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Roles of chromosomal and gonadal sex in the fetal and placental responses to maternal food restriction in mice [junctional zone/decidua]

GSE291544 Mus musculus (mouse) RNA-seq (gene expression) 60 samples Submitted 2025/05/07 Platform GPL30172
At a glance

RNA-seq (gene expression) · mouse · 60 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
60 samples: 12 conditions, mostly with about 5 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
Roles of chromosomal and gonadal sex in the fetal and placental responses to maternal food restriction in miceMolecular human reproduction · 2025
Summary (written by the submitters)
It is hypothesized that male fetuses are more vulnerable to in utero insults than female fetuses due to different growth strategies, and that the placenta contributes to these sex differences. Using the Four Core Genotypes mouse model, we examined sex differences in the fetal and placental responses to maternal food restriction (~60% of ad libitum) beginning mid-gestation (day 11.5), including the independent roles of chromosomal and gonadal sex.
Read the full summary ↓
Food restriction reduced fetal and placental weights, but had no effect on the number of viable conceptuses. However, the effect of food restriction did not differ between gonadal male and female conceptuses, or between XX and XY conceptuses. Sex differences in gene expression in both the labyrinth and the combined junctional zone/ decidua, as assessed by RNA sequencing, were due entirely to chromosomal sex, and not to gonadal sex. Food restriction affected the expression of 525 and 665 genes in the labyrinth and the combined junctional zone/ decidua, respectively. However, these effects of food restriction did not differ by gonadal sex or chromosomal sex when assessed for statistical interactions. In contrast, when analysing XX and XY placentas separately, we found hundreds of genes that were affected by food restriction in one sex but not the other, including hundreds of genes not found to be significant in the combined analyses. However, estimated effect sizes were generally similar for XX and XY placentas, suggesting that these sex-stratified analyses greatly exaggerated the extent of sex-dependent responses. Overall, we did not find evidence of the hypothesized sex differences in fetal growth strategy, and found that sex differences in placental gene expression were largely due to chromosomal sex.
Published in
Roles of chromosomal and gonadal sex in the fetal and placental responses to maternal food restriction in mice
Hercus JC, Salcedo Rubio DA, Osorio Nieto ME et al. · Molecular human reproduction 2025 · PMID 40286295 · doi:10.1093/molehr/gaaf015
This dataset
Open GSE291544 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 GSE291544_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 PRJNA1234125 and SRA study SRP569179. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40286295) ↗
Study design
12 conditions, mostly with about 5 replicates each
JunctionalZone/Decidua, FCG_XXF_FoodRest, ×5 JunctionalZone/Decidua, WT_F_FoodRest, ×5 JunctionalZone/Decidua, WT_F_Control, ×5 JunctionalZone/Decidua, FCG_XYF_Control, ×5 JunctionalZone/Decidua, WT_M_Control, ×5 JunctionalZone/Decidua, FCG_XXM_FoodRest, ×5 JunctionalZone/Decidua, WT_M_FoodRest, ×5 JunctionalZone/Decidua, FCG_XYM_FoodRest, ×5 +4 more

Supports a between-group comparison across 60 samples.

How we read this: 12 replicated groups read from 60 sample titles; they account for 60 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

+ 20 more — browse all 60 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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