Epilepsy study with ATAC-seq, ChIP-Seq + 2 more data on dbGaP (89 participants)

phs001373 — Brain Cell Type-Specific Enhancer-Promoter Connectivity Maps and Disease    Risk Association

<p>These studies map the epigenetic landscape of microglia, neurons, astrocytes and oligodendrocytes. The initial study compared acutely isolated microglia to cultured microglia from the same donors, to identify changes that occur when microglia are removed from the brain microenvironment. In collaboration with the <a href="https://www.rchsd.org/">Rady Children's Hospital</a>, we obtained brain tissue samples from pediatric patients representing putative normal tissue resected to gain access to brain tumors as well as tissue resected to remove epileptic foci. We assayed microglia isolated from these samples using RNA-seq, ATAC-seq and ChIP-seq for PU.1, H3K4me2, and H3K27ac. For patients from whom a sufficient cell number was obtained, we additionally cultured their microglia for up to 7 days and subjected these to the same suite of assays. In a follow-up study, we obtained brain tissue from a comparable cohort of pediatric epilepsy patients from <a href="https://www.rchsd.org/">Rady Children's Hospital</a>. We isolated nuclei from microglia, neurons, astrocytes and oligodendrocytes, and assayed for ATAC-seq, ChIP-seq for H3K4me3, and H3K27ac, and PLAC-seq (Proximity Ligated ChIP-seq). We isolated microglia from human fetal and postnatal sample and assayed for bulk RNA-seq, bulk ATAC-seq, bulk H3K27ac ChIP-seq, single-cell RNA-seq (scRNA-seq) and single-cell ATAC-seq. For these studies, human microglia are defined by signature genes/proteins, such as <a href="https://www.ncbi.nlm.nih.gov/gene/64805">P2RY12</a>, <a href="https://www.ncbi.nlm.nih.gov/gene/6299">SALL1</a>, and <a href="https://www.ncbi.nlm.nih.gov/gene/1524">CX3CR1</a>.</p>