GEO series

The metabolic cofactor Coenzyme A enhances alternative macrophage activation via MyD88-linked signaling [ATAC-seq]

GSE324240 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 18 samples Submitted 2026/03/13 Platform GPL21103

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 18 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: Mus musculus (mouse)
Samples: 18 samples: 6 conditions, mostly in triplicateGroups 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.

Summary (written by the submitters)

Metabolites and metabolic co-factors can shape the innate immune response, though the pathways by which these molecules adjust inflammation remain incompletely understood. Here we show that the metabolic cofactor Coenzyme A (CoA) enhances IL-4 driven alternative macrophage activation [M(IL-4)] in vitro and in vivo. Unexpectedly, we found that perturbations in intracellular CoA metabolism did not influence M(IL-4) differentiation.

Read the full summary ↓

Rather, we discovered that exogenous CoA is a weak TLR4 agonist which primes macrophages for increased receptivity to IL-4 signals and resolution of inflammation via MyD88. Mechanistic studies revealed MyD88- linked signals enhance IL-4 responsiveness, in part, by reshaping chromatin accessibility to enhance transcription of IL-4-linked genes. The results identify CoA as a host metabolic co-factor that influences macrophage function through an extrinsic TLR4-dependent mechanism and suggest that damage-associated molecular patterns (DAMPs) can prime macrophages for alternative activation and resolution of inflammation.

This dataset

Open GSE324240 in finder → Find more mouse 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 GSE324240_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 PRJNA1434287 and SRA study SRP682164. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

6 conditions, mostly in triplicate

BMDM, NT,12hrs, ×3 BMDM, IL-4,12hrs, ×3 BMDM, IL-4+TLR2,12hrs, ×3 BMDM, NT,24hrs, ×3 BMDM, IL-4,24hrs, ×3 BMDM, IL-4+TLR2,24hrs, ×3

Supports a between-group comparison across 18 samples.

How we read this: 6 replicated groups read from 18 sample titles; they account for 18 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

GSM9571690 BMDM, NT,12hrs, rep1 BMDM, NT,12hrs,
GSM9571691 BMDM, NT,12hrs, rep2 BMDM, NT,12hrs,
GSM9571692 BMDM, NT,12hrs, rep3 BMDM, NT,12hrs,
GSM9571693 BMDM, IL-4,12hrs, rep1 BMDM, IL-4,12hrs,
GSM9571694 BMDM, IL-4,12hrs, rep2 BMDM, IL-4,12hrs,
GSM9571695 BMDM, IL-4,12hrs, rep3 BMDM, IL-4,12hrs,
GSM9571696 BMDM, IL-4+TLR2,12hrs, rep1 BMDM, IL-4+TLR2,12hrs,
GSM9571697 BMDM, IL-4+TLR2,12hrs, rep2 BMDM, IL-4+TLR2,12hrs,
GSM9571698 BMDM, IL-4+TLR2,12hrs, rep3 BMDM, IL-4+TLR2,12hrs,
GSM9571699 BMDM, NT,24hrs, rep1 BMDM, NT,24hrs,
GSM9571700 BMDM, NT,24hrs, rep2 BMDM, NT,24hrs,
GSM9571701 BMDM, NT,24hrs, rep3 BMDM, NT,24hrs,
GSM9571702 BMDM, IL-4,24hrs, rep1 BMDM, IL-4,24hrs,
GSM9571703 BMDM, IL-4,24hrs, rep2 BMDM, IL-4,24hrs,
GSM9571704 BMDM, IL-4,24hrs, rep3 BMDM, IL-4,24hrs,
GSM9571705 BMDM, IL-4+TLR2,24hrs, rep1 BMDM, IL-4+TLR2,24hrs,
GSM9571706 BMDM, IL-4+TLR2,24hrs, rep2 BMDM, IL-4+TLR2,24hrs,
GSM9571707 BMDM, IL-4+TLR2,24hrs, rep3 BMDM, IL-4+TLR2,24hrs,

Datasets on a similar topic

GSE298001 Stage-specific Epigenetic Priming Amplifies Gene Activation During Lineage Commitment [ATAC-Seq] 36 samples shares activation, atac-seq
GSE327645 BACH1 acts as a pioneer repressor to enable macrophage plasticity and adaptation across tissues and inflammatory contexts [RNA-seq/ATAC-seq] 28 samples shares macrophage, atac-seq
GSE245648 The Heme-regulated transcriptional repressor, BACH1 safeguards macrophage enhancer selection, activation andtissue adaptation [RNA-seq_BMDM] 24 samples shares macrophage, activation
GSE99296 α-ketoglutarate orchestrates macrophage activation through metabolic and epigenetic reprogramming 18 samples shares macrophage, activation
GSE297574 H3K9 di-methylation dynamics underlies mouse minor zygotic genome activation [spike-in ChIP-seq of mESC] 64 samples shares activation
GSE326173 Nuclear receptor Nur77 resolves the inflammatory response of macrophages primarily by regulating expression of AP-1 transcription factors and their target genes [ChIP-seq] 42 samples shares macrophage
GSE298002 Stage-specific Epigenetic Priming Amplifies Gene Activation During Lineage Commitment [CUT&Run] 38 samples shares activation
GSE266022 Nrf2-mediated chromatin activation of hyperosmotic response genes attenuates heat-induced renal injury [ChIP-seq] 24 samples shares activation

Search all mouse ChIP / ATAC / CUT&Tag 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.