GEO series

Indolent primary cutaneous B cell lymphomas resemble persistent antigen reactions without signs of dedifferentiation

GSE218861 Homo sapiens (human) Single-cell RNA-seq 27 samples Submitted 2025/12/30 Platform GPL20301

At a glance

Single-cell RNA-seq · human · 27 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: 27 samples: 27 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: Indolent primary cutaneous B-cell lymphomas resemble persistent antigen reactions without signs of dedifferentiationNature communications · 2026

Summary (written by the submitters)

Primary cutaneous B-cell lymphoma encompass clinically heterogeneous entities. While primary cutaneous diffuse large B-cell lymphoma, leg type (pcDLBCL-LT) is aggressive, primary cutaneous follicle centre lymphoma (pcFCL) and primary cutaneous marginal zone lymphoma (pcMZL) typically follow an indolent course. To clarify their pathophysiological basis, we perform single-cell RNA sequencing on pcFCL, pcMZL, and pcDLBCL-LT, alongside reactive B-cell rich lymphoid proliferations (rB-LP), gastric mucosa-associated lymphoid tissue (MALT) lymphoma, and systemic counterparts.

Read the full summary ↓

Here we show that the indolent pcMZL, pcFCL, and rB-LP exhibit a persistent germinal centre reaction, not observed in pcDLBCL-LT or gastric MALT lymphoma. Further, pcMZL top expanded clones develop within lesions from naïve and not post-germinal centre B cells as currently presumed. Our data thus indicate that pcMZL and pcFCL, similar to rB-LP may be driven by (a yet unknown) antigen. While our data indicates that pcFCL exhibits some features of true lymphomas, it clearly supports the classification of pcMZL as a lymphoproliferative disease.

Published in

Indolent primary cutaneous B-cell lymphomas resemble persistent antigen reactions without signs of dedifferentiation

Griss J, Gansberger S, Oyarzun I et al. · Nature communications 2026 · PMID 41639106 · doi:10.1038/s41467-026-69210-9

This dataset

Open GSE218861 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 GSE218861_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 PRJNA906036. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41639106) ↗

Study design

27 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 27 sample titles: 27 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

GSM8268337 rB-LP 3 – Transcriptome
GSM8268338 rB-LP 4 – Transcriptome
GSM8268339 rB-LP 5 – Transcriptome
GSM8268340 pcMZL 1 – Transcriptome
GSM8268341 pcMZL 2 – Transcriptome
GSM8268342 pcMZL 3 – Transcriptome
GSM8268343 pcMZL 4 – Transcriptome
GSM8268344 pcMZL 5 – Transcriptome
GSM8268345 pcMZL 6 – Transcriptome
GSM8268346 pcMZL 7 – Transcriptome
GSM8268347 pcFCL 1 – Transcriptome
GSM8268348 pcDLBCL-LT 1 – Transcriptome
GSM8268349 pcDLBCL-LT 2 – Transcriptome
GSM8268350 pcDLBCL-LT 3 – Transcriptome
GSM8268351 pcMZL 8 – Tanscriptome
GSM8268352 rB-LP 1 – Transcriptome
GSM8268353 rB-LP 2 – Transcriptome
GSM8268354 MALT 1 – Transcriptome
GSM8268355 MALT 2 – Transcriptome
GSM8268356 MALT 3 – Transcriptome
GSM8268357 MALT 4 – Transcriptome
GSM8268358 pcFCL 2 – Transcriptome
GSM8268359 pcFCL 3 – Transcriptome
GSM8268360 pcFCL 4 – Transcriptome
GSM8617965 pcMZL 9 – Tanscriptome
GSM8617966 pcFCL 5 – Tanscriptome
GSM8617967 pcDLBCL-LT 4 – Tanscriptome

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