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Evidence that inflammation-associated fibroblasts (IAFs) originate from Edil3 stromal "mesitocytes" in the colon following radiation injury

GSE268790 Mus musculus (mouse) Single-cell RNA-seq 16 samples Submitted 2024/06/01 Platform GPL24247
At a glance

Single-cell RNA-seq · mouse · 16 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
Mus musculus (mouse)
Samples
16 samples: 9 × Stromal cells (CD45-, EPCAM -) of colon from control miceGroups 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)
Stromal cells present in the colon crypt provide proliferation and differentiation signals to the epithelial cells, thereby maintaining their integrity and stimulating the regeneration process. Cancer patients treated for tumors located in the abdominopelvic region may develop radiation proctitis, a condition characterized by a strong mucosal inflammation.
Read the full summary ↓
In this work, single-cell RNA sequencing approaches were combined with spatial transcriptomics to characterize colonic stromal cells in depth, both in control conditions and in the context of radiation-induced ulceration. The present study identifies a novel stromal marker, Edil3 (EGF-like repeats and discoidin domains 3), which defines the major stromal population of the colon. This population is spatially and functionally distinct from telocytes and trophocytes and is expressed along the crypt with a functional proliferation-differentiation axis . This population, which we propose to name "mesitocytes," cooperates with vascular cells to control inflammation and epithelial proliferation. We demonstrate that radiation-induced ulcerated areas are characterized by the presence of inflammation-associated fibroblasts (IAFs) deriving from mesitocytes.
This dataset
Open GSE268790 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 GSE268790_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 PRJNA1118758 and SRA study SRP511097. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
9 × Stromal cells (CD45-, EPCAM -) of colon from control mice

Supports a between-group comparison across 9 samples.

How we read this: 1 replicated groups read from 16 sample titles; they account for 9 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.