The Use of the Fluidigm C1 for RNA Expression Analyses of Single Cells

Curr Protoc Mol Biol. 2018 Apr;122(1):e55. doi: 10.1002/cpmb.55.


Understanding the transcriptional heterogeneity that occurs on the level of a single cell is critical to understanding the gene-regulatory mechanisms underlying development and disease. Population-level whole-transcriptome profiling approaches average gene expression across thousands to millions of cells and are unable to delineate the transcriptional signature of individual cells. Considerable biological heterogeneity between individual cells arises from differences in cell lineage, environment, or response to stimulus. The development of single-cell RNA sequencing (RNA-seq) enabled a high-resolution and unbiased analysis of cell transcriptomes. This unit describes a procedure utilizing an automated microfluidic platform, the Fluidigm C1 system, to simultaneously isolate dozens of single cells in a size- and shape-dependent manner. The microfluidic platform processes cells in individual nanoliter-scale reactions to convert their contents into double-stranded cDNA. This cDNA is used to make dual-indexed libraries using the Illumina Nextera XT library preparation kit for eventual RNA-seq analysis. © 2018 by John Wiley & Sons, Inc.

Keywords: Fluidigm C1; RNA-seq; single-cell.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Gene Expression*
  • Gene Library
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Microfluidics / methods*
  • Polymerase Chain Reaction
  • RNA / genetics
  • RNA / metabolism*
  • Reverse Transcription / genetics
  • Single-Cell Analysis / methods*


  • RNA