title: Single Cell Gene Expression Profiling of Skeletal Muscle-Derived Cells.
abstract: 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.
authors.affiliation: Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Toreey Pines Road, La Jolla, CA, USA.
authors.forename: Sole
authors.initials: S
authors.lastname: Gatto
authors.affiliation: Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Toreey Pines Road, La Jolla, CA, USA.|IRCCS Fondazione Santa Lucia, Rome, Italy.
authors.forename: Pier Lorenzo
authors.initials: PL
authors.lastname: Puri
authors.affiliation: Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Toreey Pines Road, La Jolla, CA, USA. barboramalecova22@gmail.com.|Regulus Therapeutics, 10614 Science Center Dr., San Diego, CA, 92121, USA. barboramalecova22@gmail.com.
authors.forename: Barbora
authors.initials: B
authors.lastname: Malecova
mesh_terms: D000818:Animals; D015415:Biomarkers; D018929:Cell Culture Techniques; D002469:Cell Separation / Q000379:methods; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D005434:Flow Cytometry / Q000379:methods; D015870:Gene Expression; D020869:Gene Expression Profiling / Q000379:methods; D016130:Immunophenotyping / Q000379:methods; D051379:Mice; D024510:Muscle Development / Q000235:genetics*; D018482:Muscle, Skeletal / Q000166:cytology*; D011786:Quality Control; D060888:Real-Time Polymerase Chain Reaction; D059010:Single-Cell Analysis / Q000379:methods; D012984:Software; D013223:Statistics as Topic; D059467:Transcriptome; D064878:Web Browser
chemical_list: D015415:Biomarkers
keywords: Bar plots; Data analysis; Fibro-Adipogenic Progenitors (FAPs ); Flow cytometry; Fluidigm ® technology; Fluorescence Activated Cell Sorting (FACS ); Hierarchical clustering heatmap; Muscle regeneration; Principal component analysis; Single cell gene expression; Violin plots