Tabula Microcebus

Native to Madagascar, mouse lemurs are the smallest, fastest reproducing, and among the most abundant primates in the world, and an emerging model organism for primate biology, behavior, health and conservation (Ezran et al (2017) Genetics 206, 651-664). Although much has been learned about their physiology and their ecology and phylogeny, little is known about their cellular and molecular biology. The Tabula Microcebus is the result of an international collaborative effort involving the CZ Biohub, many groups at Stanford, the CNRS-MNHN (Museum National d'Histoire Naturelle in Brunoy, France), and groups at HKUST, Cornell, A*STAR (Agency for Science, Technology and Research in Singapore), and UCSF. We used droplet- and plate-based single cell RNA sequencing to profile over 220,000 cells from 27 mouse lemur organs humanely procured. We defined hundreds of mouse lemur cell types and their full gene expression profiles, including most classical cell types plus dozens of apparently novel cell types and cell states. The atlas provides a cellular and molecular foundation for studying this primate model organism, and a general approach for establishing other emerging model organisms. Tabula Microcebus, now available on biorxiv (https://www.biorxiv.org/content/10.1101/2021.12.12.469460v1), is a valuable community resource and with the goal of enabling more research avenues we are making the sequence data rapidly and broadly available. We provide the cell by gene count data for the Tabula Microcebus mouse lemur scRNAseq cell atlas in Python’s h5ad and Matlab’s mat formats, as well as scripts to export the files to R’s Seurat format. Datasets are organized as described in https://tabula-microcebus.ds.czbiohub.org/. Datasets can also be explored and reannotated interactively using the cellxgene browser on the same web link. We ask the scientific community to please read our Data Release Policy (https://tabula-microcebus.ds.czbiohub.org/whereisthedata) before you use it and to reach out using the contact form available from our data portal (https://tabula-microcebus.ds.czbiohub.org/).