Transcriptomic and chromatin profiling of familial Alzheimer’s disease mutations in PSEN1, PSEN2, APP
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 24 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
- 24 samples: 24 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
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.
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.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE206603_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA851445 and SRA study SRP382946. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 24 sample titles: 24 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.
- GSM6257296 NDC replicate 1 [ATAC-seq]
- GSM6257297 NDC replicate 2 [ATAC-seq]
- GSM6257298 NDC replicate 3 [ATAC-seq]
- GSM6257299 APP-V717I replicate 1 [ATAC-seq]
- GSM6257300 APP-V717I replicate 2 [ATAC-seq]
- GSM6257301 APP-V717I replicate 3 [ATAC-seq]
- GSM6257302 PSEN1-A79V replicate 1 [ATAC-seq]
- GSM6257303 PSEN1-A79V replicate 2 [ATAC-seq]
- GSM6257304 PSEN1-A79V replicate 3 [ATAC-seq]
- GSM6257305 PSEN2-N141I replicate 1 [ATAC-seq]
- GSM6257306 PSEN2-N141I replicate 2 [ATAC-seq]
- GSM6257307 PSEN2-N141I replicate 3 [ATAC-seq]
- 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]
- GSE204912 Mapping genotypes to chromatin accessibility profiles in single cells 55 samples shares app, chromatin
- GSE204911 Mapping genotypes to chromatin accessibility profiles in single cells [Genotyping GoT-ChA amplicon] 27 samples shares app, chromatin
- GSE268035 STAG2 Mutations Reshape the Cohesin-Structured Spatial Chromatin Architecture to Drive Gene Regulation in Acute myeloid Leukemia 541 samples shares chromatin, mutations
- GSE240343 STAG2 mutations and 3D genome organization, chromatin loops, and polycomb signaling in glioblastoma multiforme 20 samples shares chromatin, mutations
- GSE304074 RAD51 proximity mapping reveals spatial constraints on homology search during DNA double-stranded break repair 118 samples shares app
- GSE330130 A multi-omics characterization of the human lumbar spinal cord and motor cortex reveals non-overlapping molecular signatures in ALS [snRNA-Seq; snATAC-Seq] 87 samples shares app
- GSE264314 Topical application of Urolithin A slows intrinsic skin aging and protects from UVB-mediated photodamage: Findings from Randomized Clinical Trials 57 samples shares app
- GSE296831 Epigenetic Context Defines the Transcriptional Activity of Canonical and Noncanonical NF-kappaB Signaling in Pancreatic Cancer [ChIP-Seq] 48 samples shares app
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.