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Exploring the Differential Host Responses to DSS and UC-Derived Microbiota in a Mouse Model of Colitis

GSE305760 Mus musculus (mouse) RNA-seq (gene expression) 14 samples Submitted 2025/08/20 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 14 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
14 samples: 4 × colon mucosa, DSS and UC FMT treatment, day 5, vs 4 × colon mucosa, UC FMT treatment, day 5, vs 3 × colon mucosa, control, day 0, vs 3 × colon mucosa, DSS treatment, day 5,Groups 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
Exploring new animal models of ulcerative colitis: evaluating chemical and patient-derived microbial triggers to advance translational relevanceLaboratory animal research · 2026
Summary (written by the submitters)
Ulcerative colitis (UC) is a chronic inflammatory condition of the colon, characterized by recurring mucosal inflammation. Current evidence suggests that dysbiosis may drive the disease, but mechanistic links remain incompletely understood. To further investigate the host-microbiome interactions, three UC-induction methods were used on a pseudo germ-free mouse model: (1) DSS, (2) fecal microbiota transplantation (FMT) from a UC patient, and (3) combination of both DSS and FMT simultaneously.
Read the full summary ↓
Disease severity (DAI), immune cell profiles (flow cytometry), colon transcriptomics (RNA sequencing), and microbiota composition (16S rRNA sequencing) were assessed. Our study revealed distinct effects of DSS and FMT on experimental colitis. DSS had a more pronounced impact on disease severity, while FMT exerted a stronger influence on several immune populations and downregulation of genes associated with tight junctions and mucins. Microbiome analysis demonstrated distinct compositional profiles across all experimental groups. The combined FMT and DSS model exhibited features of both induction methods, resulting in exacerbated clinical scores, barrier dysfunction, and inflammatory responses. Our study provides valuable insight into host–microbiome interactions in UC and introduces a dual-hit approach that may more accurately recapitulate its multifactorial pathogenesis than DSS alone.
Published in
Exploring new animal models of ulcerative colitis: evaluating chemical and patient-derived microbial triggers to advance translational relevance
Rynikova M, Gancarcikova S, Lauko S et al. · Laboratory animal research 2026 · PMID 42260597 · doi:10.1186/s42826-026-00283-9
This dataset
Open GSE305760 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 GSE305760_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 PRJNA1307556 and SRA study SRP609760. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42260597) ↗
Study design
4 × colon mucosa, DSS and UC FMT treatment, day 5, vs 4 × colon mucosa, UC FMT treatment, day 5, vs 3 × colon mucosa, control, day 0, vs 3 × colon mucosa, DSS treatment, day 5,

Supports a between-group comparison across 14 samples.

How we read this: 4 replicated groups read from 14 sample titles; they account for 14 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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