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Seattle Alzheimer’s Disease Brain Cell Atlas

Seattle Alzheimer’s Disease Brain Cell Atlas (SEA-AD)

The Seattle Alzheimer’s Disease Brain Cell Atlas (SEA-AD) consortium strives to gain a deep molecular and cellular understanding of the early pathogenesis of Alzheimer’s disease. To accomplish this, we are leveraging advances in next-generation single-cell molecular profiling technologies developed through the BRAIN Initiative and at the Allen Institute for Brain Science. We are integrating single-cell profiling technologies with quantitative neuropathology and deep clinical phenotyping through collaboration with the University of Washington Alzheimer's Disease Research Center (ADRC) and Kaiser Permanente Washington Health Research Institute (KPWHRI), to create a multifaceted open data resource. We seek to understand the cellular and molecular changes that underlie Alzheimer’s disease initiation and progressive cognitive decline, with the ultimate goal of identifying targets for therapeutic intervention.

Explore The Data

Cell Types

Cellular level transcriptomic data has the power to help uncover and understand cell type vulnerabilities in Alzheimer’s and related diseases.

Two resources are provided to explore gene expression relationships in cell types of the middle temporal gyrus (MTG). For neurotypical reference brains and brains from the SEA-AD aged cohort that span the spectrum of Alzheimer’s disease, the SEA-AD Transcriptomics Comparative Viewer enables side by side comparison of gene expression in matched cells for any gene, comparison with essential donor metadata, and quantification of expression differences. The Transcriptomics Explorer shows the set of MTG brain cell types from younger neurotypical donors, illustrating the gene expression basis for defining cell types in the SEA-AD aged donor cohort.

Transcriptomics Comparative Viewer 

Transcriptomics Explorer (Reference MTG)

Donors and Neuropathology

Review demographic, clinical, cognitive, and neuropathological information on the Seattle Alzheimer's Disease Brain Cell Atlas (SEA-AD) cohort via the SEA-AD Donor Index. Data is derived from a full spectrum of aged donors, from healthy controls to those with high Alzheimer's disease pathology and dementia.

Examine images of donor brain tissue sections from the middle temporal gyrus (MTG) stained for key pathological proteins and cell types of interest to Alzheimer’s disease via the SEA-AD Neuropathology Image Viewer. Observe how quantitative measurements were made on stained tissue sections from the SEA-AD donors to assess pathological proteins, neuroinflammation, and neurodegeneration.

Data and specimens were obtained from the Adult Changes in Thought (ACT) Study from Kaiser Permanente Washington Health Research Institute (KPWHRI), and the University of Washington Alzheimer’s Disease Research Center (ADRC).

Donor Index

Neuropathology Image Viewer

Chan Zuckerberg CELL by GENE

Visualize and explore gene expression and metadata from the SEA-AD study using Chan-Zuckerberg CELL by GENE. CZ CELLxGENE is a tool that helps scientists to explore and visualize high dimensional single-cell datasets in an interactive way, allowing them to surface important information that could lead to discoveries in treating disease.

CZ CELLxGENE

Epigenetics: Chromatin Accessibility

Explore the open chromatin landscape and assess changes in chromatin accessibility as a function of Alzheimer's Disease neuropathological change by viewing single nucleus ATAC-seq data from the SEA-AD cohort in the UCSC Genome Browser.

UCSC Genome Browser - ATAC-seq data

Documentation, Data, and Downloads

Access to raw and processed data, quantifications, and documentation.

Documentation, Data, and Downloads





The Seattle Alzheimer's Disease Brain Cell Atlas (SEA-AD) consortium is supported by the National Institutes on Aging (NIA) grant U19AG060909.

 

Study data were generated from postmortem brain tissue obtained from the University of Washington BioRepository and Integrated Neuropathology (BRaIN) laboratory and Precision Neuropathology Core, which is supported by the NIH grants for the UW Alzheimer's Disease Research Center (NIA grants: P50AG005136 and P30AG066509) and the Adult Changes in Thought Study (NIA grants: U01AG006781 and U19AG066567).

 

The ACT study is a longitudinal population-based prospective cohort study of brain aging and incident dementia in the Seattle metropolitan area. ACT is a repository at the Kaiser Permanente Washington Health Research Institute, which has established policies and procedures for sharing data with external investigators. Data available from this study web site do not require any additional Institutional Review Board (IRB) approval or permissions. Linking those data with other ACT study or Kaiser Permanente Washington data would require additional review. All of those steps are initiated after contacting KPWA.actproposals@kp.org.