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Related Experiment Video

Updated: Nov 15, 2025

High Throughput MicroRNA Profiling: Optimized Multiplex qRT-PCR at Nanoliter Scale on the Fluidigm Dynamic ArrayTM IFCs
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Single-cell qPCR Assay with Massively Parallel Microfluidic System.

Marta Prieto-Vila1,2, Takahiro Ochiya1,2, Yusuke Yamamoto2

  • 1Department of Molecular and Cellular Medicine, Institute of Medical Science, Tokyo Medical University, Tokyo, Japan.

Bio-Protocol
|March 4, 2021
PubMed
Summary

Single-cell quantitative polymerase chain reaction (qPCR) offers a simpler method for analyzing gene expression in individual cells. This protocol details steps for single-cell isolation to gene amplification, aiding research without complex bioinformatics.

Keywords:
Cell heterogeneityMicrofluidic systemSingle-cellSingle-cell qPCRTranscriptomicsmRNA

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Area of Science:

  • Molecular Biology
  • Genomics
  • Biotechnology

Background:

  • Single-cell transcriptomes are highly variable, reflecting cellular responses to environmental conditions.
  • Bulk sample analysis averages gene expression, masking heterogeneity and minority cell populations.
  • Single-cell technologies offer deeper insights into cellular diversity.

Purpose of the Study:

  • To present a standardized protocol for single-cell quantitative polymerase chain reaction (qPCR).
  • To provide an accessible method for analyzing gene expression at the single-cell level.
  • To facilitate research on cellular heterogeneity without complex bioinformatics.

Main Methods:

  • Single-cell isolation
  • Cell lysis
  • Complementary DNA (cDNA) reverse-transcription synthesis
  • cDNA library amplification
  • Quantitative polymerase chain reaction (qPCR)

Main Results:

  • The protocol outlines key steps for performing single-cell qPCR.
  • Single-cell qPCR is presented as a relatively simple analysis method.
  • The technique allows gene expression analysis without extensive bioinformatics.

Conclusions:

  • Standardized protocols are needed for novel single-cell techniques.
  • Single-cell qPCR provides a valuable, accessible approach to studying cellular heterogeneity.
  • This method enables detailed analysis of gene expression in individual cells.