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Transcriptomic and epigenetic investigation of Zika virus (ZIKV) and Dengue virus (DENV) infection in human monocyte-derived dendritic cells

GSE220842 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 45 samples Submitted 2025/02/22 Platform GPL18573Platform GPL24676Platform GPL20301
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 45 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
45 samples: 45 samples, each with a distinct title — no replicated groupsGroups 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
Zika but not Dengue virus infection limits NF-κB activity in human monocyte-derived dendritic cells and suppresses their ability to activate T cellsNature communications · 2025
Summary (written by the submitters)
Dendritic cells are key targets for ZIKV and DENV infection. To identify host pathways manipulated by ZIKV and DENV in dendritic cells, we developed a system that enables characterization of genome-wide transcriptional and epigenetic changes in virus-infected and neighboring (bystander), uninfected primary human dendritic cells.
Published in
Zika but not Dengue virus infection limits NF-κB activity in human monocyte-derived dendritic cells and suppresses their ability to activate T cells
Wang YT, Branche E, Xie J et al. · Nature communications 2025 · PMID 40133263 · doi:10.1038/s41467-025-57977-2
This dataset
Open GSE220842 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 GSE220842_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 PRJNA911746 and SRA study SRP412797. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40133263) ↗
Study design
45 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 45 sample titles: 45 distinct titles with little repetition. 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

+ 5 more — browse all 45 samples with per-sample file links →

Datasets on a similar topic

Search all human RNA-seq datasets in GEO →

Share this dataset

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.