father’s diets. Our current study demonstrates that poor paternal diet at the time of mating can influence the patterns of maternal metabolism and gestation-associated adaptations to her physiology. Such changes could have significant consequences for the long-term health of his offspring and the mother.

Published in

Sub-Optimal Paternal Diet at the Time of Mating Disrupts Maternal Adaptations to Pregnancy in the Late Gestation Mouse

Khoshkerdar A, Eid N, Batra V et al. · Nutrients 2024 · PMID 38931234 · doi:10.3390/nu16121879

This dataset

Open GSE265783 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 GSE265783_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 PRJNA1104197 and SRA study SRP503805. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38931234) ↗

Study design

5 conditions, mostly with about 6 replicates each

CD ×6 LPD ×6 MDL ×6 WD ×6 MDWD ×6

Supports a between-group comparison across 30 samples.

How we read this: 5 replicated groups read from 30 sample titles; they account for 30 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

GSM8229120 CD1 CD
GSM8229121 CD4 CD
GSM8229122 CD5 CD
GSM8229123 CD6 CD
GSM8229124 CD7 CD
GSM8229125 CD9 CD
GSM8229126 LPD3 LPD
GSM8229127 LPD4 LPD
GSM8229128 LPD6 LPD
GSM8229129 LPD8 LPD
GSM8229130 LPD9 LPD
GSM8229131 LPD10 LPD
GSM8229132 MDL1 MDL
GSM8229133 MDL3 MDL
GSM8229134 MDL4 MDL
GSM8229135 MDL6 MDL
GSM8229136 MDL7 MDL
GSM8229137 MDL8 MDL
GSM8229138 WD2 WD
GSM8229139 WD4 WD
GSM8229140 WD5 WD
GSM8229141 WD6 WD
GSM8229142 WD7 WD
GSM8229143 WD8 WD
GSM8229144 MDWD1 MDWD
GSM8229145 MDWD2 MDWD
GSM8229146 MDWD3 MDWD
GSM8229147 MDWD4 MDWD
GSM8229148 MDWD6 MDWD
GSM8229149 MDWD8 MDWD

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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.