Single Cell Gene Expression Profiling of Skeletal Muscle-Derived Cells

  • Sole Gatto
  • Pier Lorenzo Puri
  • Barbora MalecovaEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1556)


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 words

Fibro-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.

Supplementary material

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Copyright information

© Springer Science+Business Media LLC 2017

Open Access This chapter is distributed under the terms of the Creative Commons Attribution Noncommercial License, which permits any noncommercial use, distribution, and reproduction in any medium, provided the original author(s) and source are credited.

Authors and Affiliations

  • Sole Gatto
    • 1
  • Pier Lorenzo Puri
    • 1
    • 2
  • Barbora Malecova
    • 1
    • 3
    Email author
  1. 1.Development, Aging and Regeneration ProgramSanford Burnham Prebys Medical Discovery InstituteLa JollaUSA
  2. 2.IRCCS Fondazione Santa LuciaRomeItaly
  3. 3.Regulus Therapeutics10614 Science Center Dr.San DiegoUSA

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