The APOE isoforms differentially shape the transcriptomic and epigenomic landscapes of human microglia in a xenotransplantation model of Alzheimer’s disease [ATAC-seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 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
- Homo sapiens (human)
- 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
- The APOE isoforms differentially shape the transcriptomic and epigenomic landscapes of human microglia xenografted into a mouse model of Alzheimer's diseaseNature communications · 2025
Read the full summary ↓
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 GSE271384_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 PRJNA1131283 and SRA study SRP517720. 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 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.
- GSM8375867 Microglia, APOE2, replicate 1 [ATAC-seq]
- GSM8375868 Microglia, APOE2, replicate 2 [ATAC-seq]
- GSM8375869 Microglia, APOE2, replicate 3 [ATAC-seq]
- GSM8375870 Microglia, APOE2, replicate 4 [ATAC-seq]
- GSM8375871 Microglia, APOE2, replicate 5 [ATAC-seq]
- GSM8375872 Microglia, APOE3, replicate 1 [ATAC-seq]
- GSM8375873 Microglia, APOE3, replicate 2 [ATAC-seq]
- GSM8375874 Microglia, APOE3, replicate 3 [ATAC-seq]
- GSM8375875 Microglia, APOE3, replicate 4 [ATAC-seq]
- GSM8375876 Microglia, APOE3, replicate 5 [ATAC-seq]
- GSM8375877 Microglia, APOE4, replicate 1 [ATAC-seq]
- GSM8375878 Microglia, APOE4, replicate 2 [ATAC-seq]
- GSM8375879 Microglia, APOE4, replicate 3 [ATAC-seq]
- GSM8375880 Microglia, APOE4, replicate 4 [ATAC-seq]
- GSM8375881 Microglia, APOE4, replicate 5 [ATAC-seq]
- GSM8375882 Microglia, APOE-KO, replicate 1 [ATAC-seq]
- GSM8375883 Microglia, APOE-KO, replicate 2 [ATAC-seq]
- GSM8375884 Microglia, APOE-KO, replicate 3 [ATAC-seq]
- GSM8375885 Microglia, APOE-KO, replicate 4 [ATAC-seq]
- GSM8375886 Microglia, APOE-KO, replicate 5 [ATAC-seq]
- GSE271385 The APOE isoforms differentially shape the transcriptomic and epigenomic landscapes of human microglia in a xenotransplantation model of Alzheimer’s disease [RNA-seq] 19 samples shares apoe, xenotransplantation, differentially, epigenomic, landscapes, microglia, alzheimer, isoforms
- GSE254205 APOE4/4 is linked to damaging lipid droplets in Alzheimer's microglia 102 samples shares apoe, microglia, alzheimer
- GSE243743 SEX-DEPENDENT APOE4 NEUTROPHIL-MICROGLIA INTERACTIONS DRIVE COGNITIVE IMPAIRMENT IN ALZHEIMER'S DISEASE [Human_F_M_HC_MCI_AD_E33_34] 94 samples shares apoe, microglia, alzheimer
- GSE243744 SEX-DEPENDENT APOE4 NEUTROPHIL-MICROGLIA INTERACTIONS DRIVE COGNITIVE IMPAIRMENT IN ALZHEIMER'S DISEASE [Human_Female_HC_MCI_APOE23_33_34] 47 samples shares apoe, microglia, alzheimer
- GSE260461 Sex-dependent APOE4 Neutrophil-microglia interactions drive cognitive impairment in Alzheimer's Disease 39 samples shares apoe, microglia, alzheimer
- GSE250249 LPS stimulation of APOE knock-out iPSC-derived microglia with different ApoE isoforms 24 samples shares apoe, microglia, isoforms
- GSE243745 SEX-DEPENDENT APOE4 NEUTROPHIL-MICROGLIA INTERACTIONS DRIVE COGNITIVE IMPAIRMENT IN ALZHEIMER'S DISEASE [Human_IL18R1] 10 samples shares apoe, microglia, alzheimer
- GSE237718 APOE determines cell type-specific pathological landscape of Alzheimer's disease 56 samples shares apoe, alzheimer
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.