GEO series

Single-nuclei multiome (ATAC + Gene Expression) sequencing of CD40L-activated human plasmacytoid dendritic cells

GSE267099 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 2 samples Submitted 2025/06/13 Platform GPL24676

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 2 samples

What it is: ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism: Homo sapiens (human)
Samples: 2 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: 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 GSE267099 in finder → Find more human ChIP / ATAC / CUT&Tag 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 GSE267099_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA1109766 and SRA study SRP506784. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40796660) ↗

Samples in this study

The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.

+ 2 more — browse all 2 samples with per-sample file links →

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Search all human ChIP / ATAC / CUT&Tag datasets in GEO →

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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.