Single-Cell Isolation and Gene Analysis: Pitfalls and Possibilities

Int J Mol Sci. 2015 Nov 10;16(11):26832-49. doi: 10.3390/ijms161125996.


During the last two decades single-cell analysis (SCA) has revealed extensive phenotypic differences within homogenous cell populations. These phenotypic differences are reflected in the stochastic nature of gene regulation, which is often masked by qualitatively and quantitatively averaging in whole tissue analyses. The ability to isolate transcripts and investigate how genes are regulated at the single cell level requires highly sensitive and refined methods. This paper reviews different strategies currently used for SCA, including harvesting, reverse transcription, and amplification of the RNA, followed by methods for transcript quantification. The review provides the historical background to SCA, discusses limitations, and current and future possibilities in this exciting field of research.

Keywords: Analysis; RT; amplification qPCR; harvesting; single-cell.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Cell Separation / instrumentation
  • Cell Separation / methods*
  • Electrophoresis, Capillary / instrumentation
  • Electrophoresis, Capillary / methods
  • Escherichia coli / chemistry
  • Flow Cytometry / instrumentation
  • Flow Cytometry / methods
  • Gene Expression Profiling / instrumentation
  • Gene Expression Profiling / methods*
  • Gene Expression Regulation*
  • Humans
  • Laser Capture Microdissection / instrumentation
  • Laser Capture Microdissection / methods
  • Microfluidics / instrumentation
  • Microfluidics / methods
  • Phenotype
  • RNA, Messenger / genetics*
  • RNA, Messenger / metabolism
  • Real-Time Polymerase Chain Reaction / instrumentation
  • Real-Time Polymerase Chain Reaction / methods
  • Reverse Transcription
  • Single-Cell Analysis / instrumentation
  • Single-Cell Analysis / methods*
  • Thermus / chemistry


  • RNA, Messenger