Learn more about the reference taxonomies available in MapMyCells.
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:
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
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:
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
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:
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
Species: Human (Homo sapiens), Rhesus macaque (Macaca mulatta), Common marmoset (Callithrix jacchus)
Description: The Consensus Basal Ganglia Taxonomy is a multi-species, multi-omic cell type atlas of the primate basal ganglia developed by the BICAN Human and Mammalian Brain Atlas consortium. The taxonomy integrates over two million single nuclei from eight major basal ganglia structures profiled using single-nucleus RNA-seq, ATAC-seq, spatial transcriptomics, morphology, and electrophysiology. Cross-species alignment with existing mouse and human whole-brain atlases identifies approximately 60 homologous cell types conserved across 80 million years of evolution. The dataset refines the taxonomy of medium spiny neurons and other GABAergic populations, revealing both conserved and species-divergent molecular signatures. Comparative cis-regulatory analysis defines deeply conserved enhancer grammars that encode cell identity and inform viral targeting strategies. The taxonomy provides a foundational resource for understanding basal ganglia evolution, circuit function, and disease association.
Additional resources:
Citation: Johansen N.J., Fu Y., Schmitz M., et al. Cross-species consensus atlas of primate basal ganglia. Preprint in preparation.
