A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain
The mammalian brain consists of millions to billions of cells that are organized into many cell types with specific spatial distribution patterns and structural and functional properties1–3. Here we report a comprehensive and high-resolution transcriptomic and spatial cell-type atlas for the whole adult mouse brain. The cell-type atlas was created by combining a single-cell RNA-sequencing (scRNA-seq) dataset of around 7 million cells profiled (approximately 4.0 million cells passing quality control), and a spatial transcriptomic dataset of approximately 4.3 million cells using multiplexed error-robust fluorescence in situ hybridization (MERFISH). The atlas is hierarchically organized into 4 nested levels of classification: 34 classes, 338 subclasses, 1,201 supertypes and 5,322 clusters. We present an online platform, Allen Brain Cell Atlas, to visualize the mouse whole-brain cell-type atlas along with the single-cell RNA-sequencing and MERFISH datasets. We systematically analysed the neuronal and non-neuronal cell types across the brain and identified a high degree of correspondence between transcriptomic identity and spatial specificity for each cell type. The results reveal unique features of cell-type organization in different brain regions—in particular, a dichotomy between the dorsal and ventral parts of the brain. The dorsal part contains relatively fewer yet highly divergent neuronal types, whereas the ventral part contains more numerous neuronal types that are more closely related to each other. Our study also uncovered extraordinary diversity and heterogeneity in neurotransmitter and neuropeptide expression and co-expression patterns in different cell types. Finally, we found that transcription factors are major determinants of cell-type classification and identified a combinatorial transcription factor code that defines cell types across all parts of the brain. The whole mouse brain transcriptomic and spatial cell-type atlas establishes a benchmark reference atlas and a foundational resource for integrative investigations of cellular and circuit function, development and evolution of the mammalian brain.
Datasets (16)
- Whole Mouse Brain Taxonomy, Near and corticothalamic projecting cortical glutamatergic neurons310,198 cells
- Whole Mouse Brain Taxonomy, Pons neurons44,995 cells
- Whole Mouse Brain Taxonomy, Intra-and extratelencephalic projecting cortical glutamatergic neurons1,095,484 cells
- Whole Mouse Brain Taxonomy, Thalamic excitatory neurons115,401 cells
- Whole Mouse Brain Taxonomy, Olfactory-bulb/immature GABAergic neurons107,502 cells
- Whole Mouse Brain Taxonomy, Dentate-Gyrus /immature glutamatergic neurons84,352 cells
- Whole Mouse Brain Taxonomy, Lateral septal complex GABAergic neurons30,313 cells
- Whole Mouse Brain Taxonomy, Habenula glutamatergic neurons10,770 cells
- Whole Mouse Brain Taxonomy, Olfactory bulb and Cajal Retzius neurons4,767 cells
- Whole Mouse Brain Taxonomy, Cerebral nuclei neurons258,176 cells
- Whole Mouse Brain Taxonomy, Cerebellar neurons191,986 cells
- Whole Mouse Brain Taxonomy, Pallium GABAergic interneurons261,117 cells
- Whole Mouse Brain Taxonomy, Hypothalamic neurons171,281 cells
- Whole Mouse Brain Taxonomy, non_neuronal1,085,569 cells
- Whole Mouse Brain Taxonomy, Midbrain neurons209,303 cells
- Whole Mouse Brain Taxonomy, Medulla neurons60,075 cells
