GEO series

Neuronal type-specific modulation of cognition and AP-1 signaling by early-life rearing conditions. [ATAC-Seq]

GSE288332 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 18 samples Submitted 2025/09/23 Platform GPL17021

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: 6 conditions, mostly in triplicateGroups 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: Neuronal type-specific modulation of cognition and AP-1 signaling by early-life rearing conditionsNature communications · 2025

Summary (written by the submitters)

Environmental conditions profoundly influence cognitive development, particularly during early life. Transcriptional and epigenetic mechanisms may serve as molecular substrates for the lasting effects of environmental enrichment (EE) and impoverished environment (IE) on cognitive abilities and hippocampal function. However, the specific gene programs driving these changes remain largely unknown.

Read the full summary ↓

In this study, we employed EE and IE paradigms to modulate cognitive abilities in opposing directions in mice. By combining hippocampal microdissection and genetic tagging of neuronal nuclei with genome-wide analyses of gene expression, chromatin accessibility, histone acetylation, and DNA methylation, we uncovered cell type-specific genomic changes induced by EE and IE in CA1 pyramidal neurons and dentate gyrus (DG) granule neurons. This multiomic screen identified the activity-regulated transcription factor AP-1 as a crucial mediator of neuroadaptation to environmental conditions during early life in both neuronal populations, albeit through distinct downstream mechanisms. Conditional deletion of Fos, a core AP-1 subunit, in excitatory neurons hampered EE-induced cognitive enhancement, further underscoring the pivotal role of this transcription factor in neuroadaptation.

Published in

Neuronal type-specific modulation of cognition and AP-1 signaling by early-life rearing conditions

Alaiz-Noya M, Miozzo F, Fuentes-Ramos M et al. · Nature communications 2025 · PMID 41193527 · doi:10.1038/s41467-025-65343-5

This dataset

Open GSE288332 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 GSE288332_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 PRJNA1216951 and SRA study SRP560583. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41193527) ↗

Study design

6 conditions, mostly in triplicate

ATAC, CA1, EE, ×3 ATAC, CA1, SC, ×3 ATAC, CA1, IE, ×3 ATAC, DG, EE, ×3 ATAC, DG, SC, ×3 ATAC, DG, IE, ×3

Supports a between-group comparison across 18 samples.

How we read this: 6 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

GSM8765491 ATAC, CA1, EE, rep1 ATAC, CA1, EE,
GSM8765492 ATAC, CA1, EE, rep2 ATAC, CA1, EE,
GSM8765493 ATAC, CA1, EE, rep3 ATAC, CA1, EE,
GSM8765494 ATAC, CA1, SC, rep1 ATAC, CA1, SC,
GSM8765495 ATAC, CA1, SC, rep2 ATAC, CA1, SC,
GSM8765496 ATAC, CA1, SC, rep3 ATAC, CA1, SC,
GSM8765497 ATAC, CA1, IE, rep1 ATAC, CA1, IE,
GSM8765498 ATAC, CA1, IE, rep2 ATAC, CA1, IE,
GSM8765499 ATAC, CA1, IE, rep3 ATAC, CA1, IE,
GSM8765500 ATAC, DG, EE, rep1 ATAC, DG, EE,
GSM8765501 ATAC, DG, EE, rep2 ATAC, DG, EE,
GSM8765502 ATAC, DG, EE, rep3 ATAC, DG, EE,
GSM8765503 ATAC, DG, SC, rep1 ATAC, DG, SC,
GSM8765504 ATAC, DG, SC, rep2 ATAC, DG, SC,
GSM8765505 ATAC, DG, SC, rep3 ATAC, DG, SC,
GSM8765506 ATAC, DG, IE, rep1 ATAC, DG, IE,
GSM8765507 ATAC, DG, IE, rep2 ATAC, DG, IE,
GSM8765508 ATAC, DG, IE, rep3 ATAC, DG, IE,

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GSE200461 The maternal X chromosome impairs cognition and accelerates brain aging through epigenetic modulation in female mice 30 samples shares modulation, cognition
GSE270835 Sex-Specific modulation of Anxiety-Like behavior by Forebrain Neuronal SMC3 in Mice 22 samples shares modulation, neuronal

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