MapMyCells: Cell type references

10x Whole mouse brain taxonomy (CCN20230722)

Name: A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain

Species: Mouse

Description: The Mouse Whole Brain Atlas is a high-resolution transcriptomic and spatial cell-type atlas across the entire mouse brain, integrating several whole-brain single-cell RNA-sequencing (scRNA-seq) datasets. The datasets contain a total of ~4 million cells passing rigorous quality-control (QC) criteria. The integrated transcriptomic taxonomy contains 5,322 clusters that are organized in a hierarchical manner with nested groupings of 34 classes, 338 subclasses, 1,201 supertypes and 5,322 types/clusters. The scRNA-seq data reveal transcriptome-wide gene expression and co-expression patterns for each cell type. The anatomical location of each cell type has been annotated using a comprehensive brain-wide MERFISH dataset with a total of ~4 million segmented and QC-passed cells, probed with a 500-gene panel and registered to the Allen Mouse Brain Common Coordinate Framework (CCF v3). Learn more... .

Additional resources:

• Download the data on GitHub.

• Explore the scRNA-seq and MERFISH data using the ABC Atlas

• To learn more about cell type annotations including cell type hierarachy, marker genes, anatomic locations, and more, download this detailed cell type annotation table.

• See what the abbreviations mean through this table.

Citation: Yao Z., et al. A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain. Nature; 624, 317-332 (2023). Available from: https://doi.org/10.1038/s41586-023-06812-z

10x Human MTG SEA-AD taxonomy (CCN20230505)

Name: A high-resolution transcriptomic atlas of cell types from middle temporal gyrus from the SEA-AD aged human cohort that spans the spectrum of Alzheimer’s disease. 

Species: Human

Description: The Seattle Alzheimer’s Disease Brain Cell Atlas (SEA-AD) is a consortium focused on gaining a deep molecular and cellular understanding of the early pathogenesis of Alzheimer’s Disease. SEA-AD is a collaboration of the Allen Institute for Brain Science, the University of Washington Alzheimer’s Disease Research Center, and Kaiser Permanente Washington Research Institute. This taxonomy is a high-resolution transcriptomic cell type atlas from middle temporal gyrus (MTG) from the SEA-AD aged human cohort that spans the spectrum of Alzheimer’s disease. The atlas was created from a single nucleus RNA-sequencing (snRNAseq) and multiomics dataset of ~2.0 million cells profiled (~1.4 million cells after QC) from 84 aged donors. The atlas is hierarchically organized into nested levels of classification: 3 classes, 24 subclasses, and 139 supertypes.

Additional resources: 

• Download the raw data at Sage Bionetworks’ AD Knowledge Portal 

• Download the processed/annotated data from AWS Open Data 

• Explore the data at SEA-AD.org or using the ABC Atlas

Citation: Gabitto M.I. and Travaglini K.J., et al. Integrated Multimodal Cell Atlas of Alzheimer’s Disease. Nat Neurosci (2024). Available from: https://doi.org/10.1038/s41593-024-01774-5 

10x Whole human brain taxonomy (CCN20240330)

Name: Transcriptomic diversity of cell types in adult human brain. 

Species: Human

Description: This dataset includes more than three million cells sampled from the adult human brain. Samples were isolated from ~100 dissections from three donors and assayed using single-nucleus RNA sequencing. The resulting cells were clustered into hierarchical groups of 31 superclusters, 461 clusters, and 3313 subclusters. Additionally, categorical neurotransmitter type annotations were assigned to clusters based on expression (or lack thereof) of one or more neurotransmitter-associated marker genes. Learn more...

Additional resources: 

• Access the data via the Allen Institute GitHub page.

• Explore the scRNA-seq using the ABC Atlas.

• Access additional paper content, code, data, and visualizations from the Linnarsson lab GitHub page.

• See what the abbreviations mean through this table.

Citation: Siletti, K., et al. Transcriptomic diversity of cell types in adult human brain. Science (2024). Available from: https://doi.org/10.1126/science.add7046

Additional information on the cell type reference taxonomies available at the ABC Atlas and the Cell Type Resource Catalog.

ABC Atlas Cell Type Resource Catalog