Human-Mammalian Brain - Basal Ganglia 10X snRANSeq data: Aligned gene expression across species#
Data 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 dataset.
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: Mammalian Basal Ganglia Consensus Cell Type Atlas.
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-Aligned/20250531/ |
33.6 GB |
Cell and gene metadata |
s3://allen-brain-cell-atlas/metadata/HMBA-10xMultiome-BG-Aligned/20250531/ |
429 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 aligned dataset. (HMBA-BG-taxonomy-CCN20250428)
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]