GEO series

The macrophage response to LPS is marked by dynamic nucleosome positioning and increases in nucleosome sensitivity corresponding with immune regulatory factor footprints

GSE279622 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 24 samples Submitted 2025/02/19 Platform GPL24676

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 24 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: 24 samples: 24 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.

Summary (written by the submitters)

Macrophages detect lipopolysaccharide (LPS) through toll-like receptor 4 (TLR-4) on the cell surface which initiates a signaling cascades resulting in the recruitment of regulatory factors to chromatin and subsequent expression of chemokine and cytokine genes. Primary response genes, which are marked by poised promoters and enhancers, are rapidly expressed after LPS stimulation and activate secondary response genes via paracrine and autocrine signaling pathways.

Read the full summary ↓

While immune signaling following macrophage activation is well understood, the dynamics of nucleosome architecture and regulatory factor binding in promoter regions during early and late LPS responses remain unclear. Here, we stimulated THP-1 derived macrophages with LPS and assessed nucleosome distribution, MNase sensitivity, and small factor footprints across promoters at eight time points. We found that while nucleosome distribution was static over most promoters, LPS stimulation resulted in transient remodeling of immune and DNA repair gene promoters. We also observed distinct MNase sensitivity alterations in two phases which aligned with early/late gene expression patterns. Notably, while most Pol II promoters showed altered chromatin sensitivity, only a subset exhibited transcriptional changes, suggesting widespread chromatin remodeling uncoupled from gene expression. Small factor footprints suggested regulatory factor binding increased at promoters with altered nucleosome distributions or sensitivity, implying that nucleosome sensitivity may result from a combination of histone modifications, genome accessibility, and protein-DNA interactions. These findings provide new temporal insight into the transient and long term effects of immune stimulation on promoter architecture. This also provides a methodological framework for additional time-resolved studies of chromatin remodeling in other systems.

This dataset

Open GSE279622 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 GSE279622_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 PRJNA1173713 and SRA study SRP538935. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41032087) ↗

Study design

24 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 24 sample titles: 24 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

GSM8577131 THP-1, 0hr LPS, merged digests
GSM8577132 THP-1, 5min LPS, merged digests
GSM8577133 THP-1, 30min LPS, merged digests
GSM8577134 THP-1, 1hr LPS, merged digests
GSM8577135 THP-1, 4hr LPS, merged digests
GSM8577136 THP-1, 12hr LPS, merged digests
GSM8577137 THP-1, 24hr LPS, merged digests
GSM8577138 THP-1, 48hr LPS, merged digests
GSM8577139 THP-1, 0hr LPS, light digest
GSM8577140 THP-1, 5min LPS, light digest
GSM8577141 THP-1, 30min LPS, light digest
GSM8577142 THP-1, 1hr LPS, light digest
GSM8577143 THP-1, 4hr LPS, light digest
GSM8577144 THP-1, 12hr LPS, light digest
GSM8577145 THP-1, 24hr LPS, light digest
GSM8577146 THP-1, 48hr LPS, light digest
GSM8577147 THP-1, 0hr LPS, heavy digest
GSM8577148 THP-1, 5min LPS, heavy digest
GSM8577149 THP-1, 30min LPS, heavy digest
GSM8577150 THP-1, 1hr LPS, heavy digest
GSM8577151 THP-1, 4hr LPS, heavy digest
GSM8577152 THP-1, 12hr LPS, heavy digest
GSM8577153 THP-1, 24hr LPS, heavy digest
GSM8577154 THP-1, 48hr LPS, heavy digest

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