Human-Mammalian Brain - Basal Ganglia 10X snRANSeq data: Individual species gene expression#
The basal ganglia are a set of subcortical structures critical for motor control, particularly in the context of action selection, motor learning and emotional state, whose coarse functional organization is well-described in the literature.
Gene expression data and metadata for each individual species in the Human-Mammalian Brain - Basal Ganglia (HMBA-BG) 10X dataset. Currently this includes:
1,683,105 Human cells, 36,601 genes
839,102 Macaque cells, 35,219 genes
414,575 Marmoset cells, 35,787 genes
This release also includes data for running MapMyCells for each of the currently released species using the associated taxonomy.
For more information on the dataset, please refer to the following webpage: Mammalian Basal Ganglia Consensus Cell Type Atlas.
The expression matrices and associated metadata are hosted in a AWS S3 bucket as a AWS Public Dataset:
Component |
Current Version |
Size |
|---|---|---|
Expression Matrices |
s3://allen-brain-cell-atlas/expression_matrices/HMBA-10xMultiome-BG/20250630/ |
50.5 GB |
Cell and gene metadata |
s3://allen-brain-cell-atlas/metadata/HMBA-10xMultiome-BG/20250630/ |
778.8 MB |
Data is being shared under the CC BY NC 4.0 license.
Related resources:
Taxonomy and Clustering analysis of ~2 million single cell transcriptomes from the aligned dataset. (HMBA-BG-taxonomy-CCN20250428)
~2 million single cell transcriptomes with aligned genes across species. (HMBA-10XMultiome-BG-Aligned)
Spatial transcriptomic data for three species and donors (HMBA-Spatial-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]
Spatial transcriptomic slab coordinates and annotation: Learn about the HMBA-BG spatial data/metadata structure and mapping to the BG taxonomy through example use cases and visualization. [notebooks/hmba_bg_spatial_slabs_and_taxonomy.ipynb]
Spatial transcriptomic gene expression: Interact with HMBA-BG spatial transcriptomic gene expression data. [notebooks/hmba_bg_spatial_genes.ipynb]