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RNAseq analysis of human neutrophils from people with rheumatoid arthritis

GSE274598 Homo sapiens (human) RNA-seq (gene expression) 41 samples Submitted 2025/05/14 Platform GPL11154
At a glance

RNA-seq (gene expression) · human · 41 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
41 samples: 22 × Blood neutrophil, 0h, SRA vs 13 × Blood neutrophil, 0h, ERA vs 6 × Blood neutrophil, 0h, HCGroups 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
The small molecule inhibitor 3PO is a modulator of neutrophil metabolism, ROS production, and NET releaseClinical and experimental immunology · 2025
Summary (written by the submitters)
We report gene expression profiles of blood neutrophils from (1) people newly-diagnosed with rheumatoid arthritis (early RA) before commencement of disease-modifying anti-rheumatic drug therapy, (2) DMARD-refractory RA (severe RA) before commencement of anti-TNF therapy and (3) healthy controls.
Published in
The small molecule inhibitor 3PO is a modulator of neutrophil metabolism, ROS production, and NET release
Fresneda Alarcon M, Abdullah GA, Nolan A et al. · Clinical and experimental immunology 2025 · PMID 39969221 · doi:10.1093/cei/uxaf012
This dataset
Open GSE274598 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 GSE274598_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 PRJNA1147260 and SRA study SRP525924. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39969221) ↗
Study design
22 × Blood neutrophil, 0h, SRA vs 13 × Blood neutrophil, 0h, ERA vs 6 × Blood neutrophil, 0h, HC

Supports a between-group comparison across 41 samples.

How we read this: 3 replicated groups read from 41 sample titles; they account for 41 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

+ 1 more — browse all 41 samples with per-sample file links →

Datasets on a similar topic

Search all human 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.