Single-Cell mRNA-Seq Using the Fluidigm C1 System and Integrated Fluidics Circuits

  • Haibiao Gong
  • Devin Do
  • Ramesh Ramakrishnan
Part of the Methods in Molecular Biology book series (MIMB, volume 1783)


Single-cell mRNA-seq is a valuable tool to dissect expression profiles and to understand the regulatory network of genes. Microfluidics is well suited for single-cell analysis owing both to the small volume of the reaction chambers and easiness of automation. Here we describe the workflow of single-cell mRNA-seq using C1 IFC, which can isolate and process up to 96 cells. Both on-chip procedure (lysis, reverse transcription, and preamplification PCR) and off-chip sequencing library preparation protocols are described. The workflow generates full-length mRNA information, which is more valuable compared to 3′ end counting method for many applications.

Key words

Single-cell mRNA-seq Gene expression Integrated fluidic circuit 


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Fluidigm CorporationSouth San FranciscoUSA
  2. 2.Dovetail Genomics LLCSanta CruzUSA

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