Human-Mammalian Brain - Basal Ganglia 10X snRNASeq data: Cross-Species gene expression across species#
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.
This page describes and links to and metadata for the HMBA-BG 10X gene expression data, with 16,630 genes aligned across the species. In total there are 2,035,898 cells in this gene aligned, cross-species dataset. These data are a QCed subset of those from described in the (HMBA-10XMultiome-BG) page.
These data from the basis of the cross species Basal Ganglia (BG) taxonomy.
For more information on the dataset, please refer to the following webpage: Human and Mammalian Brain Atlas Release: Basal Ganglia.
The expression matrices and associated metadata are hosted on AWS S3 bucket as a AWS Public Dataset:
Component |
Current Version |
Size |
|---|---|---|
Expression Matrices |
s3://allen-brain-cell-atlas/expression_matrices/HMBA-10xMultiome-BG-Cross-Species/20261031/ |
30.7 GB |
Cell and gene metadata |
s3://allen-brain-cell-atlas/metadata/HMBA-10xMultiome-BG-Cross-Species/20261031/ |
535.2 MB |
Data is being shared under the CC BY NC 4.0 license.
Related resources:
Single cell transcriptomes for each individual species in the HMBA-BG dataset.(HMBA-10XMultiome-BG)
Taxonomy and Clustering analysis of ~2 million single cell transcriptomes from the cross-species dataset. (HMBA-BG-taxonomy)
Spatial transcriptomic data for three species and donors (HMBA-Spatial-BG)
717 Macaque Patch-Seq cells with summary electro-physiology and morphology features. (HMBA-Macaque-PatchSeq-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-Cross-Species 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]
Macaque Patch-Seq notebooks: Interact with HMBA-BG spatial transcriptomic gene expression data. [notebooks/hmba_bg_macaque_patchseq.ipynb]