Using Fluidigm C1 to Generate Single-Cell Full-Length cDNA Libraries for mRNA Sequencing

  • Robert Durruthy-Durruthy
  • Manisha Ray
Part of the Methods in Molecular Biology book series (MIMB, volume 1706)


Single-cell RNA sequencing has evolved into a benchmark application to study cellular heterogeneity, advancing our understanding of cellular differentiation, disease progression, and gene regulation in a multitude of research areas. The generation of high-quality cDNA, an important step in the experimental workflow when generating sequence-ready libraries, is critical to maximizing data quality. Here we describe a strategy that uses a microfluidic device (i.e., the C1™ IFC) to synthesize full-length cDNA from single cells in a fully automated, nanoliter-scale format. The device also facilitates confirmation of the presence of a single, viable cell and recording of phenotypic information, quality control measures that are crucial for streamlining downstream data processing and enhancing overall data validity.

Key words

Single-cell RNA-seq Gene expression profiling Full-length cDNA Single-cell transcriptomics Cell characterization 


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Copyright information

© Springer Science+Business Media, LLC 2018

Authors and Affiliations

  • Robert Durruthy-Durruthy
    • 1
  • Manisha Ray
    • 1
  1. 1.Fluidigm CorporationSouth San FranciscoUSA

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