This supplement to our R01AG076949 aims to harmonize and jointly analyze our multiome datasets from 100 neurotypical normally aging (NA) subjects from adolescence into the 90s, and 40 Alzheimer’s Disease (AD) brains, with BRAIN Initiative-generated datasets from human brain tissue. We are implementing high resolution mass spectrometry (HRMS) (Stephens et al., 2018; Wobma et al., 2018a; Wobma et al., 2018b), 10X Genomics single nuclei RNA sequencing (snRNA-seq), sn Assay for Transposase-Accessible Chromatin sequencing (snATAC-seq), Visium spatial transcriptomics (10X Genomics), and our custom-made slide-seq technology, using deterministic barcoding in tissue for spatial omics sequencing (DBiT-seq), for co-mapping mRNAs and proteins (Liu et al., 2020), ATAC spatial sequencing (Deng et al., 2022) and RNA-ATAC co-profiling (Zhang et al., 2023). We will integrate our data with publicly available datasets from GEO (Gene Expression Omnibus), SCORCH (Single Cell Opioid Responses in the Context of HIV), PsychENCODE Consortium, NeMO (Neuroscience Multi-Omic Data Archive), SEA-AD (Seattle Alzheimer’s Disease Brain Cell Atlas), Psych-AD (Neuropsychiatric Symptoms in Alzheimer’s Disease) and the BICCN (BRAIN Initiative Cell Census Network). We will include external datasets on hippocampus and other brain regions, to implement analyses on gene regulatory networks (GRNs) that are common to neurons and glial cells across brain regions, and identify GRNs that synergistically regulate functional brain circuits involved in cognitive, emotional, and behavioral changes in AD. The hippocampus, fundamental for memory, the amygdala, regulating emotional responses to stress and “fight or flight” reactions, and the prefrontal cortex (PFC), involved in set shifting, attentional control, and decision making, are all progressively affected in AD, and they are involved in AD neuropsychiatric symptoms (NPS), such as disinhibition, impulsivity, anxiety, emotional distress, aggression, paranoid ideation, and other psychotic symptoms. Understanding how those brain regions are regulated by cell-type specific epigenetic and gene expression changes, will shed light on molecular mechanisms of AD pathogenesis and provide targets for new therapeutic approaches to AD and NPS in AD. This supplement is within the scope of the active award and improves the discovery potential of our dataset. This project will provide scalable pipelines for analyzing multimodal and spatial omics cell profiling datasets, and will deliver a developmental and adult cell atlas of cell type diversity. It will provide information on the regulome, the interaction between regulatory components that control the state of expression of genes and their isoforms, their subcellular location, tissue state, development, and pathology. These regulatory mechanisms include DNA accessibility for gene transcription, DNA methylation, transcription factors that regulate gene transcription, RNA-protein interactions, and non-coding...