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Temporal Evolution of Fibroblast Responses Following Salivary Gland Ductal Ligation Injury

GSE287797 Mus musculus (mouse) Single-cell RNA-seq 12 samples Submitted 2025/02/28 Platform GPL30172
At a glance

Single-cell RNA-seq · mouse · 12 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
12 samples: 3 × Homeostatic sample vs 3 × 1-day ligated sample vs 3 × 3-day ligated sample vs 3 × 7-day ligated sampleGroups 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)
Extracellular matrix remodeling is a natural response to injury but, excessive extracellular matrix accumulation or fibrosis, is a causative factor in hundreds of diseases that limit organ function and impede regenerative responses. Fibrosis is closely related to inflammation, both of which occur in the salivary glands of patients treated with radiation for head and neck cancers and in patients suffering from the autoimmune condition, Sjögren’s Disease.
Read the full summary ↓
Despite the known involvement of fibrosis in disease and the inhibitory effects of fibrosis on tissue regeneration, the mechanisms through which fibrosis develops in the salivary gland are poorly understood. Stromal fibroblasts are the primary matrix-producing cells and are known to drive both fibrosis and inflammation. To define the signals produced by fibroblasts in response to injury, we induced a temporary obstructive injury though ligation of the primary submandibular and sublingual salivary gland ducts and then performed single-cell RNA sequencing and pathway analysis at timepoints immediately following the injury. Using bioinformatic approaches, we identified three unique fibroblast groups that dynamically respond to the injury. We characterized the changes in matrisomal and inflammatory gene expression over a 7-day time course and identified the group 2 fibroblasts to be the primary fibrogenic cells, although all groups produced ECM genes. Understanding how fibroblasts respond at early and late injury timepoints along with defining signaling pathways regulated by fibroblasts could lead to a better understanding of the contribution of fibroblast to acute injury responses to facilitate development of therapeutics that minimize fibrosis and promote regenerative gland responses in chronic disease states.
This dataset
Open GSE287797 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 GSE287797_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 PRJNA1214712 and SRA study SRP559384. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
3 × Homeostatic sample vs 3 × 1-day ligated sample vs 3 × 3-day ligated sample vs 3 × 7-day ligated sample

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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.