Comprehensive qPCR profiling of gene expression in single neuronal cells

Nat Protoc. 2011 Dec 22;7(1):118-27. doi: 10.1038/nprot.2011.430.


A major challenge in neuronal stem cell biology lies in characterization of lineage-specific reprogrammed human neuronal cells, a process that necessitates the use of an assay sensitive to the single-cell level. Single-cell gene profiling can provide definitive evidence regarding the conversion of one cell type into another at a high level of resolution. The protocol we describe uses Fluidigm Biomark dynamic arrays for high-throughput expression profiling from single neuronal cells, assaying up to 96 independent samples with up to 96 quantitative PCR (qPCR) probes (equivalent to 9,216 reactions) in a single experiment, which can be completed within 2-3 d. The protocol enables simple and cost-effective profiling of several hundred transcripts from a single cell, and it could have numerous utilities.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Differentiation
  • Cells, Cultured
  • Gene Expression Profiling / methods*
  • Humans
  • Microfluidics
  • Neurons / metabolism*
  • Polymerase Chain Reaction / methods*
  • RNA, Messenger / metabolism
  • Single-Cell Analysis


  • RNA, Messenger