Oct. 3, 2018

  • Research lays the groundwork for the understanding of cell types and gene expression patterns relevant to human disease
  • Data is poised to enable future research in reprogramming cells and understanding the diversity of cell types in health and disease
  • The open-source annotated dataset is known as “Tabula Muris”

The Chan Zuckerberg Biohub (CZ Biohub) today announced Tabula Muris, a single-cell atlas of mouse cell types and their gene expression patterns containing nearly 100,000 cells from 20 organs and tissues. The mouse is the most important model organism used in biomedical research and plays a crucial role as a proxy for human disease. The data in Tabula Muris allow for comparison of gene expression patterns across cell types and between tissues, including an analysis of shared cell types from distinct anatomical locations, as well as a detailed understanding of how cell type identity is determined by the molecules which bind to the genome to regulate gene expression. A paper describing this research was published in this week’s issue of the journal Nature.

“We believe that this rich collection of annotated cells will be a useful resource for biomedical research,” said Dr. Spyros Darmanis, CZ Biohub Group Leader, Cell Atlas. “Through this project we uncovered gene-expression patterns that allow the identification of distinct cell types originating from a wide range of tissues across an entire organism, which can be used for cell selection, targeting and reprogramming”

This research lays the groundwork for examining and comparing healthy tissue with tissues in a disease state, including metabolic disorders like diabetes and heart disease, as well as cancer, genetic disorders and infectious disease. Investigations into specific gene expression patterns in healthy tissues offer insight into the natural cellular state and the potential to improve treatment therapies.

“The Tabula Muris represents a fantastic collaboration between the Stanford and UCSF medical schools and the Biohub,” said Stephen Quake, co-president of CZ Biohub and Lee Otterson professor of bioengineering and professor of applied physics at Stanford University. “This resource is the result of a lot of hard work by a large group of dedicated people, and it’s a great example of team science.”

The teams used two complementary technical approaches, Fluorescence Activated Cell Sorting (FACS), and microfluidics, to achieve highly sensitive and efficient results. The study examined 20 organs from 7 healthy adult mice, and mapped 100,000 cells. The data is a baseline for healthy mice, meaning that researchers studying mice with various diseases have a reference guide to determine differences for the mice in their study groups.

“Gene expression patterns are highly relevant to our aging research,” said Tony Wyss-Coray, professor of neurology focused on age-related cognitive decline at Stanford University. “It is our hope and expectation that the Tabula Muris data will prove invaluable to the Alzheimer’s work being done globally. Specifically, we think that analysis of the gene expression patterns and transcriptional regulators from brain tissue and inflammatory cell populations in healthy and aged mice may shed light on the most relevant pathways controlling disease progression. Without understanding these pivotal patterns and how they degenerate with age, we will never be able to design therapeutic interventions and treatments for a disease that claims the lives of so many.”

More information about Tabula Muris can be found here: The site provides access to the datasets, and features visualization tools including interactive plots.

The CZ Biohub is an independent non-profit medical research organization collaborating with the University of California, Berkeley, Stanford University and the University of California, San Francisco. The organization’s goal is to harness the power of science, technology and human capacity to cure, prevent or manage all disease during our children’s lifetime. For more information about the CZ Biohub, visit