Analysis of ATAC-seq Data from Human Microglia Isolated in a Xenotransplantation Model of Alzheimer’s Disease

In this report, we analyse the publicly available data set (PRJNA1131283) to explore differential chromatin accessibility between APOE genotypes.

Microglia play a pivotal role in clearing amyloid beta (Aß) deposits (Hampel et al., 2021, Mol Psychiatry) in Alzheimer’s disease (AD). Murphy and colleagues (Murphy et al., 2024, bioRxiv) hypothesised that APOE, the strongest genetic risk factor of late-onset AD, functionally alters the microglia’s response by regulating accessibility of chromatin regions. The authors generated Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) data from human microglia isolated from xenotransplantation models of AD to investigate chromatin accessibility of three APOE genotypes (APOE2/0, APOE3/0 and APOE4/0) and APOE knockout (APOE-KO). In this report, we analyse the publicly available data set (PRJNA1131283) to explore differential chromatin accessibility between APOE genotypes.

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