GEO series

Maternal Western-Style Diet alters Kupffer Cell proportion leading to Metabolic Dysfunction-Associated Steatotic Liver Disease when challenged with western diet in adulthood

GSE312316 Mus musculus (mouse) RNA-seq (gene expression) 36 samples Submitted 2025/12/05 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 36 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: 36 samples
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 western-style diet alters Kupffer cell proportion leading to metabolic dysfunction-associated steatotic liver disease when challenged with western diet in adulthoodFrontiers in immunology · 2025

Summary (written by the submitters)

Exposure to maternal western-style diet (mWD) is associated with early development of metabolic dysfunction-associated fatty liver disease (MAFLD) in offspring. Kupffer cells (KCs), the main resident macrophage population in the liver, are known to promote MAFLD progression, however, the effects of mWD on KC subtypes, ontogeny, and gene expression in offspring are not fully understood.

Read the full summary ↓

In this manuscript, we used two different models of mWD exposure and challenge in adulthood to understand the impact of mWD on KC proportion, ontogeny, and gene expression in adult offspring. Our data indicate that in the absence of challenge in adulthood, mWD results in increased KC proportion in offspring, with limited changes in KC ontogeny or liver phenotype. In contrast, mWD mice challenged with WD in adulthood had increased expression of inflammatory (Nlrp3) and fibrosis (Tgfb1) related genes compared to chow (CH)-WD fed mice. Although KC proportion and ontogeny were similar when comparing CH-WD and WD-WD fed mice, we found that WD-WD mice had a greater reduction in KC proportion and TdT labelling than CH-WD fed mice when normalized to their respective maternal diet controls. Similar results were found when mice were weaned onto normal chow and re-challenged with WD later on in adulthood. Bulk RNA sequencing data indicate that KCs from mWD mice re-challenged with WD in adulthood had increased expression of inflammatory and antigen presenting genes compared to KCs isolated from WD fed mice lacking mWD exposure. These findings highlight the intergenerational repercussions of mWD on liver phenotype as well as KC proportion and ontogeny and provide novel insight into the mechanisms dictating MAFLD.

Published in

Maternal western-style diet alters Kupffer cell proportion leading to metabolic dysfunction-associated steatotic liver disease when challenged with western diet in adulthood

Miller SJ, Janssen RC, Zhao W et al. · Frontiers in immunology 2025 · PMID 41451197 · doi:10.3389/fimmu.2025.1698609

This dataset

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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 GSE312316_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 PRJNA1373016 and SRA study SRP656107. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41451197) ↗

Samples in this study

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+ 36 more — browse all 36 samples with per-sample file links →

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