GEO series

Daratumumab in systemic lupus erythematosus: a phase 2 trial

GSE294789 Homo sapiens (human) RNA-seq (gene expression) 56 samples Submitted 2025/12/13 Platform GPL30173

At a glance

RNA-seq (gene expression) · human · 56 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: Homo sapiens (human)
Samples: 56 samples: 56 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.
Paper: Daratumumab in systemic lupus erythematosus: a single-arm phase 2 trialNature communications · 2026

Summary (written by the submitters)

Antibody-secreting cells (ASCs) play a central role in the pathophysiology of systemic lupus erythematosus (SLE). This single-arm, open-label, phase 2 clinical trial aimed to evaluate the safety and efficacy of the ASC-depleting anti-CD38 monoclonal antibody daratumumab in patients with refractory SLE. The primary endpoint was a significant reduction in serum anti-double-stranded DNA (anti-dsDNA) antibody levels.

Read the full summary ↓

Ten female patients with active disease and inadequate responses to at least two disease-modifying drugs received eight weekly subcutaneous injections of 1800 mg daratumumab. By week 12, anti-dsDNA antibody levels were significantly reduced (p=0.002), accompanied by rapid and sustained clinical improvements across all patients and organ domains. Adverse events were mild to moderate. Daratumumab treatment depleted circulating ASCs, reduced type I interferon activity, and profoundly modulated T-cell responses. These findings highlight the pivotal role of ASCs in SLE pathogenesis and support daratumumab as a promising therapeutic option for refractory SLE. ClinicalTrials.gov identifier: NCT04810754.

Published in

Daratumumab in systemic lupus erythematosus: a single-arm phase 2 trial

Ostendorf L, Zernicke J, Klotsche J et al. · Nature communications 2026 · PMID 41629292 · doi:10.1038/s41467-026-69112-w

This dataset

Open GSE294789 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 GSE294789_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 PRJNA1251604 and SRA study SRP579084. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41629292) ↗

Study design

56 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 56 sample titles: 56 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

GSM8919721 Sorted Memory B and T cells from Patient 1 week 0 – Gene Expression
GSM8919722 Sorted Memory B and T cells from Patient 1 week 0 – BCR
GSM8919723 Sorted Memory B and T cells from Patient 1 week 0 – TCR
GSM8919724 Sorted Memory B and T cells from Patient 2 week 0 – Gene Expression
GSM8919725 Sorted Memory B and T cells from Patient 2 week 0 – BCR
GSM8919726 Sorted Memory B and T cells from Patient 2 week 0 – TCR
GSM8919727 Sorted Memory B and T cells from Patient 1 week 9 – Gene Expression
GSM8919728 Sorted Memory B and T cells from Patient 1 week 9 – BCR
GSM8919729 Sorted Memory B and T cells from Patient 1 week 9 – TCR
GSM8919730 Sorted Memory B and T cells from Patient 2 week 9 – Gene Expression
GSM8919731 Sorted Memory B and T cells from Patient 2 week 9 – BCR
GSM8919732 Sorted Memory B and T cells from Patient 2 week 9 – TCR
GSM8919733 Sorted Memory B and T cells from Patient 3 week 0 – Gene Expression
GSM8919734 Sorted Memory B and T cells from Patient 3 week 0 – BCR
GSM8919735 Sorted Memory B and T cells from Patient 3 week 0 – TCR
GSM8919736 Sorted Memory B and T cells from Patient 3 week 9 – Gene Expression
GSM8919737 Sorted Memory B and T cells from Patient 3 week 9 – BCR
GSM8919738 Sorted Memory B and T cells from Patient 3 week 9 – TCR
GSM8919739 Sorted Memory B and T cells from Patient 4 week 0 – Gene Expression
GSM8919740 Sorted Memory B and T cells from Patient 4 week 0 – BCR
GSM8919741 Sorted Memory B and T cells from Patient 4 week 0 – TCR
GSM8919742 Sorted Memory B and T cells from Patient 5 week 0 and Patient 7 week 0 – Gene Expression
GSM8919743 Sorted Memory B and T cells from Patient 5 week 0 and Patient 7 week 0 – BCR
GSM8919744 Sorted Memory B and T cells from Patient 5 week 0 and Patient 7 week 0 – TCR
GSM8919745 Sorted Memory B and T cells from Patient 4 week 9 – Gene Expression
GSM8919746 Sorted Memory B and T cells from Patient 4 week 9 – BCR
GSM8919747 Sorted Memory B and T cells from Patient 4 week 9 – TCR
GSM8919748 Sorted Memory B and T cells from Patient 1 week 36 and Patient 2 week 36 – Gene Expression
GSM8919749 Sorted Memory B and T cells from Patient 1 week 36 and Patient 2 week 36 – BCR
GSM8919750 Sorted Memory B and T cells from Patient 1 week 36 and Patient 2 week 36 – TCR
GSM8919751 Sorted Memory B and T cells from Patient 5 week 9 and Patient 7 week 9 – Gene Expression
GSM8919752 Sorted Memory B and T cells from Patient 5 week 9 and Patient 7 week 9 – BCR
GSM8919753 Sorted Memory B and T cells from Patient 5 week 9 and Patient 7 week 9 – TCR
GSM8919754 Sorted Memory B and T cells from Patient 3 week 36 – Gene Expression
GSM8919755 Sorted Memory B and T cells from Patient 3 week 36 – BCR
GSM8919756 Sorted Memory B and T cells from Patient 3 week 36 – TCR
GSM8919757 Sorted Memory B and T cells from Patient 9 week 0 – Gene Expression
GSM8919758 Sorted Memory B and T cells from Patient 9 week 0 – BCR
GSM8919759 Sorted Memory B and T cells from Patient 9 week 0 – TCR
GSM8919760 Sorted Memory B and T cells from Patient 5 week 36 and Patient 10 week 0 – Gene Expression

+ 16 more — browse all 56 samples with per-sample file links →

Datasets on a similar topic

GSE250025 Impaired innate and adaptive immune responses to BNT162b2 SARS-CoV-2 vaccination in systemic lupus erythematosus 84 samples shares erythematosus, systemic, lupus
GSE250023 Impaired innate and adaptive immune responses to BNT162b2 SARS-CoV-2 vaccination in systemic lupus erythematosus 75 samples shares erythematosus, systemic, lupus
GSE226147 Modeling of Clinical Phenotypes in Systemic Lupus Erythematosus Based on the Platelet Transcriptome and FCGR2a Genotype 69 samples shares erythematosus, systemic, lupus
GSE249619 Divergent Epigenetic and Transcriptomic Remodelling during Monocyte Subset Differentiation in Systemic Lupus Erythematosus [RNA-seq] 57 samples shares erythematosus, systemic, lupus
GSE278120 Interferon activation in bone marrow long-lived plasma cells in systemic lupus erythematosus 48 samples shares erythematosus, systemic, lupus
GSE295130 Multi-omics Integration Identifies NK Cell-Mediated Cytotoxicity as a Therapeutic Target in Systemic Lupus Erythematosus 26 samples shares erythematosus, systemic, lupus
GSE297006 Endogenous retroviruses promote aberrant T cell differentiation in systemic lupus erythematosus via the RIG-I pathway [SLE] 10 samples shares erythematosus, systemic, lupus
GSE288271 Endogenous retroviruses promote aberrant T cell differentiation in systemic lupus erythematosus via the RIG-I pathway [whole transcriptomics] 10 samples shares erythematosus, systemic, lupus

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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.