Downloading and exploring -omics data from SEA-AD

How To
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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. As part of this effort, >2 million cells were collected using singleome and multiome snRNA-seq and snATAC-seq methodologies. All data is freely and publicly accessible online for download, and several tools have been developed for exploration of this data. As of November 2022, all shared data is from middle temporal gyrus (MTG), but data from additional brain regions will be included in the future.

This post aims to address several questions we’ve received about where to download and explore single nucleus omics data sets and exploration tools for this and related projects. If you still have questions about the SEA-AD omics data, please reply to this post.

Data exploration

This section includes links for on-line data exploration. If you’d like to work with our data on your own computer, please download it from one of the links in the next section.

  • Reference taxonomy: The Transcriptomics Explorer shows the set of reference brain cell types from younger neurotypical donors, illustrating the gene expression basis for defining cell types in the SEA-AD aged donor cohort.
  • SEA-AD cohort, compare gene expression: The 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.
  • SEA-AD cohort, explore gene expression: Visualize and explore gene expression and metadata from the SEA-AD study using Chan-Zuckerberg CELL by GENE.
  • SEA-AD cohort, visualize 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.

Data download

This section includes links for data and metadata access for download and off-line use.

  • Donor metadata: Donor metadata (as well as links to all of the other items in this section) is available via the main SEA-AD documentation page.
  • Reference taxonomy (processed data): Single-nucleus transcriptomes from 166,868 total nuclei derived from 5 younger healthy donors are available for download from the Cell Types Database: RNA-Seq Data “Human MTG 10x SEA-AD” page. This taxonomy of 127 transcriptomic supertypes is used to map all data omics data from the aged SEA-AD cohort.
  • SEA-AD cohort, -omics data (processed data): snRNA-seq and snATAC-seq data (both singleome and multiome) from 84 aged donors in the SEA-AD cohort are available for download from the Registry of Open Data on AWS. Details of the included files and some use cases are included in the SEA-AD documentation.
  • Cell metadata: Cell metadata is included with the count matrix as part of the above downloads for processed data.
  • Raw -omics data (e.g., FASTQ files): All snRNA-seq, snATAC-seq and multiome data described above is accessible via controlled access from the Sage Bionetworks AD Knowledge Portal SEA-AD study page.
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Hi, I was wondering if the dotplot in the SEA-AD functions as it is supposed to function? For none of the genes that I’m inputting I can see that there is a significant difference on ‘cognitive status’, or any other metdata which is supposed to be highlighted with an * in the dotplot. I only observe differential expressions in subclasses. Of course it could be my genes of interest, but I have checked quite some genes already and have never seen a difference.

Thanks!

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Hi @lcn. Few genes show significant relationships with cognitive status (or related meta-data), and those that do are typically quite subtle and hard to parse visually in the dot plot. We are working on presenting gene expression data in a way that better highlights relationships between gene expression and disease metrics and hope to have new visualizations soon.