GEO series

Single-cell analysis identifies monocyte signatures of disease activity and clinical subtypes in Behçet’s disease

GSE338165 Homo sapiens (human) Single-cell RNA-seq 22 samples Submitted 2026/07/30 Platform GPL24676

At a glance

Single-cell RNA-seq · human · 22 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism: Homo sapiens (human)
Samples: 22 samples: 11 × Sample LineGroups 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: Single-cell analysis identifies monocyte signatures of disease activity and clinical subtypes in Behçet's diseaseAnnals of the rheumatic diseases · 2026

Summary (written by the submitters)

This study used single-cell RNA sequencing of PBMCs from 34 Behçet’s disease patients and 12 healthy controls to characterize immune dysregulation across disease activity states and clinical phenotypes. BD was marked by expansion and activation of monocyte subsets, with strong IFN-γ, heat-shock, and antigen-presentation signatures, particularly during active disease.

Read the full summary ↓

These inflammatory programs decreased in remission, which showed restoration of regulatory and metabolic pathways and increased type I interferon-related gene expression, suggesting a potentially protective role. Distinct monocyte signatures were also associated with vascular, ocular, and non-organ-involved BD. Overall, the study identifies monocyte-driven inflammation as a central feature of BD and highlights activity- and phenotype-specific pathways that may guide targeted therapies.

Published in

Single-cell analysis identifies monocyte signatures of disease activity and clinical subtypes in Behçet's disease

Carmona E, Deniz R, Bes C et al. · Annals of the rheumatic diseases 2026 · PMID 42471274 · doi:10.1016/j.ard.2026.06.033

This dataset

Open GSE338165 in finder → Find more human 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 GSE338165_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 PRJNA1492640 and SRA study SRP716737. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42471274) ↗

Study design

11 × Sample Line

Supports a between-group comparison across 11 samples.

How we read this: 1 replicated groups read from 22 sample titles; they account for 11 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

GSM9868193 Sample Line 1 Sample Line
GSM9868194 Sample Line 1 HTO
GSM9868195 Sample Line 2 Sample Line
GSM9868196 Sample Line 2 HTO
GSM9868197 Sample Line 3 Sample Line
GSM9868198 Sample Line 3 HTO
GSM9868199 Sample Line 4 Sample Line
GSM9868200 Sample Line 4 HTO
GSM9868201 Sample Line 5 Sample Line
GSM9868202 Sample Line 5 HTO
GSM9868203 Sample Line 6 Sample Line
GSM9868204 Sample Line 6 HTO
GSM9868205 Sample Line 7 Sample Line
GSM9868206 Sample Line 7 HTO
GSM9868207 Sample Line 8 Sample Line
GSM9868208 Sample Line 8 HTO
GSM9868209 Sample Line 9 Sample Line
GSM9868210 Sample Line 9 HTO
GSM9868211 Sample Line 10 Sample Line
GSM9868212 Sample Line 10 HTO
GSM9868213 Sample Line 11 Sample Line
GSM9868214 Sample Line 11 HTO

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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.