GEO series

Homeostatic signals induce the development of peripheral helper T cells promoted in the pathogenesis of rheumatoid arthritis

GSE273760 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2024/11/20 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 12 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: 12 samples
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: Homeostatic signals, including IL-7 and self-MHC recognition, induce the development of peripheral helper T cells, which are enriched in the joints of rheumatoid arthritisJournal of translational autoimmunity · 2024

Summary (written by the submitters)

Dysregulated T cell homeostasis has been implicated in the pathogenesis of rheumatoid arthritis (RA), in the joint of which peripheral helper T (Tph) cells accumulate and form ectopic lymphoid organs. We examined whether homeostatic signals are involved in the development of Tph cells. Human peripheral blood mononuclear cells(PBMCs) were cultured with IL-7, resulting in the development of PD-1highCXCR5+ Tph-like cells from human peripheral blood CD4 T cells after culture.

Read the full summary ↓

These IL-7-induced Tph-like (IL-7-Tph) cells produced CXCL13 and IL-21 and helped B cells produce IgG. Comprehensive gene expression analysis further supported their similarity with Tph cells in RA joint, and synovial fluid from RA patients (RASF) greatly promoted the IL-7-induced development of Tph-like cells. Our results demonstrate an antigen-nonspecific developmental pathway of Tph cells triggered by homeostatic signals and promoted by the local joint environment, which accounts for the accumulation of Tph cells in RA joints.

Published in

Homeostatic signals, including IL-7 and self-MHC recognition, induce the development of peripheral helper T cells, which are enriched in the joints of rheumatoid arthritis

Tsurui R, Yamada H, Natori T et al. · Journal of translational autoimmunity 2024 · PMID 39554252 · doi:10.1016/j.jtauto.2024.100258

This dataset

Open GSE273760 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 GSE273760_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 PRJNA1142977 and SRA study SRP523720. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39554252) ↗

Study design

A cohort of 12 individual samples

The grouping that defines any comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Sample titles run sample1 … sample12 and carry no group information.

Samples in this study

GSM8436525 sample1
GSM8436526 sample2
GSM8436527 sample3
GSM8436528 sample4
GSM8436529 sample5
GSM8436530 sample6
GSM8436531 sample7
GSM8436532 sample8
GSM8436533 sample9
GSM8436534 sample10
GSM8436535 sample11
GSM8436536 sample12

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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.