type: basic meta: summary: | Johannssen et al, Cross-species single-nucleus multiomic atlas of the basal ganglia, bioRxiv 2025 description: | The study presents a cross-species single-nucleus multiomic atlas of the basal ganglia in human, macaque, and marmoset, covering eight major structures: caudate, putamen, nucleus accumbens, ventral pallidum, external globus pallidus, internal globus pallidus, subthalamic nucleus, and substantia nigra. It characterizes the molecular and regulatory organization of cell populations across these three primate species and integrates the main single-nucleus dataset with spatial gene-expression data and macaque Patch-seq measurements. The main dataset was generated using 10x Multiome, which jointly measures RNA expression and ATAC chromatin accessibility in the same nuclei. The study includes 518 individual 10x Multiome library preparations: 204 from human, 90 from macaque, and 224 from marmoset. Species-wide expression matrices retain a hierarchical cell taxonomy including Neighborhood, Class, Subclass, Group, and Cluster annotations. [Johannssen, et al, Cross-species single-nucleus multiomic atlas of the basal ganglia, bioRxiv 2025.](https://www.biorxiv.org/content/10.64898/2025.12.15.694496v1) 
            johansen2025Crossspecies/
            ├── comprehensive_rna_expression_matrix/          3 resources
            │   ├── Human
            │   ├── Macaque
            │   └── Marmoset
            │
            ├── rna_expression_matrix/                       15 resources
            │   ├── HMBA-10xMultiome-BG/                      6 resources
            │   ├── HMBA-10xMultiome-BG-Aligned/              2 resources
            │   ├── HMBA-Macaque-PatchSeq/                    1 resource
            │   ├── HMBA-MERSCOPE-H22.30.001-BG/              2 resources
            │   ├── HMBA-MERSCOPE-QM23.50.001-BG/             2 resources
            │   └── HMBA-Xenium-CJ23.56.004-BG/               2 resources
            │
            ├── rna_expression_metadata/                     73 resources
            │   ├── HMBA-10xMultiome-BG/                     10 resources
            │   ├── HMBA-10xMultiome-BG-Aligned/              6 resources
            │   ├── HMBA-BG-taxonomy-CCN20250428/             8 resources
            │   ├── HMBA-Macaque-PatchSeq/                   12 resources
            │   ├── HMBA-MERSCOPE-H22.30.001-BG/             13 resources
            │   ├── HMBA-MERSCOPE-QM23.50.001-BG/            12 resources
            │   └── HMBA-Xenium-CJ23.56.004-BG/              12 resources
            │
            ├── atac_fragments/                             518 resources
            │   ├── human/                                  204 resources
            │   ├── macaque/                                 90 resources
            │   └── marmoset/                               224 resources
            │
            ├── pseudobulk_atac/                            169 resources
            │   ├── human/                                   60 resources
            │   │   ├── Astrocyte/
            │   │   ├── Microglia/
            │   │   ├── Pericyte/
            │   │   └── ...
            │   ├── macaque/                                 58 resources
            │   └── marmoset/                                51 resources
            │
            └── supplementary_table/                         53 resources
The data are organized into six main resource groups. **comprehensive\_rna\_expression\_matrix** contains three species-level AnnData resources, one each for human, macaque, and marmoset, providing comprehensive RNA expression matrices from the 10x Genomics dataset. **rna\_expression\_matrix** contains 15 AnnData resources representing several expression datasets used in the study. These include species-specific 10x Multiome RNA expression matrices in raw and log2-transformed form, cross-species aligned 10x expression matrices, macaque Patch-seq data, human and macaque MERSCOPE spatial expression data, and marmoset Xenium spatial expression data. **rna\_expression\_metadata** contains 73 tabular resources associated with these expression datasets, including cell, donor, library, gene, taxonomy, anatomical, and other supporting annotations. **atac\_fragments** contains 518 sample-level ATAC fragment resources generated by 10x Multiome: 204 human, 90 macaque, and 224 marmoset resources. Each resource contains chromatin-accessibility fragments from an individual library preparation. **pseudobulk\_atac** contains 169 cell-type-specific bigWig resources derived from the 10x Multiome ATAC data: 60 human, 58 macaque, and 51 marmoset tracks. These represent chromatin-accessibility signal aggregated across nuclei belonging to the same annotated cell type. The **supplementary\_table** collection contains 53 resources derived from the supplementary tables and associated subdivisions provided with the study. labels: assay: 10x_Multiome dataset: johansen2025Crossspecies vendor: 10x_Genomics sequencing_platform: Illumina brain_region: basal ganglia