Research model, area of interest
Technique

Related tool

Project summary

Related publication

Related cell type taxonomy

Mouse, Whole Brain
‍Spatial transcriptomics & single cell RNA-Seq

ABC Atlas (Spatial & non-spatial, coronal)

MapMyCells

Whole Mouse Brain Transcriptomic Cell Type Atlas

Yao et al. (2023) A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain. DOI 10.1038/s41586-023-06812-z.

Whole adult mouse brain taxonomy of cell types

Mouse, Whole Brain
‍Spatial transcriptomics

ABC Atlas (Spatial, coronal & sagittal)

A molecularly defined and spatially resolved cell atlas of the whole mouse brain

Zhang et al. (2023) Molecularly defined and spatially resolved cell atlas of the whole mouse brain. DOI 10.1038/s41586-023-06808-9

Whole adult mouse brain taxonomy of cell types

Mouse, Whole Cortex & Hippocampus
‍Single cell RNA-Seq (SMART-Seq and 10x)‍

Transcriptomic Explorer (SMART-Seq)

Transcriptomic Explorer (10x)

Mouse - Whole Cortex & Hippocampus - SMART-seq

Mouse - Whole Cortex & Hippocampus - 10x

Yao, Z., et al. (2021). A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation. DOI 10.1016/j.cell.2021.04.021

Cell types taxonomy (2021)‍

‍Cell types taxonomy (2021) viewer

Mouse, Primary Visual Cortex & Anterior Lateral Motor Cortex
‍Single cell RNA-Seq

RNA-Seq Mouse Data Navigator

Transcriptomic cell types in the mouse brain: SMART-seq cells

Tasic, B., et al. (2018). Shared and distinct transcriptomic cell types across neocortical areas. DOI 10.1038/s41586-018-0654-5

Taxonomy embedded in VISp and ALM

Mouse, Primary Motor Cortex‍
‍Patch-Seq

Cell Type Knowledge Explorer

Patch-seq of mouse motor cortex: transcriptomics

Scala, F., et al. (2021). Phenotypic variation of transcriptomic cell types in mouse motor cortex. DOI 10.1038/s41586-020-2907-3

Taxonomy embedded in the download files for the "10x Chromium v3 (Broad)" dataset

Mouse, Primary Motor Cortex‍
‍Single cell RNA-Seq

Cell Type Knowledge Explorer

Transcriptomic cell types in the mouse brain: 10x nuclei

Yao, Z. et al. (2021) A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex. DOI 10.1038/s41586-021-03500-8

Taxonomy embedded in the download files for the first seven datasets

Mouse, Primary Visual Cortex‍
‍Patch-Seq

Mouse PatchSeq VIS

Neurons in Mouse Primary Visual Cortex

Gouwens, N. W., et al. (2020). Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells. DOI 10.1016/j.cell.2020.09.057

Subset of taxonomy embedded in VISp download; includes all GABAergic neurons and VISp glutamatergic neurons.

Mouse, (majority) Visual Cortex‍
‍Patch-Clamp

Allen Cell Types Database

Cell Types: Overview of the Data

Gouwens, N. W., et al. (2019) Classification of electrophysiological and morphological neuron types in the mouse visual cortex. DOI 10.1038/s41593-019-0417-0

No associated transcriptomic taxonomy

Human, Whole Brain‍
‍Single nucleus RNA-Seq

ABC Atlas

MapMyCells

Transcriptomic diversity of cell types in adult human brain

Siletti, K., Hodge, R., et al. (2023) Transcriptomic diversity of cell types across the adult human brain. DOI:10.1126/science.add7046

Human whole brain

Human, Multiple Cortical Areas‍
‍Single nucleus RNA-Seq

Transcriptomic Explorer

Human Multiple Cortical Areas - SMART-seq

*some of the data
‍‍Jorstad, N. L., et al. (2023) Transcriptomic cytoarchitecture reveals principles of human neocortex organization. DOI:10.1126/science.adf6812

Taxonomy for transcriptomic explorer‍‍

Taxonomy from paper (Newer Data)

Human, Primary Motor Cortex‍
‍Single nucleus RNA-Seq

Cell Type Knowledge Explorer

Transcriptomic Explorer

Transcriptomic characterization of cell types in human M1 using droplet-based single nucleus RNA sequencing

Bakken, T. E., Jorstad, N. L., Hu, Q., et al. (2021). Comparative cellular analysis of motor cortex in human, marmoset and mouse. DOI 10.1038/s41586-021-03465-8

Human M1 10x

Human, Middle Temporal Gyrus
‍Single nucleus RNA-Seq

RNA-Seq Navigator

Transcriptomic characterization of cell types in human M1 using droplet-based single nucleus RNA sequencing

Hodge, R. D., Bakken, T. E., et al. (2019). Conserved cell types with divergent features in human versus mouse cortex. DOI: 0.1038/s41586-019-1506-7.

Human MTG SMART-seq

Human, Middle Temporal Gyrus, Alzhiemer's Disease‍
‍Spatial Transcriptomics

ABC Atlas

Seattle Alzheimer's Disease Brain Cell Atlas (SEA-AD) - Spatial transcriptomics - MERFISH

Gabitto, M. I., Travaglini, K. J., et. al. (2024). Integrated multimodal cell atlas of Alzheimer’s disease

Mapped to this expanded aged/AD donor taxonomy

Human, Middle Temporal Gyrus, Alzhiemer's Disease
‍Single nucleus RNA-Seq

ABC Atlas

Transcriptomic Explorer

MapMyCells

Seattle Alzheimer's Disease Brain Cell Atlas (SEA-AD) - 10x single nucleus RNAseq

Gabitto, M. I., Travaglini, K. J., et. al. (2024). Integrated multimodal cell atlas of Alzheimer’s disease

Adult donor taxonomy

Marmoset, Primary Motor Cortex‍
‍Single nucleus RNA-Seq

Cell Type Knowledge Explorer

A Molecular and Cellular Atlas of the Marmoset Brain - Single nucleus sequencing

Bakken, T. E., Jorstad, N. L., Hu, Q., et al. (2021). Comparative cellular analysis of motor cortex in human, marmoset and mouse. DOI 10.1038/s41586-021-03465-8

Embedded in the metadata file on NeMO

Mouse, Multiple brain areas, Aging
Single cell RNA-Seq

ABC Atlas

Cellular and Molecular Characterization of the Aged Mouse Brain

Jin, K., et al. (2025). Brain-wide cell-type-specific transcriptomic signatures of healthy ageing in mice. DOI 10.1038/s41586-024-08350-8

Whole adult mouse brain taxonomy of cell types

Human, Multiple brain areas, Parkinson's disease
Single nucleus RNA-seq

ABC Atlas

ASAP Human Postmortem-Derived Brain Sequencing Collection

none

Data mapped to:
Human whole brain
SEA-AD MTG taxonomy

Cross-species, Basal Ganglia
Single nucleus RNA-seq (Multiome)

MapMyCells

Mammalian Basal Ganglia Consensus Cell Type Atlas

none

Consensus basal ganglia taxonomy