A transcriptomic atlas of mouse cerebellar cortex comprehensively defines cell types

Velina Kozareva*, Caroline Martin*, Tomas Osorno, Stephanie Rudolph, Chong Guo, Charles Vanderburg, Naeem Nadaf, Aviv Regev, Wade Regehr, Evan Macosko. 



The cerebellar cortex is a well-studied brain structure with diverse roles in motor learning, coordination, cognition and autonomic regulation. However,  a complete inventory of cerebellar cell types is currently lacking. Here, using recent advances in high-throughput transcriptional profiling, we molecularly define cell types across individual lobules of the adult mouse cerebellum. Purkinje neurons showed considerable regional specialization, with the greatest diversity occurring in the posterior lobules. For several types of cerebellar interneuron, the molecular variation within each type was more continuous, rather than discrete. In particular, for the unipolar brush cells—an interneuron population previously subdivided into discrete populations—the continuous variation in gene expression was associated with a graded continuum of electrophysiological properties. Notably, we found that molecular layer interneurons were composed of two molecularly and functionally distinct types. Both types show a continuum of morphological variation through the thickness of the molecular layer, but electrophysiological recordings revealed marked differences between the two types in spontaneous firing, excitability and electrical coupling. Together, these findings provide a comprehensive cellular atlas of the cerebellar cortex, and outline a methodological and conceptual framework for the integration of molecular, morphological and physiological ontologies for defining brain cell types.


To comprehensively sample cell types in the mouse cerebellum, we dissected and isolated nuclei from 16 different lobules, across both female and male replicates, recovering 611,034 high quality nuclei profiles. We have clustered and annotated these into 46 subclusters across 18 cell types (clusters). For a more detailed description of our findings, check out our publication here

In addition, we profiled and annotated 5,519 nuclei from the developing mouse cerebellum over 6 time points, and 150,258 nuclei from post-mortem human cerebellum samples. We identified developing interneuron clusters and several cell types shared between mouse and human, including subtypes of granule cells and molecular layer interneurons.

Data Availability:

We have made the processed and annotated nuclei data supporting our findings above available for visualization and download. The raw UMI counts are available as .mtx files (and also as part of accompanying Seurat objects). Annotations are available in CSV format as well as through the Seurat objects. Objects are available for adult mouse, developing mouse, and four cell type-specific joint mouse/human cerebellum analyses. 

Code to reproduce our analyses and visualizations is available on Github., along with additional information about annotation objects made available here. Unannotated count data is also available on GEO