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Maternal obesity remodels nutrient transporttranscriptional programs in early mouse embryonic and extraembryonic cell lineages

GSE327799 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 12 samples Submitted 2026/05/05 Platform GPL24247
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 12 samples

What it is
ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism
Mus musculus (mouse)
Samples
12 samples: 3 × Multiome E8.5 embryonic and extraembryonic cells, GEX, Biol control vs 3 × Multiome E8.5 embryonic and extraembryonic cells, ATAC, Biol control vs 3 × Multiome E8.5 embryonic and extraembryonic cells, GEX, Biol high fat vs 3 × Multiome E8.5 embryonic and extraembryonic cells, ATAC, Biol high fatGroups 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
Maternal obesity remodels nutrient transport transcriptional programs in early mouse embryonic and extraembryonic cell lineagesMolecular metabolism · 2026
Summary (written by the submitters)
Maternal obesity increases the risk of congenital anomalies and later-life metabolic disease in offspring. Still, underlying mechanisms remain unclear, particularly in extraembryonic lineages at the maternal-fetal interface, which remain poorly studied. We jointly profiled gene expression and chromatin accessibility in single nuclei from mouse embryos and extraembryonic tissues in a diet-induced obesity model at embryonic day 8.5, when multiple organogenesis programs are underway.
Read the full summary ↓
This analysis generated an atlas of 36 cell lineages, including derivatives of all three germ layers and trophoblast populations. Lineage allocation was preserved in embryos from obese dams. However, transcription was widely dysregulated. Oxidative phosphorylation genes were broadly suppressed, and genes involved in hypoxia, cytoskeleton remodeling, and cell migration were enriched among upregulated pathways. Chromatin accessibility changed in a few lineages, most notably in extraembryonic visceral endoderm and parietal trophoblast giant cells. Differently accessible chromatin was enriched in binding motifs for retinoic acid receptors. Indeed, genes involved in retinol and lipoprotein transport were suppressed, and RNA in situ hybridization confirmed reduced expression of retinol transporters Ttr, Rbp4, and Stra6, and lipoprotein transporter Apoa1 in visceral yolk sac. Thus, obesity during pregnancy causes early transcriptional dysregulation that impairs retinoic acid and lipoprotein transport at the maternal-fetal interface, suggesting a mechanism through which maternal obesity could influence long-term developmental outcomes.
Published in
Maternal obesity remodels nutrient transport transcriptional programs in early mouse embryonic and extraembryonic cell lineages
Caballero A, Chi L, Delgado-Olguín P · Molecular metabolism 2026 · PMID 42066955 · doi:10.1016/j.molmet.2026.102375
This dataset
Open GSE327799 in finder → Find more mouse ChIP / ATAC / CUT&Tag 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 GSE327799_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA1452824 and SRA study SRP691318. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42066955) ↗
Study design
3 × Multiome E8.5 embryonic and extraembryonic cells, GEX, Biol control vs 3 × Multiome E8.5 embryonic and extraembryonic cells, ATAC, Biol control vs 3 × Multiome E8.5 embryonic and extraembryonic cells, GEX, Biol high fat vs 3 × Multiome E8.5 embryonic and extraembryonic cells, ATAC, Biol high fat

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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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