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Human MTG 10x SEA-AD

This data set includes single-nucleus transcriptomes from 166,868 total nuclei derived from 5 post-mortem human brain specimens, to survey cell type diversity in the middle temporal gyrus (MTG). In total, 127 transcriptomic supertypes were identified. 

The Seattle Alzheimer's Disease Brain Cell Atlas (SEA-AD) consortium includes the Allen Institute for Brain Science, the University of Washington, and Kaiser Permanente Washington Health Research Institute and is supported by the National Institutes on Aging (NIA) grant U19AG060909.The content on this page is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

 

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General
File Size Type Description
README 197KB pdf Read-me file with additional information about the data set, taxonomy, and other files in this directory.
Cell metadata 54MB csv Metadata about cells, including various cell type assignments and donor information.
Gene expression matrix - coming soon   csv Gene expression matrix of counts (UMIs) provided as a csv (rows = genes; columns = cells).
Seurat object (all data and metadata) - coming soon   RDS Seurat (v4.0.4) object with the same UMI counts and cell metadata as in above files.
AnnData Object (all data and metadata) - coming soon   h5ad AnnData hdf5 (version 0.7.8) file with the same UMI counts and cell metadata as in above files.
AnnData Object (QC'ed data, metadata, and more) - coming soon   h5ad AnnData hdf5 (version 0.7.8) file counts, metadata, UMAP coordinates, and other information for SEA-AD cells passing QC.
Taxonomy of clusters 483KB json Serialized cluster hierarchy with all node information embedded (json format).
Taxonomy of clusters 23KB RDS Serialized cluster hierarchy with all node information embedded (RDS format).
Gene expression by cell type, trimmed means 24MB csv Gene expression aggregated per cell type, calculated as trimmed means of log-normalized counts per million.
Gene expression by cell type, medians 17MB csv Gene expression aggregated per cell type, calculated as medians of log-normalized counts per million.
2D coordinates (UMAP) + latent space (scVI) 9MB csv UMAP coordinates for each cell, as shown in the Transcriptomics Explorer, and the latent space that generated them.
scVI Model 105MB csv The trained scVI model used to project counts into the latent dimensions, which also can  allow mapping of new data.
Common Cell type Nomenclature (CCN) output 2MB zip Output files from applying CCN to this taxonomy, for linkage to other BICCN taxonomies.
Reproducibility scripts 1MB zip R scripts for generating some of these files based on gene expression matrix and cell metadata.
Gene transfer format 55MB gtf Standard format .gtf file for localizing various aspects of transcripts within a specific genome (CR6).