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Epigenetic dysregulation of transposable elements in cognitive impairment and Alzheimer’s disease

GSE270454 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 135 samples Submitted 2024/08/01 Platform GPL24676
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 135 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
135 samples: 12 conditions, mostly with about 10 replicates eachGroups 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
Epigenetic dysregulation of transposable elements in cognitive impairment and Alzheimer's diseaseGeroScience · 2025
Summary (written by the submitters)
Growing evidence implicates transposable elements (TEs) in aging and Alzheimer’s disease (AD). To evaluate potential transcriptional and epigenetic differences related to TE expression in this context, we generated whole blood total RNA-seq, and peripheral blood cell whole-genome bisulfite sequencing (WGBS), and transposase-accessible chromatin sequencing (ATAC-seq) on samples from healthy middle-aged/older adults, mild cognitive impairment (MCI), and AD patients.
Published in
Epigenetic dysregulation of transposable elements in cognitive impairment and Alzheimer's disease
Cavalier AN, Smith ME, McWilliams GT et al. · GeroScience 2025 · PMID 40779089 · doi:10.1007/s11357-025-01765-9
This dataset
Open GSE270454 in finder → Find more human 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 GSE270454_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 PRJNA1126662 and SRA study SRP515320. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40779089) ↗
Study design
12 conditions, mostly with about 10 replicates each
Whole blood, older adult, ×14 WGBS Buffy coat, older adult, ×14 ATAC-seq Buffy coat, older adult, ×14 Whole blood, middle-aged/older adult, ×11 WGBS Buffy coat, middle-aged/older adult, ×11 ATAC-seq Buffy coat, middle-aged/older adult, ×11 Whole blood, MCI patient, ×10 Whole blood, AD patient, ×10 +4 more

Supports a between-group comparison across 135 samples.

How we read this: 12 replicated groups read from 135 sample titles; they account for 135 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

+ 95 more — browse all 135 samples with per-sample file links →

Datasets on a similar topic

Search all human RNA-seq 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.