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Impact of dietary methionine, tryptophan, and niacin deficiency on intestinal gene expression in mice.

GSE300498 Mus musculus (mouse) RNA-seq (gene expression) 22 samples Submitted 2025/07/12 Platform GPL28457
At a glance

RNA-seq (gene expression) · mouse · 22 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
22 samples: 22 samples, each with a distinct title — no replicated groupsGroups 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
Deficiencies in methionine, tryptophan, and niacin remodels intestinal transcriptome and gut microbiota in female miceScientific reports · 2025
Summary (written by the submitters)
Emerging evidence indicates that selective nutrient restriction can reproduce metabolic benefits. Although methionine and branched-chain amino acid limitation improve metabolism and reshape the gut microbiome, the effects of other nutrients are still unclear. In this study, we examine the consequences of restricting methionine, tryptophan, and niacin, and find that their transient deprivation induces significant changes in intestinal gene expression.
Published in
Deficiencies in methionine, tryptophan, and niacin remodels intestinal transcriptome and gut microbiota in female mice
Hara T, Meng S, Motooka D et al. · Scientific reports 2025 · PMID 41102214 · doi:10.1038/s41598-025-18046-2
This dataset
Open GSE300498 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 GSE300498_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 PRJNA1281067 and SRA study SRP594058. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41102214) ↗
Study design
22 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 22 sample titles: 22 distinct titles with little repetition. 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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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.