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

Area of Science:

• Molecular Biology
• Genomics
• Biotechnology

Background:

• Single-cell mRNA sequencing (mRNA-seq) is crucial for dissecting gene expression and regulatory networks.
• Microfluidics offers advantages for single-cell analysis due to small reaction volumes and automation capabilities.

Purpose of the Study:

• To describe a comprehensive workflow for single-cell mRNA-seq.
• To demonstrate the utility of the C1 Integrated Fluidic Circuit (IFC) for isolating and processing up to 96 single cells.
• To highlight the generation of full-length mRNA information.

Main Methods:

• Utilized the C1 IFC for automated single-cell isolation and processing.
• Performed on-chip lysis, reverse transcription, and preamplification PCR.
• Executed off-chip sequencing library preparation.

Main Results:

• Successfully implemented a workflow for single-cell mRNA-seq using C1 IFC.
• Generated full-length mRNA sequence data from up to 96 individual cells.
• Demonstrated the value of full-length mRNA information over 3' end counting methods.

Conclusions:

• The described workflow enables efficient and high-throughput single-cell mRNA-seq.
• The C1 IFC platform facilitates comprehensive gene expression analysis at the single-cell level.
• Full-length mRNA sequencing provides richer data for biological insights compared to 3' end methods.