Stanford group draws wide expertise from Microbiome Insights & others to complete Chan Zuckerberg Biohub’s Tabula Muris project

A detailed database of transcriptomic data from over 100,000 individual cells taken from the mouse model organism Mus musculus, titled Tabula Muris, is now available for use by biomedical researchers around the world. This work, completed by the The Tabula Muris Consortium, was a project funded by the Chan Zuckerberg Biohub.

This database is the first concise and detailed collection of mouse single cell transcriptomic data from this important model organism. It reveals the individual gene expression levels of the cells from 20 different organs and tissues and is a first draft for an organism-wide representation of cellular diversity. This now-publicly-available resource will aid in the discovery of new cell types and of novel gene expression patterns, while also serving as a reference for healthy organs and tissues, making it an important baseline for future disease models. The team also made all of the data, scripts, and protocols publicly available along with an interactive data browser. The aim is to allow future groups to carry out further in depth-analysis and exact replications of their work.

In order to complete such an ambitious project, the consortium assembled expertise from several groups. Consortium members included researchers from Chan Zuckerberg Biohub, multiple faculty at Stanford University, and experts from the Palo Alto Healthcare System. Each group specialised in a tissue type (e.g. kidneys or lungs), or had specific experience (e.g. pathology or flow cytometry). A breadth of knowledge was required because the over 100,000 individual cells needed to be individually isolated. For mammalian cells, two methods were used: fluorescence-activated cell sorting and the microfluidic droplet technique. From here, DNA and RNA were extracted and sequenced. In tandem, fecal samples were collected for functional analysis of the microbiota. It was at this stage that Microbiome Insights provided their expertise by performing a customized suite of DNA extraction and library preparation services to contribute to the overall results.

“Working closely with Microbiome Insights to quickly analyze the data was critical to our ability to integrate microbiota information with the rest of the Cell Atlas project,” said KC Huang, a Stanford professor involved in the project. The sheer number of cell types and subsequent genomic information to be processed required an enormous feat of coordination—making this a remarkable example of research collaboration.

The strength of this single cell and organ approach is that it will allow researchers working with a single organ, for example, to see the changes that occur throughout the entire body. It provides a whole-body view of disease and development. This could aid in studies on prevention and potentially even cures for many important diseases such as diabetes, heart disease, and cancer. The Chan Zuckerberg group is now supporting a similar project, The Human Cell Atlas, which according to their website, is aimed at building “a collection of maps that will describe and define the cellular basis of health and disease”.