Single Cell Gene Expression Profiling of Skeletal Muscle-Derived Cells
Single cell gene expression profiling is a fundamental tool for studying the heterogeneity of a cell population by addressing the phenotypic and functional characteristics of each cell. Technological advances that have coupled microfluidic technologies with high-throughput quantitative RT-PCR analyses have enabled detailed analyses of single cells in various biological contexts. In this chapter, we describe the procedure for isolating the skeletal muscle interstitial cells termed Fibro-Adipogenic Progenitors (FAPs ) and their gene expression profiling at the single cell level. Moreover, we accompany our bench protocol with bioinformatics analysis designed to process raw data as well as to visualize single cell gene expression data. Single cell gene expression profiling is therefore a useful tool in the investigation of FAPs heterogeneity and their contribution to muscle homeostasis.
Key wordsFibro-Adipogenic Progenitors (FAPs) Muscle regeneration Single cell gene expression Fluorescence Activated Cell Sorting (FACS) Flow cytometry Data analysis Fluidigm® technology Principal component analysis Hierarchical clustering heatmap Violin plots Bar plots
This work was supported by NIH P30 pilot grant P30AR061303 and CIRM training grant TG2-01162 to B.M., and NIH grants R01AR056712, R01AR052779, and P30 AR061303 to P.L.P. We thank Thomas C. Roberts and Alessandra Dall’Agnese for critical reading of the manuscript.
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