Alzheimer's Disease Data (SEA-AD)
This repository is under review for potential modification in compliance with Administration directives.
Seattle Alzheimer's Disease Brain Cell Atlas (SEA-AD) Study Documentation, Data, and Downloads
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. This page includes links to access and download raw and processed data generated as part of SEA-AD, along with documentation describing aspects of data generation from cohort selection to tissue processing, to detailed protocols for collecting and analyzing data from each modality.
Access and download data
SEA-AD includes data from multiple brain regions and data modalities. All of the data included in our public resources, along with additional data not yet fully analyzed is freely and publicly available online. This graphic summarizes all data currently available:
Values of A+B indicate the number of SEA-AD and reference donors, respectively. Abbreviations: MTG, middle temporal gyrus; A9 (also called PFC), prefrontal cortex; STG, superior temporal gyrus; V1C, primary visual cortex; MEC/LEC/EC, medial/lateral entorhinal cortex; HIP, hippocampal formation; ITG, Inferior temporal gyrus.
The table below includes a series of files or links out to all SEA-AD data. We provide these data to the research community. Accessing, downloading, and/or using these files must be done in accordance with the Allen Institute Terms of Use and the terms of our external partners. To use our resources, you must cite them in accordance with our Allen Institute Citation Policy. To cite a dataset, cite both the primary publication and the specific dataset. Citation of the primary publication, where one exists, is required when citing the data resource in a scientific publication.
Data
| File | Size | Type | Description |
|---|---|---|---|
| Donor metadata | 44 KB | .xlsx |
Donor metadata (demographic, clinical, cognitive, and neuropathological data) |
| Link to raw single nucleus data | link |
Link to Sage Bionetworks AD Knowledge Portal SEA-AD study page. Controlled access to raw 10x snRNASeq, snATACseq, and Multiome data. |
|
| Link to processed single nucleus RNAseq and ATAC-seq data | link |
Link to processed single cell data on AWS. Open access to processed 10x snRNAseq and snATAC-seq data. |
|
| MRI volumetrics | 64KB | .xlsx | Post mortem MRI brain volumetrics. |
| Luminex (ABeta and Tau, MTG) | 24KB | .xlsx | Luminex data: ABeta and Tau measurements for Middle Temporal Gyrus (MTG). |
| Quantitative neuropathology summary data (MTG) | 253KB | .csv | Measurements of Abeta, pTau, pTDP43, a-synuclein, Neun+ cells, IBA1+ cells, and GFAP+ cells from quantitative analysis of stained neuropathology images from Middle Temporal Gyrus (MTG). |
| Neuropathology: raw and analyzed/annotated image files | link | Link to neuropathology image files on AWS. Download raw and quantified (stained images annotated and masked via the HALO image analysis software from Indica Labs). | |
| Link to spatial transcriptomics (MERFISH) data | link | Link to spatial transcriptomics: Multiplexed Error-Robust Fluorescence in situ Hybridization (MERFISH) data on AWS. | |
| Cell ID conversion for ABC Atlas | 233MB | .csv | Conversion table between cell ids used in the ABC Atlas and cell labels used in all other locations for single cell and MERFISH data sets in MTG and prefrontal cortex (A9). |
| Harmonized cognitive scores | 71KB | .xlsx | Available harmonized cogntive scores for the SEA-AD cohort. The dataset includes composite scores for memory, executive functioning, language, and visuospatial ability at each visit and their slope of overall. Each of the domains was psychometrically co-calibrated across the Adult Changes in Thought (ACT) study, the Alzheimer’s Disease Neuroimaging Initiative (ADNI), the Religious Orders Study (ROS), the Memory and Aging Project (MAP), and the University Of Pittsburgh (PITT) study. |
| Link to Mouse Mesoscale Connectivity project | link | Link to the landing page for the Mouse Mesoscale Connectivity in Aging and Alzheimer’s Disease project (unaffiliated with SEA-AD). This project involved quantifying brain-wide axonal projections and amyloid pathology in mouse models of AD and their aged littermates. |
Access the white papers
White papers’ documenting various aspects of SEA-AD cohort and data generation. Links and associated descriptions are shown in the table below.
Documentation
| File | Size | Type | Description |
|---|---|---|---|
| SEA-AD cohort information | 99KB |
SEA-AD cohort selection information, inclusion/exclusion criteria |
|
| SEA-AD cohort metadata summary graphs | 514KB |
Graphs summarizing the SEA-AD cohort's age at death, sex, APOE4 status, cognitive status, CERAD score, ADNC score, Braak stage, and Thal phase. |
|
| Transcriptomics and epigenomics data generation | 95KB | Methods for 10x snRNASeq, snATACseq, and Multiome data generation and RNA Integrity Number (RIN) determination | |
| Transcriptomics: Post-sequencing data analysis | 153KB | Methods for transcriptomics data analysis. Information on development of web tools, which present transcriptomic data. | |
| Donor metadata brief descriptions | 90KB | Brief descriptions for the donor metadata elements. | |
| Donor metadata citations | 123KB |
Citations for select donor metadata elements |
|
| Consensus clinical diagnosis | 136KB | Information on clinical AD detection and consensus clinical diagnosis generation. | |
| Dissection, MRI, neuropathological analysis | 108KB | Citation for dissection, ex vivo MRI, tissue preparation, and neuropathological analysis. | |
| Information on processed single cell profiling data | 217KB | Methods information and tutorial for processed single cell profiling data available on AWS | |
| Information on neuropathology images and image analysis data | 764KB | Methods information and tutorial for neuropathology images and image analysis data available on AWS | |
| Cell type taxonomy change-log | 764KB | Translation table between initial cell type names used in Comparative Viewer and CELLxGENE and official names used everywhere else. |
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