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Updated: May 17, 2026
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Single-cell Gene Expression Using Multiplex RT-qPCR to Characterize Heterogeneity of Rare Lymphoid Populations
Published on: January 19, 2017
Methods for qPCR gene expression profiling applied to 1440 lymphoblastoid single cells
Kenneth J Livak1, Quin F Wills, Alex J Tipping
1Fluidigm Corporation, 7000 Shoreline Court, Suite 100, South San Francisco, CA 94080, USA. ken.livak@fluidigm.com
Methods (San Diego, Calif.)
|October 20, 2012
Summary
This study presents microfluidic methods for analyzing single-cell gene expression, overcoming noise challenges. These techniques enable robust analysis of Wnt pathway activation across many cells.
Area of Science:
- Molecular Biology
- Genomics
- Biotechnology
Background:
- Eukaryotic transcript generation is inherently stochastic, posing challenges for single-cell gene expression analysis.
- Conventional quantitative polymerase chain reaction (qPCR) methods struggle with the noise and scale required for single-cell studies.
- Understanding gene expression at the single-cell level is crucial for fields like developmental biology and disease research.
Purpose of the Study:
- To detail methods for collecting and analyzing single-cell gene expression data using microfluidic arrays.
- To address the inherent noise in single-cell transcriptomics.
- To explore the effect of genotype on Wnt pathway activation using single-cell qPCR.
Main Methods:
- Utilized microfluidic arrays for high-throughput data collection on multiple genes in numerous single cells.
- Performed 96 quantitative polymerase chain reaction (qPCR) assays on 1440 lymphoblastoid cells.
- Included preliminary data processing steps for raw single-cell qPCR data.
- Contrasted single-cell qPCR methods with conventional qPCR approaches.
Main Results:
- Successfully collected and processed single-cell gene expression data from a large cohort of cells.
- Demonstrated the feasibility of using microfluidic arrays for robust single-cell qPCR.
- Generated data relevant to Wnt pathway activation influenced by genotype.
Conclusions:
- Microfluidic-based single-cell qPCR offers a viable solution to the challenges of analyzing noisy gene expression data.
- The described methods facilitate large-scale, high-resolution gene expression studies.
- This approach provides a foundation for investigating genotype-phenotype relationships at the single-cell level.
