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RNA-seq of Tph and Tfh cells proliferated in the spleens of CD8T cells depleted PBMC-transferred humanized mice

GSE308690 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2025/10/01 Platform GPL18573
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: 3 × DN cells, spleen,CD8 T cell-depleted PBMC-transferred, vs 3 × Tfh cells, spleen,CD8 T cell-depleted PBMC-transferred, vs 3 × Tph cells, spleen,CD8 T cell-depleted PBMC-transferred, vs 2 × Tfh cells, spleen, HSC-transferred,Groups 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
CD8+ T cell depletion promotes human Tph/Tfh cell proliferation and Sjögren syndrome-like symptoms in PBMC-based humanized miceJCI insight · 2025
Summary (written by the submitters)
We found that the transfer of PBMCs depleted of CD8 T cells into immunodeficient mice resulted in the proliferation of human Tph/Tfh cells in the spleen. To characterize the Tph/Tfh cells, we examined the comprehensive gene profiles of these cells in the spleen of humanized mice by RNA sequencing (RNA-seq).
Published in
CD8+ T cell depletion promotes human Tph/Tfh cell proliferation and Sjögren syndrome-like symptoms in PBMC-based humanized mice
Piruzyan M, Fujimori S, Sato R et al. · JCI insight 2025 · PMID 41277554 · doi:10.1172/jci.insight.191700
This dataset
Open GSE308690 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 GSE308690_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 PRJNA1332543 and SRA study SRP624216. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41277554) ↗
Study design
3 × DN cells, spleen,CD8 T cell-depleted PBMC-transferred, vs 3 × Tfh cells, spleen,CD8 T cell-depleted PBMC-transferred, vs 3 × Tph cells, spleen,CD8 T cell-depleted PBMC-transferred, vs 2 × Tfh cells, spleen, HSC-transferred,

Supports a between-group comparison across 11 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 11 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
Datasets on a similar topic

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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.