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.
Download
General
| File | Size | Type | Description |
|---|---|---|---|
| README | 197KB | 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 | 9.4GB | csv | Gene expression matrix of counts (UMIs) provided as a csv (rows = genes; columns = cells). |
| Seurat object (all data and metadata) | 4.4GB | RDS | Seurat (v4.0.4) object with the same UMI counts and cell metadata as in above files. |
| AnnData Object (all data and metadata) | 6.8GB | 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) | 5.9GB | 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). |
Your browser is out-of-date!
Update your browser to view this website correctly.