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Chromatin Landscape of Macrophages Following Helminth Enzyme Exposure Targeting Prostaglandin Synthesis

GSE259349 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 16 samples Submitted 2025/03/15 Platform GPL18573
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 16 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
16 samples: 16 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
A helminth enzyme subverts macrophage-mediated immunity by epigenetic targeting of prostaglandin synthesisScience immunology · 2024
Summary (written by the submitters)
The molecular mechanisms by which worm parasites evade host immunity are incompletely understood. In a mouse model of chronic intestinal helminth infection, we identify helminthic glutamate dehydrogenase (heGDH) as an essential factor for parasite chronicity by using antibody mediated neutralization or treatment with exogenous recombinant heGDH.
Read the full summary ↓
Macrophages efficiently internalize heGDH and represent a major target of the enzyme in vivo. Combining RNA-seq, ChIP-seq, targeted lipidomics and inhibitor studies, we identify prostaglandin E2 (PGE2) as a major immune regulatory mechanism of heGDH. The induction of PGE2 and further immune regulatory factors (IL-12 family cytokines, IDO1) by heGDH depended on the p300-mediated acetylation of histones. While the enzyme’s catalytic activity was dispensable for key immune regulatory functions, an N-terminal handle-like structure distinct from mammalian GDHs may confer interaction of heGDH with its targets (CD64, GPNMB), identified via proteomics. Thus, helminths employ a ubiquitous metabolic enzyme to epigenetically target macrophages and establish chronicity.
Published in
A helminth enzyme subverts macrophage-mediated immunity by epigenetic targeting of prostaglandin synthesis
Bohnacker S, Henkel FDR, Hartung F et al. · Science immunology 2024 · PMID 39642243 · doi:10.1126/sciimmunol.adl1467
This dataset
Open GSE259349 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 GSE259349_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 PRJNA1081279 and SRA study SRP491983. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39642243) ↗
Study design
16 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 16 sample titles: 16 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
Datasets on a similar topic

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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.