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Single-cell RNA sequencing of healthy mouse colon and mouse colon with acute or chronic colitis induced by DSS

GSE264408 Mus musculus (mouse) Single-cell RNA-seq 10 samples Submitted 2024/05/08 Platform GPL21273
At a glance

Single-cell RNA-seq · mouse · 10 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism
Mus musculus (mouse)
Samples
10 samples: 4 × Mouse colon, ChronicColitis vs 3 × Mouse colon, Healthy vs 3 × Mouse colon, AcuteColitisGroups 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
Integrative analysis of single-cell RNA-seq and gut microbiome metabarcoding data elucidates macrophage dysfunction in mice with DSS-induced ulcerative colitisCommunications biology · 2024
Summary (written by the submitters)
In this study, we attempted to dissect the dynamic changes during inflammation using well-prepared scRNA-seq dataset. Specifically, we tried to characterize the pathology and the biological mechanism underlying the ulcerative colitis separately for the acute and chronic colitis. We observed a significant reduction in epithelial populations during acute colitis, indicating tissue damage, with a partial recovery observed in chronic inflammation.
Read the full summary ↓
Analyses of cell-cell interactions demonstrated shifts in networking patterns among different cell types during disease progression. Notably, macrophage phenotypes exhibited diversity, with a pronounced polarization towards the pro-inflammatory M1 phenotype in chronic condition, suggesting the role of macrophage heterogeneity in disease progression. Analysis of the intestinal microbiome revealed significant alterations in composition and metabolism pathways, particularly the nicotinamide pathway. Additionally, dysbiosis was linked to dysregulation of NAD homeostasis through NAMPT, providing insights into potential therapeutic strategies. The study also highlighted the role of T cell differentiation in the context of dysbiosis and its implications in colitis progression, emphasizing the need for targeted interventions to modulate the inflammatory response and immune balance in colitis.
Published in
Integrative analysis of single-cell RNA-seq and gut microbiome metabarcoding data elucidates macrophage dysfunction in mice with DSS-induced ulcerative colitis
Hong D, Kim HK, Yang W et al. · Communications biology 2024 · PMID 38879692 · doi:10.1038/s42003-024-06409-w
This dataset
Open GSE264408 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 GSE264408_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 PRJNA1102362 and SRA study SRP502899. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38879692) ↗
Study design
4 × Mouse colon, ChronicColitis vs 3 × Mouse colon, Healthy vs 3 × Mouse colon, AcuteColitis

Supports a between-group comparison across 10 samples.

How we read this: 3 replicated groups read from 10 sample titles; they account for 10 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.