Single cell gene expression profiling of skeletal muscle-derived cells

Sole Gatto, Pier Lorenzo Puri, Barbora Malecova

Research output: Chapter in Book/Report/Conference proceedingChapter


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.

Original languageEnglish
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Number of pages29
Publication statusPublished - Jan 1 2017

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745


  • 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

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics


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