GEO series

Senescent activated naive B cells promote anti-citrullinated antigen T cell responses and the transition to clinical rheumatoid arthritis

GSE342939 Homo sapiens (human) Single-cell RNA-seq 78 samples Submitted 2026/08/07 Platform GPL34284

At a glance

Single-cell RNA-seq · human · 78 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: Homo sapiens (human)
Samples: 78 samples: 78 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)

This study profiles peripheral B cells from individuals at risk for rheumatoid arthritis (RA), including ACPA-positive converters to clinical RA, ACPA-positive non-converters, and healthy controls, at paired pre and post time points. Using 10x Genomics Chromium single-cell gene expression (scRNA-seq), antibody-derived tag / CITE-seq surface protein profiling, and B cell receptor (BCR) V(D)J sequencing, we characterize activated naive B cell states associated with progression toward clinical RA.

This dataset

Open GSE342939 in finder → Find more human 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 GSE342939_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 PRJNA1344838 and SRA study SRP632981. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

78 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 78 sample titles: 78 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

GSM9943404 Peripheral B cells, healthy control, pre, scRNA-seq, NN1A
GSM9943405 Peripheral B cells, healthy control, pre, CITE-seq, NN1A
GSM9943406 Peripheral B cells, healthy control, pre, BCR-seq, NN1A
GSM9943407 Peripheral B cells, healthy control, post, scRNA-seq, NN1B
GSM9943408 Peripheral B cells, healthy control, post, CITE-seq, NN1B
GSM9943409 Peripheral B cells, healthy control, post, BCR-seq, NN1B
GSM9943410 Peripheral B cells, healthy control, pre, scRNA-seq, NN2A
GSM9943411 Peripheral B cells, healthy control, pre, CITE-seq, NN2A
GSM9943412 Peripheral B cells, healthy control, pre, BCR-seq, NN2A
GSM9943413 Peripheral B cells, healthy control, post, scRNA-seq, NN2B
GSM9943414 Peripheral B cells, healthy control, post, CITE-seq, NN2B
GSM9943415 Peripheral B cells, healthy control, post, BCR-seq, NN2B
GSM9943416 Peripheral B cells, healthy control, pre, scRNA-seq, NN3A
GSM9943417 Peripheral B cells, healthy control, pre, CITE-seq, NN3A
GSM9943418 Peripheral B cells, healthy control, pre, BCR-seq, NN3A
GSM9943419 Peripheral B cells, healthy control, post, scRNA-seq, NN3B
GSM9943420 Peripheral B cells, healthy control, post, CITE-seq, NN3B
GSM9943421 Peripheral B cells, healthy control, post, BCR-seq, NN3B
GSM9943422 Peripheral B cells, ACPA-positive converter to clinical RA, pre, scRNA-seq, PC1A
GSM9943423 Peripheral B cells, ACPA-positive converter to clinical RA, pre, CITE-seq, PC1A
GSM9943424 Peripheral B cells, ACPA-positive converter to clinical RA, pre, BCR-seq, PC1A
GSM9943425 Peripheral B cells, ACPA-positive converter to clinical RA, post, scRNA-seq, PC1B
GSM9943426 Peripheral B cells, ACPA-positive converter to clinical RA, post, CITE-seq, PC1B
GSM9943427 Peripheral B cells, ACPA-positive converter to clinical RA, post, BCR-seq, PC1B
GSM9943428 Peripheral B cells, ACPA-positive converter to clinical RA, pre, scRNA-seq, PC2A
GSM9943429 Peripheral B cells, ACPA-positive converter to clinical RA, pre, CITE-seq, PC2A
GSM9943430 Peripheral B cells, ACPA-positive converter to clinical RA, pre, BCR-seq, PC2A
GSM9943431 Peripheral B cells, ACPA-positive converter to clinical RA, post, scRNA-seq, PC2B
GSM9943432 Peripheral B cells, ACPA-positive converter to clinical RA, post, CITE-seq, PC2B
GSM9943433 Peripheral B cells, ACPA-positive converter to clinical RA, post, BCR-seq, PC2B
GSM9943434 Peripheral B cells, ACPA-positive converter to clinical RA, pre, scRNA-seq, PC3A
GSM9943435 Peripheral B cells, ACPA-positive converter to clinical RA, pre, CITE-seq, PC3A
GSM9943436 Peripheral B cells, ACPA-positive converter to clinical RA, pre, BCR-seq, PC3A
GSM9943437 Peripheral B cells, ACPA-positive converter to clinical RA, post, scRNA-seq, PC3B
GSM9943438 Peripheral B cells, ACPA-positive converter to clinical RA, post, CITE-seq, PC3B
GSM9943439 Peripheral B cells, ACPA-positive converter to clinical RA, post, BCR-seq, PC3B
GSM9943440 Peripheral B cells, ACPA-positive converter to clinical RA, pre, scRNA-seq, PC4A
GSM9943441 Peripheral B cells, ACPA-positive converter to clinical RA, pre, CITE-seq, PC4A
GSM9943442 Peripheral B cells, ACPA-positive converter to clinical RA, pre, BCR-seq, PC4A
GSM9943443 Peripheral B cells, ACPA-positive converter to clinical RA, post, scRNA-seq, PC4B

+ 38 more — browse all 78 samples with per-sample file links →

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