The gene-regulatory landscape of the brain is highly dynamic in health and disease, coordinating a menagerie of biological processes across distinct cell types. Understanding these regulatory programs requires a holistic experimental and analytical approach. Here, we present a single-cell study of 380,000 nuclei in late-stage Alzheimer’s Disease (AD) using parse biosciences whole transcriptome kit, profiling gene expression in thousands of genes and uncovering vast neuronal and glial heterogeneity in late-stage AD.