ATAC-seq of human plasmacytoid dendritic cells in adult and elderly donors
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 12 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
- 12 samples: 12 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
- TNF and type I interferon crosstalk controls the fate and function of plasmacytoid dendritic cellsNature immunology · 2025
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.
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.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE279911_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1175372 and SRA study SRP539680. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 12 sample titles: 12 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.
- GSM8583252 Ue2 [ATAC-Seq]
- GSM8583253 Ue3 [ATAC-Seq]
- GSM8583254 Ue4 [ATAC-Seq]
- GSM8583255 Ue5 [ATAC-Seq]
- GSM8583256 Ue6 [ATAC-Seq]
- GSM8583257 Ue7 [ATAC-Seq]
- GSM8583258 UY1 [ATAC-Seq]
- GSM8583259 UY2 [ATAC-Seq]
- GSM8583260 UY4 [ATAC-Seq]
- GSM8583261 UY5 [ATAC-Seq]
- GSM8583262 UY6 [ATAC-Seq]
- GSM8583263 UY7 [ATAC-Seq]
- GSE254707 Single-cell transcriptomic analysis identifies infiltrating plasmacytoid dendritic cells in psoriasis epidermis 4988 samples shares plasmacytoid, dendritic
- GSE315440 LncRNAs coordinate doxycycline-induced gene expression response in human iPSCs (ATAC-seq) 341 samples shares atac-seq
- GSE243003 Metabolic adaptation pilots the differentiation of human hematopoietic cells (bulk ATAC-Seq) 41 samples shares atac-seq
- GSE333876 Epigenetic landscape, key transcriptional regulators, and in vivo identification of human Tr1 cells [ATAC-seq] 33 samples shares atac-seq
- GSE237807 Multi-omics analysis of FOXO3 pioneer factor activity reveals distinct networks in proliferating and DNA damage induced senescent cells [ATAC-Seq] 42 samples shares atac-seq
- GSE334112 Reversible epiblast regionalisation determines differentiation potential of human PSCs [ATAC-seq] 38 samples shares atac-seq
- GSE303329 Systematic investigation reveals extensive Epstein-Barr virus transcriptional regulation of the human genome [ATAC-seq] 30 samples shares atac-seq
- GSE338484 Somatic mutations reveal the ontogeny of microglia in human aging [snATAC-seq] 29 samples shares atac-seq
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.