GEO series

Gene expression + ATAC multiome profiling of mPFC engram cells after OSK partial reprogramming

GSE276656 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 20 samples Submitted 2026/02/10 Platform GPL24247

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 20 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: 20 samples: 20 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: Cognitive rejuvenation through partial reprogramming of engram cellsNeuron · 2026

Summary (written by the submitters)

Counteracting cognitive decline is an important goal in regenerative medicine. Recently, partial cellular reprogramming has emerged as a promising strategy to restore cellular function and promote tissue regeneration, but whether this approach can also reverse cognitive frailty is not known. In old mice and mouse models of Alzheimer’s Disease (AD) engram cells responsible for memory formation are functionally impaired, which prompted us to test the potential of their reprogramming to recover cognitive capacities.

Read the full summary ↓

Here, by performing single nucleis multiome sequencing on the mPFC of the APP/PS1 AD mouse model, we found that partial reprogramming of its engram cells re-established aberrant epigenetic and transcriptional alterations.

Published in

Cognitive rejuvenation through partial reprogramming of engram cells

Berdugo-Vega G, Sierra C, Astori S et al. · Neuron 2026 · PMID 41672073 · doi:10.1016/j.neuron.2025.11.028

This dataset

Open GSE276656 in finder → Find more mouse RNA-seq 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 GSE276656_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 PRJNA1158460 and SRA study SRP531369. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41672073) ↗

Study design

20 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 20 sample titles: 20 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

GSM8503729 WT mPFC, replicate 1, snRNAseq
GSM8503730 WT mPFC, replicate 2, snRNAseq
GSM8503731 WT mPFC, replicate 3, snRNAseq
GSM8503732 APP/PS1 mPFC, replicate 1, snRNAseq
GSM8503733 APP/PS1 mPFC, replicate 2, snRNAseq
GSM8503734 APP/PS1 mPFC, replicate 3, snRNAseq
GSM8503735 APP/PS1 + OSK mPFC, replicate 1, snRNAseq
GSM8503736 APP/PS1 + OSK mPFC, replicate 2, snRNAseq
GSM8503737 APP/PS1 + OSK mPFC, replicate 3, snRNAseq
GSM8503738 APP/PS1 + OSK mPFC, replicate 4, snRNAseq
GSM8503739 WT mPFC, replicate 1, snATACseq
GSM8503740 WT mPFC, replicate 2, snATACseq
GSM8503741 WT mPFC, replicate 3, snATACseq
GSM8503742 APP/PS1 mPFC, replicate 1, snATACseq
GSM8503743 APP/PS1 mPFC, replicate 2, snATACseq
GSM8503744 APP/PS1 mPFC, replicate 3, snATACseq
GSM8503745 APP/PS1 + OSK mPFC, replicate 1, snATACseq
GSM8503746 APP/PS1 + OSK mPFC, replicate 2, snATACseq
GSM8503747 APP/PS1 + OSK mPFC, replicate 3, snATACseq
GSM8503748 APP/PS1 + OSK mPFC, replicate 4, snATACseq

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