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SMART-seq2 of activated human plasmacytoid dendritic cells

GSE266889 Homo sapiens (human) Single-cell RNA-seq 383 samples Submitted 2025/06/13 Platform GPL24676
At a glance

Single-cell RNA-seq · human · 383 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism
Homo sapiens (human)
Samples
383 samples: 34 conditions, mostly with about 12 replicates eachGroups 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
TNF and type I interferon crosstalk controls the fate and function of plasmacytoid dendritic cellsNature immunology · 2025
Summary (written by the submitters)
Plasmacytoid and conventional dendritic cells (pDCs and cDCs, respectively) are closely related immune lineages with distinct functions. Whether pDCs can switch fate into the cDC lineage has remained controversial. Here, we sequenced purified pDCs and DCs to create a reference map of the transcriptome and chromatin landscape of all major human blood DC populations (GSE267174 and GSE267100).
Read the full summary ↓
We compared this reference map to the transcriptomic and epigenetic profile of activated pDCs (GSE267099 and GSE266889). We show that activation of purified, bona fide human pDCs induces transcriptional and epigenetic heterogeneity at the single-cell level. A fraction of activated pDCs retains classical pDC features, while others acquire a cDC2-like identity through an intermediate state resembling transitional dendritic cells (tDCs). These datasets—generated using single-cell multiomic profiling (scRNA-seq and scATAC-seq) and SMART-seq—provide a resource to investigate the molecular basis of pDC-to-cDC2 fate transition.
Published in
TNF and type I interferon crosstalk controls the fate and function of plasmacytoid dendritic cells
Arroyo Hornero R, Maqueda-Alfaro RA, Solís-Barbosa MA et al. · Nature immunology 2025 · PMID 40796660 · doi:10.1038/s41590-025-02234-3
This dataset
Open GSE266889 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 GSE266889_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 PRJNA1108680 and SRA study SRP506163. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40796660) ↗
Study design
34 conditions, mostly with about 12 replicates each
Plate1_A ×12 Plate1_B ×12 Plate1_C ×12 Plate1_D ×12 Plate2_A ×12 Plate2_B ×12 Plate2_C ×12 Plate2_D ×12 +26 more

Supports a between-group comparison across 383 samples.

How we read this: 34 replicated groups read from 383 sample titles; they account for 383 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

+ 343 more — browse all 383 samples with per-sample file links →

Datasets on a similar topic

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