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Unique CD8+ T Cell Priming by Antigen Presenting Plasmacytoid Dendritic Cells Compared to Conventional Dendritic Cells

GSE261447 Homo sapiens (human) RNA-seq (gene expression) 15 samples Submitted 2025/02/01 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 15 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
15 samples: 5 conditions, mostly in triplicateGroups 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
Distinctive CD8(+) T cell activation by antigen-presenting plasmacytoid dendritic cells compared to conventional dendritic cellsCell reports · 2025
Summary (written by the submitters)
Plasmacytoid dendritic cells (pDCs) play a crucial role in orchestrating immune responses, especially against viral infections, and have traditionally been well recognized for their ability to produce type I and type III interferons. However, recent discoveries reveal pDCs to be heterogeneous with more complex functions that include antigen uptake, processing, and presentation.
Read the full summary ↓
We investigated the antigen cross-presentation ability of pDCs and their role in CD8+ T cell priming, a subject of ongoing debate. Utilizing a novel culturing system of CD8+ T cells and autologous pDCs derived from human blood circulating CD34+ hematopoietic stem and progenitor cells (cHSPCs), we demonstrate that pDCs can efficiently prime CD8+ T cells through cross-presentation, thereby contributing to their expansion and cytotoxic activity. The pDCs’ antigen presentation ability is comparable to that of monocyte-derived dendritic cells (moDCs), which are traditionally known for their efficient antigen presentation capacity. Bioinformatic analysis of the primed CD8+ T cells to uncover their transcriptomic profile following priming by pDCs versus moDCs, revealed distinct genetic signatures, indicating that pDCs prime CD8+ T cells differently than cDCs. These findings challenge the traditional view of pDCs as mere IFN-producing cells, highlighting their significant role in antigen presentation and T cell activation.
Published in
Distinctive CD8(+) T cell activation by antigen-presenting plasmacytoid dendritic cells compared to conventional dendritic cells
van der Sluis RM, García-Rodríguez JL, Nielsen IH et al. · Cell reports 2025 · PMID 40073016 · doi:10.1016/j.celrep.2025.115413
This dataset
Open GSE261447 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 GSE261447_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 PRJNA1086965 and SRA study SRP494869. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40073016) ↗
Study design
5 conditions, mostly in triplicate
CD3+CD8+CD69+ cells after co-culturing with c… ×3 CD3+CD8+CD69+ cells after co-culturing with c… ×3 CD3+CD8+CD69+ cells after co-culturing with m… ×3 CD3+CD8+CD69+ cells after co-culturing with m… ×3 CD3+CD8+CD69- cells (P5) ×3

Supports a between-group comparison across 15 samples.

How we read this: 5 replicated groups read from 15 sample titles; they account for 15 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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