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Paneth cell gene expression with and wihout zinc in different microbiome contexts (antibiotics, germ-free, normal)

GSE281682 Mus musculus (mouse) RNA-seq (gene expression) 21 samples Submitted 2025/02/26 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 21 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
21 samples: 6 conditions, mostly with about 4 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
Detection of chimeric alpha-defensin transcripts and peptides in mouse Paneth cellsFrontiers in immunology · 2025
Summary (written by the submitters)
We investigated the differences in paneth cell gene expression in different intestinal microbiome contexts and with and without zinc supplementation. We used mice housed in an SPF animal house that wre untreated, mice housed in ans SPF animal house that were treated with antobiotics for 3 weeks and germ-free mice to investigated the effect of the microbiome on paneth cell gene expression.
Read the full summary ↓
Zinc is an essential element for paneth cell fuction. Mice of each group were further divide in zinc supplemented and non-zinc supplemented drinking water subgroups. This allowed us to check if zinc would enhance the differences between SPF, atibioicts and germ-free mice or reduce them.
Published in
Detection of chimeric alpha-defensin transcripts and peptides in mouse Paneth cells
Timmermans S, Wallaeys C, De Beul S et al. · Frontiers in immunology 2025 · PMID 39981239 · doi:10.3389/fimmu.2025.1543059
This dataset
Open GSE281682 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 GSE281682_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 PRJNA1185219 and SRA study SRP544717. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39981239) ↗
Study design
6 conditions, mostly with about 4 replicates each
paneth cell, SPF MQ + antibiotica, replicaat ×4 paneth cell, SPF Zn + antibiotica, replicaat ×4 paneth cell, Germ-free Zn, replicaat ×4 paneth cell, Germ-free MQ, replicaat ×3 paneth cell, SPF MQ, replicaat ×3 paneth cell, SPF Zn, replicaat ×3

Supports a between-group comparison across 21 samples.

How we read this: 6 replicated groups read from 21 sample titles; they account for 21 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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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.