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An orally active, gut-enriched AhR agonist demonstrates therapeutic efficacy in colitis through regulation of inflammation, barrier homeostasis, and fibrosis

GSE338894 Mus musculus (mouse) RNA-seq (gene expression) 50 samples Submitted 2026/07/17 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 50 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
50 samples: 5 conditions, mostly with about 10 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.
Summary (written by the submitters)
Inflammatory bowel disease (IBD) is characterised by chronic intestinal inflammation, epithelial barrier dysfunction, and maladaptive stromal remodelling that can progress to fibrosis. Current therapies primarily target inflammatory pathways and rarely achieve durable remission or structural disease modification, highlighting a major unmet clinical need.
Read the full summary ↓
Here, we evaluated the therapeutic potential of YUQ-A1007, an orally active, gut-enriched small-molecule aryl hydrocarbon receptor (AhR) agonist, across multiple translational models of colitis. The anti-inflammatory, barrier-restorative, and anti-fibrotic effects of YUQ-A1007 were assessed using in vitro cell systems, patient-derived colonic biopsies and organoids, permeability assays, and three murine colitis models. YUQ-A1007 partially activated AhR signalling, suppressed pro-inflammatory cytokine production, enhanced regulatory T cell differentiation, increased tight junction protein expression, and inhibited fibrotic gene programs. In vivo, oral YUQ-A1007 administration reduced disease severity, restored epithelial barrier integrity, and broadly downregulated inflammatory cytokines, chemokines, fibrosis-associated genes, pro-inflammatory mesenchymal stromal cell biomarkers, and matrix metalloproteinases. In ulcerative colitis patient-derived colonic explants, YUQ-A1007 dose-dependently reduced inflammatory mediator secretion while preserving barrier function. Collectively, these findings support further development of YUQ-A1007 as a gut-targeted AhR therapeutic for ulcerative colitis and broader inflammatory bowel disease.
This dataset
Open GSE338894 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 GSE338894_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 PRJNA1496325 and SRA study SRP718588. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
5 conditions, mostly with about 10 replicates each
Colon_TNBS_A1007_10mpk ×10 Colon_TNBS_A1007_30mpk ×10 Colon_TNBS_A1007_90mpk ×10 Colon_Sham ×10 Colon_TNBS_Vehicle ×10

Supports a between-group comparison across 50 samples.

How we read this: 5 replicated groups read from 50 sample titles; they account for 50 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

+ 10 more — browse all 50 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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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.