GEO series

Accute and repeated DSS exposure induce distinct immune responses with differential relevance to human Ulcerative Colitis

GSE306845 Homo sapiens (human) Single-cell RNA-seq 10 samples Submitted 2025/10/31 Platform GPL34290Platform GPL34284

At a glance

Single-cell RNA-seq · human · 10 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism: Homo sapiens (human)
Samples: 10 samples: 9 distinct titles, 1 of them repeatedGroups 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: Repeated Dextran Sulfate Sodium Exposure Elicits Distinct Immune Responses Reflecting Human Ulcerative ColitisCellular and molecular gastroenterology and hepatology · 2026

Summary (written by the submitters)

Dextran sulfate sodium (DSS)-induced colitis is a widely used model to study ulcerative colitis (UC). However, the extent to which acute versus repeated DSS exposure mimics human disease remains unclear. Using histopathology, flow cytometry, single-cell RNA sequencing (scRNA-seq) and 16S rRNA profiling we compared disease outcomes, immune infiltrate, transcriptional programs and changes in the microbiome in mice subjected to a single (acute) versus two (repeated) DSS cycles.

Read the full summary ↓

We found that repeated cycles of DSS-induced colitis in mice result in more severe intestinal inflammation compared to a single exposure, with increased PMN and T cell infiltration, mucosal remodeling, and microbiota normalization. Single-cell transcriptomics revealed that acute vs repeated DSS exposure drives differential programs in immune cell subtypes distinctly overlapping with human UC. Overall, our findings suggest that repeated DSS exposure may more accurately models human disease, highlighting its utility for translational IBD research.

Published in

Repeated Dextran Sulfate Sodium Exposure Elicits Distinct Immune Responses Reflecting Human Ulcerative Colitis

Manzanares LD, Dehghani Z, Herrnreiter CJ et al. · Cellular and molecular gastroenterology and hepatology 2026 · PMID 41453640 · doi:10.1016/j.jcmgh.2025.101714

This dataset

Open GSE306845 in finder → Find more 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 GSE306845_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1312498 and SRA study SRP614703. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41453640) ↗

Study design

9 distinct titles, 1 of them repeated

Colon digest of cycle 2 (2.5%) DSS, sample ×2

How we read this: Read from 10 sample titles: 9 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

GSM9210595 Colon biopsy from Inactive UC patient, sample B
GSM9210596 Colon biopsy from Inactive UC patient, sample C
GSM9210597 Colon biopsy from Inactive UC patient, sample D
GSM9210598 Colon biopsy from Inactive UC patient, sample E
GSM9210599 Colon biopsy from Inactive UC patient, sample F
GSM9210600 Colon biopsy from Inactive UC patient, sample G
GSM9210601 Colon digest of cycle 1 (2.5%) DSS, sample 1
GSM9210602 Colon digest of cycle 1(2.5%)DSS, sample 2
GSM9210603 Colon digest of cycle 2 (2.5%) DSS, sample 1
GSM9210604 Colon digest of cycle 2 (2.5%) DSS, sample 2

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