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Maternal indole supplementation protects offspring from NAFLD through altered microbiota- and AHR-mediated ceramide metabolism

GSE247323 Mus musculus (mouse) RNA-seq (gene expression) 40 samples Submitted 2026/01/21 Platform GPL30172Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 40 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
40 samples: 8 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
Reprogramming offspring liver health: maternal indole supplementation as a preventive strategy against MASLDEBioMedicine · 2026
Summary (written by the submitters)
MaternalWestern-style diet (WD) disrupts early life gut microbiota in the offspring and is associated with pediatric nonalcoholic fatty liver disease (NAFLD). Here, we report that oral supplementation with gut-derived tryptophan metabolites indole (Ind) or indole-3-acetate (I3A) during pregnancy and lactation in WD-fed dams had persistent effects in offspring liver, acting on key upstream regulators in WD-challenged offspring that suppress pathways for steatosis, fibrosis, and oxidative stress.
Read the full summary ↓
Maternal Ind or I3A activated aryl hydrocarbon receptor (AHR) signaling, leading to increases in long-chain and very long-chain (VLC) ceramides in offspring liver and small intestine. These effects were evident as early as postnatal day 14. The tryptophan metabolite 5-hydroxyindoleacetate (5-HIAA), an AHR ligand, was depleted in offspring by maternal WD and restored by maternal I3A treatment. Fecal transplantation studies demonstrated that VLC ceramides and liver fibrosis remodeling were mediated by maternal indoles altering the gut microbiota, with strong associations with Lactobacillaceae. Collectively, these findings define a novel and persistent protective effect of maternal Ind and I3A to prevent NAFLD, acting both directly on the liver and through the microbiota. These tryptophan metabolites may serve as therapeutic targets for future interventional studies aimed at prevention of pediatric NAFLD.
Published in
Reprogramming offspring liver health: maternal indole supplementation as a preventive strategy against MASLD
Mandala A, Undi RB, Janssen RC et al. · EBioMedicine 2026 · PMID 41447757 · doi:10.1016/j.ebiom.2025.106098
This dataset
Open GSE247323 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 GSE247323_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 PRJNA1037105 and SRA study SRP470928. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41447757) ↗
Study design
8 conditions, mostly with about 5 replicates each
Maternal CH diet mouse ×5 Maternal WD diet mouse ×5 Maternal WD diet + Ind mouse ×5 Maternal WD diet + I3A mouse ×5 Maternal CH diet mouse FMT ×5 Maternal WD diet mouse FMT ×5 Maternal WD diet + Ind mouse FMT ×5 Maternal WD diet + I3A mouse FMT ×5

Supports a between-group comparison across 40 samples.

How we read this: 8 replicated groups read from 40 sample titles; they account for 40 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
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