Fluidigm C1 Single Cell Capture and Genomics

Fluidigm C1 Single Cell Auto Prep

Technology Overview

The C1 instrument utilizes microfluidics on integrated fluidic circuits (IFCs) to capture, lyse and prepare cDNA or genomic DNA from 96 and up to 800 single cells in extremely small reaction volumes.

Our Fluidigm C1 Single Cell Genomics platform will enable clients to perform next generation sequencing or multiplexed targeted PCR analysis of single cells from bulk or sorted populations. We offer users training on preparation of the IFC, C1 instrument operation, and downstream analysis. The platform consists of the C1 Single Cell Auto Prep instrument and Biomark HD high throughput PCR instrument.

A background video detailing the technology can be found here.

IFCs: Available for three (3) cell size ranges: 5-10, 10-17, and 17-25 microns, pricing for IFCs varies according to the downstream application: RT-PCR, RNA-Seq and DNA-Seq. Clients should order IFCs for their C1 experiments directly from Fluidigm, https://www.fluidigm.com/ifcs. IFCs can also be customized for any single cell application using the Fludigm C1 OpenApp.

For more info on the Fluidigm C1 Auto Prep visit: Fludigm C1 OpenApp


  • C1 Single Cell Auto Prep Instrument (CCW 5145)
  • Biomark HD High Throughput PCR Instrument (CCW 5211)
  • Fluorescent Microscope for post-capture annotation of IFCs
  • Accurate pipetman, suitable for use with the C1 IFCs are available in the facility.

Services Available

At the current time we do not provide full service support for this platform. Following initial training, use of the instrumentation is self-service. Assistance for infrequent users may be available.

  • C1 System
    • Single cell capture and pre-amplification using Delta Gene Assays and TaqMan Assays for mRNA or miRNA
    • Single-cell cDNA library preparation for RNA-Seq using Nextera library prep
  • BioMark HD System
    • Real-time PCR of single cell (C1 isolated) or bulk populations
    • SNP Genotyping
    • Digital PCR analysis
    • Access Array system for Illumina sequencing systems
    • Access Array system for the Ion Torrent PGM sequencing system
  • EP1 System (https://www.fluidigm.com/productsupport/biomark-support-hub#documents)
    • BioMark/EP1 data collection
    • Singular Analysis

Using the Single Cell Genomics Facility

Please contact Pearl Campbell (pcampbell@ohri.ca) to discuss training and access to the facility. We will work closely with you until you can work with the instruments unaccompanied, as this will be a walk up facility after initial training. However, we are always there to answer any questions or concerns that you may have in order for you to get quality results for your analysis. Trained users will be able to book time on the instruments.