GEO series

Enhancement of activation-induced T cell proliferation by SIRPG in a CD47-independent manner

GSE296196 Homo sapiens (human) RNA-seq (gene expression) 46 samples Submitted 2025/12/10 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 46 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: 46 samples: 22 conditions, mostly in duplicateGroups 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: Enhancement of activation-induced T cell proliferation by SIRPG in a CD47-independent mannerFrontiers in immunology · 2025

Summary (written by the submitters)

SIRPG, a primate-specific type 1 transmembrane protein in the Signal Regulatory Protein (SIRP) family, is predominantly expressed in T cells. It contains a short cytoplasmic domain, which does not contain any known signaling motif, and its only known ligand is CD47. Several genetic variations in SIRPG, including the V263A (rs6043409) polymorphism, linked to increased type 1 diabetes risk, highlight its potential importance.

Read the full summary ↓

However, its expression and physiological role remain largely unclear due to its absence in rodents. Here, we demonstrate that SIRPG and GzmB exhibit near mutually exclusive expression in resting peripheral CD8+ T cells. We further show that SIRPG serves as a valuable marker for GzmK-expressing CD8+ T cells in peripheral blood and inflamed synovial fluid and that its expression in both CD4+ and CD8+ T cells is upregulated by anti-CD3 stimulation, with further enhancement by the TNFα inhibitor adalimumab, but not certolizumab. While SIRPG ablation minimally affects T cell activation and IFNγ/TNFα production, it impairs the expression of mitosis-regulating genes like UBE2C and TOP2A, leading to reduced proliferation, and alters the expression of certain activation-induced surface molecules, including CRTAM. Notably, SIRPG-mediated proliferation and CRTAM expression are cell-autonomous and CD47-independent. Structural and functional analyses reveal that SIRPG-driven proliferation is independent of its extracellular D1 domain, not significantly affected by the V263 variant, but dependent on its cytoplasmic domain. Collectively, our findings offer novel insights into the expression, function, and mechanism of action of SIRPG in T cells.

Published in

Enhancement of activation-induced T cell proliferation by SIRPG in a CD47-independent manner

Marguerie F, Saifi MA, Geary B et al. · Frontiers in immunology 2025 · PMID 41357240 · doi:10.3389/fimmu.2025.1668361

This dataset

Open GSE296196 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 GSE296196_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 PRJNA1258190 and SRA study SRP582796. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41357240) ↗

Study design

22 conditions, mostly in duplicate

Donor 30 – SIRPG WT CD4+ T cells, Day ×2 Donor 30 – SIRPG KO CD4+ T cells, Day ×2 Donor 30 – SIRPG WT CD8+ T cells, Day ×2 Donor 30 – SIRPG KO CD8+ T cells, Day ×2 Donor 32 – SIRPG WT CD4+ T cells, Day ×2 Donor 32 – SIRPG KO CD4+ T cells, Day ×2 Donor 32 – SIRPG WT CD8+ T cells, Day ×2 Donor 32 – SIRPG KO CD8+ T cells, Day ×2 +16 more

Supports a between-group comparison across 44 samples.

How we read this: 22 replicated groups read from 46 sample titles; they account for 44 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

GSM8966844 Donor 30 – SIRPG WT CD4+ T cells, Day 2 Donor 30 – SIRPG WT CD4…
GSM8966845 Donor 30 – SIRPG KO CD4+ T cells, Day 2 Donor 30 – SIRPG KO CD4…
GSM8966846 Donor 30 – SIRPG WT CD4+ T cells, Day 4 Donor 30 – SIRPG WT CD4…
GSM8966847 Donor 30 – SIRPG KO CD4+ T cells, Day 4 Donor 30 – SIRPG KO CD4…
GSM8966848 Donor 30 – SIRPG WT CD8+ T cells, Day 2 Donor 30 – SIRPG WT CD8…
GSM8966849 Donor 30 – SIRPG KO CD8+ T cells, Day 2 Donor 30 – SIRPG KO CD8…
GSM8966850 Donor 30 – SIRPG WT CD8+ T cells, Day 4 Donor 30 – SIRPG WT CD8…
GSM8966851 Donor 30 – SIRPG KO CD8+ T cells, Day 4 Donor 30 – SIRPG KO CD8…
GSM8966852 Donor 32 – SIRPG WT CD4+ T cells, Day 2 Donor 32 – SIRPG WT CD4…
GSM8966853 Donor 32 – SIRPG KO CD4+ T cells, Day 2 Donor 32 – SIRPG KO CD4…
GSM8966854 Donor 32 – SIRPG WT CD4+ T cells, Day 4 Donor 32 – SIRPG WT CD4…
GSM8966855 Donor 32 – SIRPG KO CD4+ T cells, Day 4 Donor 32 – SIRPG KO CD4…
GSM8966856 Donor 32 – SIRPG WT CD8+ T cells, Day 2 Donor 32 – SIRPG WT CD8…
GSM8966857 Donor 32 – SIRPG KO CD8+ T cells, Day 2 Donor 32 – SIRPG KO CD8…
GSM8966858 Donor 32 – SIRPG WT CD8+ T cells, Day 4 Donor 32 – SIRPG WT CD8…
GSM8966859 Donor 32 – SIRPG KO CD8+ T cells, Day 4 Donor 32 – SIRPG KO CD8…
GSM8966860 Donor 36 – SIRPG WT CD4+ T cells, Day 4
GSM8966861 Donor 36 – SIRPG KO CD4+ T cells, Day 4
GSM8966862 Donor 36 – SIRPG WT CD8+ T cells, Day 2 Donor 36 – SIRPG WT CD8…
GSM8966863 Donor 36 – SIRPG KO CD8+ T cells, Day 2 Donor 36 – SIRPG KO CD8…
GSM8966864 Donor 36 – SIRPG WT CD8+ T cells, Day 4 Donor 36 – SIRPG WT CD8…
GSM8966865 Donor 36 – SIRPG KO CD8+ T cells, Day 4 Donor 36 – SIRPG KO CD8…
GSM8966866 Donor 49 – SIRPG WT CD4+ T cells, Day 2 Donor 49 – SIRPG WT CD4…
GSM8966867 Donor 49 – SIRPG KO CD4+ T cells, Day 2 Donor 49 – SIRPG KO CD4…
GSM8966868 Donor 49 – SIRPG WT CD4+ T cells, Day 4 Donor 49 – SIRPG WT CD4…
GSM8966869 Donor 49 – SIRPG KO CD4+ T cells, Day 4 Donor 49 – SIRPG KO CD4…
GSM8966870 Donor 49 – SIRPG WT CD8+ T cells, Day 2 Donor 49 – SIRPG WT CD8…
GSM8966871 Donor 49 – SIRPG KO CD8+ T cells, Day 2 Donor 49 – SIRPG KO CD8…
GSM8966872 Donor 49 – SIRPG WT CD8+ T cells, Day 4 Donor 49 – SIRPG WT CD8…
GSM8966873 Donor 49 – SIRPG KO CD8+ T cells, Day 4 Donor 49 – SIRPG KO CD8…
GSM8966874 Donor 50 – SIRPG WT CD4+ T cells, Day 2 Donor 50 – SIRPG WT CD4…
GSM8966875 Donor 50 – SIRPG KO CD4+ T cells, Day 2 Donor 50 – SIRPG KO CD4…
GSM8966876 Donor 50 – SIRPG WT CD4+ T cells, Day 4 Donor 50 – SIRPG WT CD4…
GSM8966877 Donor 50 – SIRPG KO CD4+ T cells, Day 4 Donor 50 – SIRPG KO CD4…
GSM8966878 Donor 50 – SIRPG WT CD8+ T cells, Day 2 Donor 50 – SIRPG WT CD8…
GSM8966879 Donor 50 – SIRPG KO CD8+ T cells, Day 2 Donor 50 – SIRPG KO CD8…
GSM8966880 Donor 50 – SIRPG WT CD8+ T cells, Day 4 Donor 50 – SIRPG WT CD8…
GSM8966881 Donor 50 – SIRPG KO CD8+ T cells, Day 4 Donor 50 – SIRPG KO CD8…
GSM8966882 Donor 55 – SIRPG WT CD4+ T cells, Day 2 Donor 55 – SIRPG WT CD4…
GSM8966883 Donor 55 – SIRPG KO CD4+ T cells, Day 2 Donor 55 – SIRPG KO CD4…

+ 6 more — browse all 46 samples with per-sample file links →

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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.