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Emergency Myelopoiesis in Murine Arthritis Results in Cell-Intrinsic Changes in Dendritic Cell Development and Function

GSE291186 Mus musculus (mouse) RNA-seq (gene expression) 26 samples Submitted 2026/06/17 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 26 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Mus musculus (mouse)
Samples
26 samples: 26 samples, each with a distinct title — no replicated groupsGroups 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)
Rheumatoid arthritis (RA) is a chronic autoimmune disease that affects up to 0.5-1% of the adult global population.. Immune and inflammatory tissue damage is the main pathogenic mechanism in RA, and involves a hyperactivation of both innate and adaptive immune systems. Trained immunity, an important feature of the innate immune system, allows the host to mount functionally altered immune responses based on their previous history of immune exposures, independently of the classical adaptive immunological memory.
Read the full summary ↓
However, the role of trained immunity in systemic autoimmune and inflammatory disorders remains poorly understood, with the effects on monocyte and macrophage differentiation and function being most widely studied. We demonstrate that emergency myelopoiesis is induced in chronic rheumatoid arthritis in murine models and acts not only to enhance the counts but also to produce functionally altered innate immune cells. Such effects are cell-intrinsic affecting hematopoietic stem and progenitor cells (HSPCs) and persist independently of the inflammatory disease milieu. Importantly, these trained immunity mechanisms impact not only macrophages but also dendritic cells, which are the major professional antigen presenting cells, bridging the innate and adaptive immune responses. Such mechanisms result in changes in the global transcriptional profiles of dendritic cells, and significantly alter their responses to recall immune stimulation and capacity for T cell activation. This study therefore represents the first demonstration of ‘dendritic cell trained immunity’ in rheumatoid arthritis.
This dataset
Open GSE291186 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 GSE291186_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1232157 and SRA study SRP568122. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
26 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 26 sample titles: 26 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
Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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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.