Specification of diverse cell types during early neurogenesis of the mouse cerebellum

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Abstract

We applied single-cell RNA sequencing to profile genome-wide gene expression in about 9,400 individual cerebellar cells from the mouse embryo at embryonic day 13.5. Reiterative clustering identified the major cerebellar cell types and subpopulations of different lineages. Through pseudotemporal ordering to reconstruct developmental trajectories, we identified novel transcriptional programs controlling cell fate specification of populations arising from the ventricular zone and the rhombic lip, two distinct germinal zones of the embryonic cerebellum. Together, our data revealed cell-specific markers for studying the cerebellum, gene-expression cascades underlying cell fate specification, and a number of previously unknown subpopulations that may play an integral role in the formation and function of the cerebellum. Our findings will facilitate new discovery by providing insights into the molecular and cell type diversity in the developing cerebellum.

Data availability

Sequencing data have been deposited in GEO under accession codes GSE120372.

The following data sets were generated

1. James Li
(2018) Sinle-cell RNA sequecing of E13.5 mouse cerebella
NCBI Gene Expression Omnibus, GSE120372.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE120372

Article and author information

Author details

John W Wizeman

Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, United States

Competing interests
The authors declare that no competing interests exist.
Qiuxia Guo

Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, United States

Competing interests
The authors declare that no competing interests exist.
Elliot M Wilion

Department of Physiology and Neurobiology, University of Connecticut, Storrs, United States

Competing interests
The authors declare that no competing interests exist.
James YH Li

Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, United States

For correspondence
jali@uchc.edu

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-9231-2698

Funding

NIH Office of the Director (R01NS106844)

James YH Li

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Ethics

Animal experimentation: All procedures involving animals were approved by the Animal Care Committee at the University of Connecticut Health Center and were in compliance with national and state laws and policies. (protocol #101849-0621

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.