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An in vitro methodology demonstrates the five steps of trained immunity in mice: implications on biomarker discovery, adaptive immune responses, mouse strains, sample cryopreservation and genetic ablation [ATAC-Seq]

GSE290032 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 17 samples Submitted 2026/01/07 Platform GPL21103
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 17 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
17 samples: 6 × BMDMs from C57BL/6 mice cultured with M-CSF, naive vs 6 × BMDMs from C57BL/6 mice cultured with M-CSF, stimulated with 10 µg/mL β-glucan (day 0) and 10 ng/mL LPS (day 6) vs 5 × BMDMs from C57BL/6 mice cultured with M-CSF, stimulated with 10 ng/mL LPS (day 6)Groups 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
In vitro protocol demonstrating five functional steps of trained immunity in mice: Implications on biomarker discovery and translational researchCell reports · 2025
Summary (written by the submitters)
Trained immunity is defined by increased inflammatory cytokine production by macrophages that are sequentially activated by two stimuli, separated by a resting period. The models used to study trained immunity should reflect the definition of this process, which includes five different steps. Here, we developed an in vitro methodology to study trained immunity using murine bone marrow-derived macrophages (BMDM), following sequential stimulation with β-glucan and lipopolysaccharide (LPS).
Read the full summary ↓
Kinetic analysis of cytokine production demonstrated, for the first time, that trained BMDM secrete high levels of tumor necrosis factor (TNF) and interleukin 6 (IL6) following stimulation with β-glucan (stimulus 1), compared to unstimulated BMDM (step 1). After a resting period, trained BMDM do not secrete significant levels of these cytokines (step 2), but rapidly produce enhanced levels of TNF and IL6 after secondary stimulation with LPS (stimulus 2), compared to BMDM stimulated with either β-glucan (step 3) or LPS (step 4) alone. In addition, the sum of cytokine levels produced by both BMDM stimulated with either β-glucan (stimulus 1) or LPS (stimulus 2) individually, was significantly lower than the cytokine levels produced by trained BMDM stimulated with both β-glucan and LPS (stimulus 1+2) (step 5). Our findings also demonstrate that trained BMDM produce higher levels of serum amyloid A3 (SAA3) protein due to metabolic and epigenetic reprogramming. Functionally, trained BMDM upregulate the expression of stimulatory molecules such as MHC-II, CD80, CD86, OX40L and PDL1; downregulate the inhibitory molecules ICOSL and CD206; and induce CD4+ and CD8+ T cell proliferation in vitro through a cell contact-dependent mechanism. Our results also revealed strain-specific differences in the training response among mice, the negative impact of cell cryopreservation on trained immunity, and the potential use of genetically modified mice in elucidating mechanistic pathways through which different training stimuli may induce long-lived memory macrophages. These results also highlight the applicability of mouse in vitro methods as an additional tool to study trained immunity, as the use of inbred mice reduce the genetic variability present in humans and minimize variables that affect trained immunity such as infections, vaccinations and lifestyle-related stimuli. The standardization of trained immunity protocols using murine BMDM will facilitate the development of therapeutic strategies that target the innate immune memory response for the treatment of multiple immune-based diseases.
Published in
In vitro protocol demonstrating five functional steps of trained immunity in mice: Implications on biomarker discovery and translational research
González-Pérez M, Baranda J, Pérez-Rodríguez L et al. · Cell reports 2025 · PMID 41014560 · doi:10.1016/j.celrep.2025.116202
This dataset
Open GSE290032 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 GSE290032_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 PRJNA1225843 and SRA study SRP565123. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41014560) ↗
Study design
6 × BMDMs from C57BL/6 mice cultured with M-CSF, naive vs 6 × BMDMs from C57BL/6 mice cultured with M-CSF, stimulated with 10 µg/mL β-glucan (day 0) and 10 ng/mL LPS (day 6) vs 5 × BMDMs from C57BL/6 mice cultured with M-CSF, stimulated with 10 ng/mL LPS (day 6)

Supports a case/control comparison: 11 samples read as cases, 6 as controls.

How we read this: 3 replicated groups read from 17 sample titles; they account for 17 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
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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.