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Microglia innate immune memory is retained after enforced repopulation [ATAC-seq]

GSE270935 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 13 samples Submitted 2025/05/01 Platform GPL19057
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 13 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
13 samples: 13 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.
Paper
Microglia endotoxin tolerance is retained after enforced repopulationBrain, behavior, and immunity · 2025
Summary (written by the submitters)
Microglia are crucial for CNS homeostasis and involved in a wide range of neurodegenerative and neuroinflammatory diseases. Systemic inflammation and infections can contribute to neurodegeneration later in life by affecting microglia. Like other innate immune cells, microglia can develop innate immune memory in response to a challenge, altering their response to future stimuli.
Read the full summary ↓
Innate immune memory can ameliorate or worsen CNS pathology, but its persistence is unclear. Recently, several methods have been developed to stimulate microglia turnover. Here, we investigated whether colony-stimulating factor 1 (CSF1R)-dependent microglia depletion followed by repopulation reversed microglial tolerance to systemic inflammation in mice. Repopulated microglia displayed a reduced expression of homeostatic genes and genes related to mitochondrial respiration and TCA cycle metabolism and an increased expression of immune effector and activation genes. Nonetheless, the blunted inflammatory gene expression induced by the LPS-preconditioning was retained after a depletion-repopulation cycle. Our study highlights the persistence of epigenetic changes underlying microglial tolerance and indicates potential implications of microglia depletion and repopulation therapies on microglia functions.
Published in
Microglia endotoxin tolerance is retained after enforced repopulation
Medeiros-Furquim T, Miedema A, Schilder E et al. · Brain, behavior, and immunity 2025 · PMID 40274001 · doi:10.1016/j.bbi.2025.04.014
This dataset
Open GSE270935 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 GSE270935_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 PRJNA1129070 and SRA study SRP516579. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40274001) ↗
Study design
13 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 13 sample titles: 13 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
Datasets on a similar topic

Search all mouse ChIP / ATAC / CUT&Tag datasets in GEO →

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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.