GEO series

Coordinated transcription factor and chromatin dynamics enable innate immune memory in single macrophages

GSE261647 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 18 samples Submitted 2025/03/14 Platform GPL24247

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: 9 conditions, mostly in duplicateGroups 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: Macrophage memory emerges from coordinated transcription factor and chromatin dynamicsCell systems · 2025

Summary (written by the submitters)

Cells of the innate immune system need to interpret dynamic microenvironments and rapidly respond to sequential signals to control inflammation and infection. It is unclear how complex immune signals are encoded and decoded through a small number of transcription factors and ultimately coordinate cellular decision-making. Here, we use single live cell analysis and ATAC sequencing to show that sequential inflammatory signals via the NFκB network induce memory through reprogramming of signaling network state and chromatin accessibility in primary macrophages.

Read the full summary ↓

We use transcriptomic profiling and deep learning to show that these regulatory modes combine to explain macrophage decision-making in response to new inflammatory signals. Macrophage response to prior stimulus predicts memory state and transcriptional response to subsequent stimulus. Surprisingly, we find that innate immune memory is mediated via intracellular individual-cell factors and not via paracrine signaling between macrophages. This work comprehensively profiles the dynamic regulation of signaling networks and chromatin accessibility and their role in tuning macrophage responses to evolving inflammatory signals.

Published in

Macrophage memory emerges from coordinated transcription factor and chromatin dynamics

Wang AG, Son M, Gorin A et al. · Cell systems 2025 · PMID 39938520 · doi:10.1016/j.cels.2025.101171

This dataset

Open GSE261647 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 GSE261647_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 PRJNA1088160 and SRA study SRP495321. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39938520) ↗

Study design

9 conditions, mostly in duplicate

BMDM_CL ×2 BMDM_CT ×2 BMDM_MC ×2 BMDM_ML ×2 BMDM_MM ×2 BMDM_MP ×2 BMDM_MT ×2 BMDM_PL ×2 +1 more

Supports a between-group comparison across 18 samples.

How we read this: 9 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

GSM8147873 BMDM_CL_rep1 BMDM_CL
GSM8147874 BMDM_CL_rep2 BMDM_CL
GSM8147875 BMDM_CT_rep1 BMDM_CT
GSM8147876 BMDM_CT_rep2 BMDM_CT
GSM8147877 BMDM_MC_rep1 BMDM_MC
GSM8147878 BMDM_MC_rep2 BMDM_MC
GSM8147879 BMDM_ML_rep1 BMDM_ML
GSM8147880 BMDM_ML_rep2 BMDM_ML
GSM8147881 BMDM_MM_rep1 BMDM_MM
GSM8147882 BMDM_MM_rep2 BMDM_MM
GSM8147883 BMDM_MP_rep1 BMDM_MP
GSM8147887 BMDM_MP_rep2 BMDM_MP
GSM8147891 BMDM_MT_rep1 BMDM_MT
GSM8147895 BMDM_MT_rep2 BMDM_MT
GSM8147898 BMDM_PL_rep1 BMDM_PL
GSM8147902 BMDM_PL_rep2 BMDM_PL
GSM8147906 BMDM_PT_rep1 BMDM_PT
GSM8147909 BMDM_PT_rep2 BMDM_PT

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