GEO series

Transcriptomic and chromatin profiling of familial Alzheimer’s disease mutations in PSEN1, PSEN2, APP [RNA-seq]

GSE206602 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2025/01/06 Platform GPL20301

At a glance

RNA-seq (gene expression) · human · 12 samples

What it is: RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism: Homo sapiens (human)
Samples: 12 samples: 12 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: Integrative multiomics reveals common endotypes across PSEN1, PSEN2, and APP mutations in familial Alzheimer's diseaseAlzheimer's research & therapy · 2025

Summary (written by the submitters)

Mutations in PSEN1, PSEN2, and APP cause familial Alzheimer’s Disease (FAD) with an early age at onset and progressive cognitive decline. We mechanistically characterize mutations in these three FAD genes using patient-derived neurons by integrating RNA- and ATAC-sequencing. Here, we demonstrate that FAD mutations share common disease endotypes with varying severity, particularly activation of non-ectoderm lineage and loss of neuron mitochondrial energy production, paving the way for potential therapeutic interventions.

Published in

Integrative multiomics reveals common endotypes across PSEN1, PSEN2, and APP mutations in familial Alzheimer's disease

Valdes P, Caldwell AB, Liu Q et al. · Alzheimer's research & therapy 2025 · PMID 39754192 · doi:10.1186/s13195-024-01659-6

This dataset

Open GSE206602 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 GSE206602_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA851439 and SRA study SRP382946. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39754192) ↗

Study design

12 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 12 sample titles: 12 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

GSM6257605 NDC replicate 1 [RNA-seq]
GSM6257606 NDC replicate 2 [RNA-seq]
GSM6257607 NDC replicate 3 [RNA-seq]
GSM6257608 APP-V717I replicate 1 [RNA-seq]
GSM6257609 APP-V717I replicate 2 [RNA-seq]
GSM6257610 APP-V717I replicate 3 [RNA-seq]
GSM6257611 PSEN1-A79V replicate 1 [RNA-seq]
GSM6257612 PSEN1-A79V replicate 2 [RNA-seq]
GSM6257613 PSEN1-A79V replicate 3 [RNA-seq]
GSM6257614 PSEN2-N141I replicate 1 [RNA-seq]
GSM6257615 PSEN2-N141I replicate 2 [RNA-seq]
GSM6257616 PSEN2-N141I replicate 3 [RNA-seq]

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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.