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.
NOTE: This cell type taxonomy has been extended to additional brain regions and cell types in the SEA-AD Multi-region Taxonomy (CCN20260630) below.
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. bioRxiv (2026). Available from: https://doi.org/10.64898/2025.12.15.694496
Name: A high-resolution transcriptomic and epigenomic cell-type atlas of the developing mouse visual cortex
Species: Mouse
Description: The Developing Mouse – Visual Cortex atlas is a high-resolution transcriptomic and epigenomic cell-type atlas of the mouse visual cortex spanning embryonic to postnatal development. It is built from a single-cell RNA-sequencing (scRNA-seq) dataset of 568,654 high-quality single-cell transcriptomes and a single-nucleus Multiome (paired snRNA-seq and snATAC-seq) dataset of 200,061 high-quality nuclei, densely sampled across development from embryonic day 11.5 (E11.5) to postnatal day 56 (P56) in wild-type C57BL/6J mice. Adult cell-type identities were assigned by label transfer from the Allen Brain Cell–Whole Mouse Brain (ABC–WMB) Atlas and then propagated to younger cells across densely sampled ages, enabling reconstruction of a transcriptomic developmental trajectory map of all excitatory, inhibitory, and non-neuronal cell types. The trajectory map identifies branching points that mark the emergence of new cell types at specific developmental ages and defines molecular signatures of cellular diversification, revealing that increasingly refined cell types continue to emerge throughout postnatal differentiation, including during eye opening and the onset of the critical period. The accompanying Multiome data reconstruct a matched chromatin-accessibility landscape and cell-type-specific, temporally resolved gene regulatory networks. The atlas is organized in a hierarchical manner with nested groupings of 15 classes, 40 subclasses, 148 clusters, and 714 subclusters.
Additional resources:
Citation: Gao Y., et al. Continuous cell-type diversification in mouse visual cortex development. Nature; 647, 127–142 (2025). Available from: https://doi.org/10.1038/s41586-025-09644-1
Name: A multimodal, multiregional cell atlas of Alzheimer's disease spanning ten neo- and allocortical brain regions
Species: Human
Description: The Seattle Alzheimer's Disease Brain Cell Atlas (SEA-AD) is a more than a dozen site consortium focused on gaining a deep molecular and cellular understanding of the early pathogenesis of Alzheimer's disease. This taxonomy extends the SEA-AD atlas across ten neo- and allocortical brain regions that span the full arc of canonical Alzheimer's disease staging, from the same 84-donor aged cohort used in the SEA-AD MTG taxonomy. This atlas was created from single-nucleus RNA-sequencing (snRNA-seq), ATAC-sequencing (snATAC-seq), and Multiome profiling of approximately seven million nuclei, paired with quantitative neuropathology and whole-genome sequencing. Three key regions along Braak staging (MEC, MTG, and PFC/A9) were profiled in the full cohort of 84 donors, which includes cases with severe common AD comorbidities, while seven additional regions (HIP, LEC, ITG, STG, FI, AnG, and V1C) were profiled in a subset of 43 donors without severe comorbidities. Nuclei were hierarchically mapped to an expanded reference taxonomy that adds five regionally specialized subclasses (EC-IT, Sub-CA1, CA2–4, DG, and Ependymal) and 70 new molecularly distinct cell types to the original SEA-AD MTG taxonomy, while retaining the existing cell type nomenclature (e.g., SST 25 in both taxonomies represent the same cell type). The atlas is hierarchically organized into nested levels of classification: 3 classes, 28 subclasses, and 207 supertypes.
Additional resources:
Citation: Travaglini K.J., Gabitto, M.I., Ding Y., et al. A multiregional, multimodal cell atlas of Alzheimer's disease. bioRxiv (2026). https://doi.org/10.64898/2025.12.15.694496.
