# 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](https://portal.brain-map.org/atlases-and-data/bkp/mapmycells) for each of the currently released species using the associated [taxonomy](HMBA-BG-taxonomy-CCN20250428.md).

For more information on the dataset, please refer to the following webpage:
[Human and Mammalian Brain Atlas Release: Basal Ganglia](https://brain-map.org/consortia/hmba/hmba-release-basal-ganglia).

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/](https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/index.html#expression_matrices/HMBA-10xMultiome-BG/20250630/) | 50.5 GB |
| Cell and gene metadata | [s3://allen-brain-cell-atlas/metadata/HMBA-10xMultiome-BG/20250630/](https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/index.html#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](HMBA-BG-taxonomy-CCN20250428.md))
* ~2 million single cell transcriptomes with aligned genes across species.
  ([HMBA-10XMultiome-BG-Aligned](HMBA-10XMultiome-BG-Aligned.md))
* Spatial transcriptomic data for three species and donors ([HMBA-Spatial-BG](HMBA-Spatial-BG.md))
* 717 Macaque Patch-Seq cells with summary electro-physiology and morphology features.
([HMBA-Macaque-PatchSeq-BG](HMBA-Macaque-PatchSeq-BG.md))

Associated notebooks:
* [**Getting started**](../notebooks/getting_started.ipynb):
  Learn how to use the ABCProjectCache object to facilitate data download and
  usage.
* [**Accessing 10X gene expression data**](../notebooks/general_accessing_10x_snRNASeq_tutorial.ipynb):
  Learn how to load individual genes from the 10X expression data.
* [**10X scRNA-seq clustering analysis and annotation**](../notebooks/hmba_bg_clustering_analysis_and_annotation.ipynb):
  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**](../notebooks/hmba_bg_10X_snRNASeq_tutorial.ipynb):
  Interact with HMBA-BG 10X-Aligned gene expression data. [*notebooks/hmba_bg_10X_snRNASeq_tutorial.ipynb*]
* [**Spatial transcriptomic slab coordinates and annotation**](../notebooks/hmba_bg_spatial_slabs_and_taxonomy.ipynb):
  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**](../notebooks/hmba_bg_spatial_genes.ipynb):
  Interact with HMBA-BG spatial transcriptomic gene expression data. [*notebooks/hmba_bg_spatial_genes.ipynb*]
* [**Macaque Patch-Seq notebooks**](../notebooks/hmba_bg_macaque_patchseq.ipynb):
  Interact with HMBA-BG spatial transcriptomic gene expression data. [*notebooks/hmba_bg_macaque_patchseq.ipynb*]