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Alzheimer's Disease Data (SEA-AD)

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.)

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).

 

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 .pdf
SEA-AD cohort selection information, inclusion/exclusion criteria
SEA-AD cohort metadata summary graphs 514KB .pdf
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 .pdf Methods for 10x snRNASeq, snATACseq, and Multiome data generation and RNA Integrity Number (RIN) determination
Transcriptomics: Post-sequencing data analysis 153KB .pdf Methods for transcriptomics data analysis. Information on development of web tools, which present transcriptomic data. 
Donor metadata brief descriptions 90KB .pdf Brief descriptions for the donor metadata elements.
Donor metadata citations 123KB .pdf
Citations for select donor metadata elements 
Consensus clinical diagnosis 136KB .pdf Information on clinical AD detection and consensus clinical diagnosis generation.
Dissection, MRI, neuropathological analysis 108KB .pdf Citation for dissection, ex vivo MRI, tissue preparation, and neuropathological analysis.
Information on processed single cell profiling data 217KB .pdf Methods information and tutorial for processed single cell profiling data available on AWS
Information on neuropathology images and image analysis data 764KB .pdf Methods information and tutorial for neuropathology images and image analysis data available on AWS
Cell type taxonomy change-log 764KB .pdf Translation table between initial cell type names used in Comparative Viewer and CELLxGENE and official names used everywhere else.