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Spatiotemporal molecular profiling of macrophage-fibroblast crosstalk defines checkpoints orchestrating onset and resolution of inflammation [RNA-seq]

GSE316918 Mus musculus (mouse) Single-cell RNA-seq 18 samples Submitted 2026/01/21 Platform GPL34290
At a glance

Single-cell RNA-seq · mouse · 18 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
18 samples: 6 conditions, mostly in triplicateGroups 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
Spatiotemporal molecular profiling of macrophage-fibroblast crosstalk defines checkpoints orchestrating onset and resolution of inflammationCell reports · 2026
Summary (written by the submitters)
The molecular details of macrophage-fibroblast crosstalk during the onset and resolution of inflammatory disease remain incompletely understood. Here, we apply a scRNAseq-, scATACseq- and bulk RNAseq-based bioinformatic modelling approach to map heterocellular signaling circuits of synovial macrophage and synovial fibroblast (SF) subsets during various stages of inflammatory arthritis.
Read the full summary ↓
While SFs function as key pacemakers of synovial inflammation, individual subsets of synovial macrophages support both the perpetuation and the resolution of arthritis. While pro-inflammatory Il1b+ macrophages dominate the early stages of inflammation, these cells also retain a substantial intrinsic plasticity that is characterized by chromatin remodeling and an eventual differentiation into Spp1+ macrophages. These cells display a terminally-differentiated phenotype, suppresses activation of pro-inflammatory SFs, and initiates the resolution of arthritis by secretion of regulatory mediators including osteopontin. Our data highlight the dichotomous character of macrophage-fibroblast crosstalk and define the cellular and molecular checkpoints that control the onset and resolution of immune-mediated inflammatory diseases.
Published in
Spatiotemporal molecular profiling of macrophage-fibroblast crosstalk defines checkpoints orchestrating onset and resolution of inflammation
Weishaupt K, Chambers D, Dzamukova M et al. · Cell reports 2026 · PMID 41832953 · doi:10.1016/j.celrep.2026.117091
This dataset
Open GSE316918 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 GSE316918_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 PRJNA1405535 and SRA study SRP664682. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41832953) ↗
Study design
6 conditions, mostly in triplicate
isolated fibroblasts from STIA mice, ×3 isolated fibroblasts from STIA mice, stimulat… ×3 isolated fibroblasts from WT mice, ×3 isolated fibroblasts from WT mice, stimulated… ×3 isolated fibroblasts from WT mice, stimulated… ×3 isolated fibroblasts from WT mice, stimulated… ×3

Supports a case/control comparison: 3 samples read as cases, 3 as controls.

How we read this: 6 replicated groups read from 18 sample titles; they account for 18 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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