Advances in single-cell RNA sequencing (scRNA-seq) technologies and the coordination of multi-laboratory consortia have set the stage for the generation of transcriptome data from the many thousands of cells that are required for deep characterization of tissues or whole organisms. A new study reports the ‘Tabula Muris’, an atlas of >100,000 cells across 20 mouse tissues.

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The Tabula Muris Consortium harvested multiple organs from the same mice to control for potentially confounding factors, such as age and environment. On the dissociated cell samples they used two scRNA-seq methods, which provide complementary data types. Microplate-based scRNA-seq was applied to all 20 organs and provided high-depth full-length transcript data. Such full-length data enable additional downstream analyses of transcript isoform features, such as alternative splicing. By contrast, the droplet-based scRNA-seq applied to 12 of the organs provides more of a transcriptome snapshot by sequencing just the 3′ ends at lower depth. However, the high scalability of cellular throughput of the droplet method facilitates data generation from thousands of cells (for example, >11,000 trachea cells analysed by droplet scRNA-seq), which enables the identification of rare cell types.

The main analyses performed were clustering of cells into putative groups of cell types on the basis of similarities in gene expression patterns, identification of those cell types from the expression of key marker genes, and then further inferences from any notable features of the clustering or gene expression patterns. Importantly, both scRNA-seq platforms performed comparably for cell-type clustering, thus highlighting the interoperability of the data types and opportunity for merged analyses.

Analysing data for single organs revealed various individual genes with putative roles in the development of those organs. However, a major strength of the project is that the methodological standardization across organs allows global clustering of cells for cross-tissue inferences. For example, the authors identified similar endothelial, mesenchymal and stromal cells across multiple organs, and could infer differentiation and activation statuses across T cells resident in different organs. Finally, they characterized the key transcription factor expression patterns that define cell types across organs, which may help to refine protocols for directed cell differentiation or reprogramming.

The Tabula Muris project complements other related efforts such as the Mouse Cell Atlas and Human Cell Atlas projects. Together, these valuable community resources will deepen our understanding of numerous phenomena, such as organ development, cell type diversity and gene regulatory networks.