Skeletal muscle is a heterogeneous tissue comprised of muscle fiber and mononuclear cell types that, in addition to movement, influences immunity, metabolism and cognition. We investigated the gene expression patterns of skeletal muscle cells using RNA-seq of subtype-pooled single human muscle fibers and single cell RNA-seq of mononuclear cells from human vastus lateralis, mouse quadriceps, and mouse diaphragm. We identified 11 human skeletal muscle mononuclear cell types, including two fibro-adipogenic progenitor (FAP) cell subtypes. The human FBN1+ FAP cell subtype is novel and a corresponding FBN1+ FAP cell type was also found in single cell RNA-seq analysis in mouse. Transcriptome exercise studies using bulk tissue analysis do not resolve changes in individual cell-type proportion or gene expression. The cell-type gene signatures provide the means to use computational methods to identify cell-type level changes in bulk studies. As an example, we analyzed public transcriptome data from an exercise training study and revealed significant changes in specific mononuclear cell-type proportions related to age, sex, acute exercise and training. Our single-cell expression map of skeletal muscle cell types will further the understanding of the diverse effects of exercise and the pathophysiology of muscle disease.Skeletal muscle is a complex heterogeneous tissue consisting of multinucleated muscle fibers, immune cells, endothelial cells, muscle stem cells (satellite cells), non-myogenic mesenchymal progenitors (e.g., fibro-adipogenic progenitors, or FAPs), and other mononuclear cells 1 . To improve the understanding of skeletal muscle cell types and their transcriptional signatures, we studied human and mouse skeletal muscle mononuclear cells by single-cell RNA-sequencing and single human muscle fiber subtypes by RNA-seq.The majority of skeletal muscle is composed of the multinucleated fibers that facilitate movement. These muscle fibers include several fiber types of differing metabolic and functional properties 2-4 . While slow-twitch (or Type I) muscle fibers possess high oxidative capacity, fast-twitch (or Type II) muscle fibers have a high glycolytic capacity and are capable of supplying more power than Type I fibers 2-4 . Fiber-type composition differs across individuals and can change by as much as 10-30% during exercise training regimens 5-7 . Furthermore, the transcriptomic response to physical activity is different in each fiber-type as each fiber-type responds differently to different modes of exercise 8,9 . Crucially, muscle fibers secrete myokines, which both act locally within muscle tissue as well as influence other organs and tissues via hormone-like signaling 10 . Myokines may be responsible for the immune-, metabolism-, and cognition-related benefits of physical activity, as well as the chronic diseases that are caused by lack of physical activity (insulin resistance, cardiovascular disease, etc.) 10 .Besides multinucleated fibers, skeletal muscle contains many mononuclear cells, such as immune cells,...