Human-Mammalian Brain - Basal Ganglia 10X snRANSeq data: clustering and annotations#
The basal ganglia (BG) are a system of interconnected brain structures that play a crucial role in motor control, learning, behavior, and emotion. With approximately 200 million neurons in the human basal ganglia alone, these structures are involved in a wide range of neurological processes and are implicated in numerous disorders affecting human health, including Parkinson’s disease, Huntington’s disease, and substance abuse disorders. To further understand the complexity of the basal ganglia, researchers have historically classified its neurons into various types based on their cytoarchitecture, connectivity, molecular profile, and functional properties. However, recent advancements in high-throughput transcriptomic profiling have revolutionized our ability to systematically categorize these cell types within species, while the maturation of machine learning technologies have enabled the integration of these taxonomies across species.
Our consensus basal ganglia cell type taxonomy is the result of iterative clustering and cross-species integration of transcriptomic data. The taxonomy encompasses neurons from key structures within the basal ganglia, including the caudate (Ca), putamen (Pu), nucleus accumbens (NAc), the external and internal segments of the globus pallidus (GPe, GPi), subthalamic nucleus (STN), and substantia nigra (SN). By combining data from multiple primate and rodent species, we have developed a consensus taxonomy that highlights both conserved and species-specific cell types. We validate our taxonomy through marker gene expression analysis, comparison with previously published taxonomies, and self-projection, ensuring the accuracy and robustness of each level in the taxonomic hierarchy.
For more information on the dataset, please refer to the following webpage: Mammalian Basal Ganglia Consensus Cell Type Atlas.
The associated metadata is hosted in a AWS S3 bucket as a AWS Public Dataset:
Component |
Current Version |
Size |
|---|---|---|
Cell taxonomy metadata |
s3://allen-brain-cell-atlas/metadata/HMBA-BG-taxonomy-CCN20250428/20250531/ |
196.6 MB |
Data is being shared under the CC BY NC 4.0 license.
Related resources :
~2 million single cell transcriptomes with aligned genes across species. (HMBA-10XMultiome-BG-Aligned)
Single cell transcriptomes for each individual species in the HMBA-BG dataset.(HMBA-10XMultiome-BG)
Associated notebooks:
Getting started: Learn how to use the ABCProjectCache object to facilitate data download and usage.
Accessing 10X gene expression data: Learn how to load individual genes from the 10X expression data.
10X scRNA-seq clustering analysis and annotation: Learn about the HMBA-BG data/metadata structure and taxonomy through example use cases and visualization. [notebooks/hmba_bg_clustering_analysis_and_annotation.ipynb]
10X scRNA-seq gene expression: Interact with HMBA-BG 10X-Aligned gene expression data. [notebooks/hmba_bg_10X_snRNASeq_tutorial.ipynb]