TOOLS AND RESOURCES Transcriptional profiling reveals extraordinary diversity among skeletal muscle tissues Erin E Terry1, Xiping Zhang2, Christy Hoffmann1, Laura D Hughes3, Scott A Lewis1, Jiajia Li1, Matthew J Wallace1, Lance A Riley2, Collin M Douglas2, Miguel A Gutierrez-Monreal2, Nicholas F Lahens4, Ming C Gong5, Francisco Andrade5, Karyn A Esser2, Michael E Hughes1* 1Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, United States; 2Department of Physiology and Functional Genomics, University of Florida College of Medicine, Gainesville, United States; 3Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, United States; 4Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States; 5Department of Physiology, University of Kentucky School of Medicine, Lexington, United States Abstract Skeletal muscle comprises a family of diverse tissues with highly specialized functions. Many acquired diseases, including HIV and COPD, affect specific muscles while sparing others. Even monogenic muscular dystrophies selectively affect certain muscle groups. These observations suggest that factors intrinsic to muscle tissues influence their resistance to disease. Nevertheless, most studies have not addressed transcriptional diversity among skeletal muscles. Here we use RNAseq to profile mRNA expression in skeletal, smooth, and cardiac muscle tissues from mice and rats. Our data set, MuscleDB, reveals extensive transcriptional diversity, with greater than 50% of transcripts differentially expressed among skeletal muscle tissues. We detect mRNA expression of *For correspondence: hundreds of putative myokines that may underlie the endocrine functions of skeletal muscle. We
[email protected] identify candidate genes that may drive tissue specialization, including Smarca4, Vegfa, and Competing interests: The Myostatin.