allen-sea-ad-atlas.yaml

Name: Seattle Alzheimer’s Disease Brain Cell Atlas (SEA-AD)
Description: |
  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 and is funded by the National Institutes on Aging (NIA U19AG060909). The SEA-AD datasets available here comprise single cell profiling (transcriptomics and epigenomics) and quantitative neuropathology. To explore gene expression and chromatin accessibility information, the single-cell profiling data includes: snRNAseq and snATAC-seq data from the SEA-AD donor cohort (aged brains which span the spectrum of Alzheimer's Disease pathology) and neurotypical reference brains. To explore key pathological proteins and cell types of interest to Alzheimer’s disease, the neuropathology data includes: full resolution brightfield images, images processed and segmented in HALO® image analysis software, image annotations, and quantification summary files for the relevant stains including Abeta (6E10), IBA1, a-Synuclein, GFAP, H&E-LFB, NeuN, pTau(AT8), and pTDP43.
Documentation: https://portal.brain-map.org/explore/seattle-alzheimers-disease/seattle-alzheimers-disease-brain-cell-atlas-download?edit&language=en
Contact: awspublicdataset@alleninstitute.org
ManagedBy: "[Allen Institute](http://www.alleninstitute.org/)"
UpdateFrequency: Annually
Tags: 
  - biology
  - cell biology
  - cell imaging
  - epigenomics
  - gene expression
  - histopathology 
  - Homo sapiens
  - imaging
  - medicine
  - microscopy
  - neurobiology
  - neuroscience
  - single-cell transcriptomics 
  - transcriptomics
License: https://alleninstitute.org/legal/terms-use/
Resources:
  - Description: Single cell profiling (transcriptomics and epigenomics) data files in a public bucket
    ARN: arn:aws:s3:::sea-ad-single-cell-profiling
    Region: us-west-2
    Type: S3 Bucket
    Explore:
    - '[Browse Bucket](https://sea-ad-single-cell-profiling.s3.amazonaws.com/index.html)'
  - Description: Quantitative neuropathology (full resolution images, processed images, and quantifications) in a public bucket
    ARN: arn:aws:s3:::sea-ad-quantitative-neuropathology
    Region: us-west-2
    Type: S3 Bucket
    Explore:
    - '[Browse Bucket](https://sea-ad-quantitative-neuropathology.s3.amazonaws.com/index.html)'
  - Description: Spatial transcriptomics data files in a public bucket
    ARN: arn:aws:s3:::sea-ad-spatial-transcriptomics
    Region: us-west-2
    Type: S3 Bucket
    Explore:
    - '[Browse Bucket](https://sea-ad-spatial-transcriptomics.s3.amazonaws.com/index.html)'
DataAtWork:
  Tools & Applications:
    - Title: Seattle Alzheimer’s Disease Brain Cell Atlas
      URL: http://sea-ad.org
      AuthorName: Lein, E et al.
      AuthorURL: www.alleninstitute.org