This dataset 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.
File
Size
Type
Description
197KB
Read-me file with additional information about the data set, taxonomy, and other files in this directory.
54MB
csv
Metadata about cells, including various cell type assignments and donor information.
9.4GB
csv
Gene expression matrix of counts (UMIs) provided as a csv (rows = genes; columns = cells).
4.4GB
RDS
Seurat (v4.0.4) object with the same UMI counts and cell metadata as in above files.
6.8GB
h5ad
AnnData hdf5 (version 0.7.8) file with the same UMI counts and cell metadata as in above files.
5.9GB
h5ad
AnnData hdf5 (version 0.7.8) file counts, metadata, UMAP coordinates, and other information for SEA-AD cells passing QC.
483KB
json
Serialized cluster hierarchy with all node information embedded (json format).
23KB
RDS
Serialized cluster hierarchy with all node information embedded (RDS format).
24MB
csv
Gene expression aggregated per cell type, calculated as trimmed means of log-normalized counts per million.
17MB
csv
Gene expression aggregated per cell type, calculated as medians of log-normalized counts per million.
9MB
csv
UMAP coordinates for each cell, as shown in the Transcriptomics Explorer, and the latent space that generated them.
105MB
csv
The trained scVI model used to project counts into the latent dimensions, which also can allow mapping of new data.
2MB
zip
Output files from applying CCN to this taxonomy, for linkage to other BICCN taxonomies.
1MB
zip
R scripts for generating some of these files based on gene expression matrix and cell metadata.
55MB
gtf
Standard format .gtf file for localizing various aspects of transcripts within a specific genome (CR6).
