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Human Macrophages Encode Stimulus-Specific Information of Prior Exposures Through Trained Immunity

GSE323311 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 48 samples Submitted 2026/03/26 Platform GPL30173
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 48 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
48 samples: 24 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
Human macrophages encode stimulus-specific information of prior exposures through trained immunityCell systems · 2026
Summary (written by the submitters)
Trained immunity (a form of innate immune memory), defined in part by heightened responses to pathogen restimulation, can be generated by many different stimuli. However, both the quantitative differences in trained states generated by different stimuli and the downstream consequences of those differences remain unclear. Here, we used primary human monocyte-derived macrophages to demonstrate phenotypic and molecular stimulus specificity of trained immunity six days after initial exposure.
Read the full summary ↓
Quantification of cytokine production with single-molecule RNA imaging demonstrated stimulus-specific patterns of response to restimulation, with trained cells showed stronger responses to secondary stimuli more similar to their initial stimulation. Differential licensing of inflammatory transcription factors was associated with encoding of specificities in chromatin six days after training, while memory of some, but not all, training stimuli is lost by eleven days post-training in vitro. Overall, our findings demonstrate that different training stimuli can impart specific memories which generate distinct training phenotypes.
Published in
Human macrophages encode stimulus-specific information of prior exposures through trained immunity
O'Farrell A, Niu Z, Li J et al. · Cell systems 2026 · PMID 42320478 · doi:10.1016/j.cels.2026.101647
This dataset
Open GSE323311 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 GSE323311_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 PRJNA1432078 and SRA study SRP681030. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42320478) ↗
Study design
24 conditions, mostly in duplicate
Monocyte-derived macrophages from Donor ND410… ×2 Monocyte-derived macrophages from Donor ND410… ×2 Monocyte-derived macrophages from Donor ND410… ×2 Monocyte-derived macrophages from Donor ND410… ×2 Monocyte-derived macrophages from Donor ND650… ×2 Monocyte-derived macrophages from Donor ND650… ×2 Monocyte-derived macrophages from Donor ND650… ×2 Monocyte-derived macrophages from Donor ND650… ×2 +16 more

Supports a between-group comparison across 48 samples.

How we read this: 24 replicated groups read from 48 sample titles; they account for 48 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

+ 8 more — browse all 48 samples with per-sample file links →

Datasets on a similar topic

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