The Tabula Muris Consortium has created a comprehensive compendium of single-cell transcriptomic data from 20 organs and tissues in the mouse (*Mus musculus*). This resource, comprising over 100,000 cells, provides a new tool for cell biology research, revealing gene expression in previously understudied cell populations and enabling direct comparison of gene expression in shared cell types across different tissues. Two technical approaches were used: microfluidic droplet-based 3′-end counting and FACS-based full-length transcript analysis. The data are publicly available, facilitating replication and cross-experiment analysis. The study defines organ-specific cell types, highlights unexpected discoveries, and demonstrates the utility of transcription factor networks in reprogramming protocols. The Tabula Muris serves as a reference for healthy young adult organs and a foundation for future studies in various physiological disciplines.The Tabula Muris Consortium has created a comprehensive compendium of single-cell transcriptomic data from 20 organs and tissues in the mouse (*Mus musculus*). This resource, comprising over 100,000 cells, provides a new tool for cell biology research, revealing gene expression in previously understudied cell populations and enabling direct comparison of gene expression in shared cell types across different tissues. Two technical approaches were used: microfluidic droplet-based 3′-end counting and FACS-based full-length transcript analysis. The data are publicly available, facilitating replication and cross-experiment analysis. The study defines organ-specific cell types, highlights unexpected discoveries, and demonstrates the utility of transcription factor networks in reprogramming protocols. The Tabula Muris serves as a reference for healthy young adult organs and a foundation for future studies in various physiological disciplines.