Functional Genomics Core


Salk Institute for Biological Studies - Functional Genomics Core - Fluidigm-BioMark


Fluidigm-BioMark – Instruments

BioMark instrumentation consists of a real-time PCR instrument and a variety of chip
loading platforms customized for your throughput research requirements.

BioMark™ Reader
The BioMark Reader is a real-time PCR instrument designed to run Fluidigm Integrated Fluidic Circuits (IFCs) in either real-time or end-point read modes. Has the multiplex capability for up to five reporter dyes. Integrated barcode scanner to identify each chip type and tracks results. Integrated high-speed computer connections.

IFC Controllers
Fluidigm’s IFC Controllers are designed to prime, load, and clean (reusable IFCs only) Dynamic Array™ and Digital Array™ IFCs.

Fluidigm-BioMark – Software

Real-Time PCR Analysis
The Fluidigm Real-Time PCR Analysis software includes:

  • Standard curve view—Allows you to easily calculate the standard curve by identifying dilutions samples
  • Delta delta Ct calculation—You can get delta delta Ct in just three easy steps
  • Automated threshold setting—Automatically determine the ideal threshold setting for each chip run
  • Automatic curve quality score—Quickly and efficiently sorts through the real-time PCR curves and exclude those that do not meet your criteria

Table and Amplification Curve Views

Results may be easily viewed in table format.

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Genotyping Analysis
The Fluidigm Genotyping Analysis software includes additional features specific to genotyping applications including:

  • Automatic cluster calling—A highly accurate cluster calling algorithm that ranks among the best in the industry and automatically increases in accuracy as it processes more samples
  • Multiple chip scoring—Combines and scores multiple experiments to decrease the analysis time and improve scoring accuracy for rare genotypes
  • Confidence score—Automatically determines the confidence level of cluster calls
  • Real time or end point—Allows you to view real-time data to aid in assay design while using end point imaging for high throughput applications

Allele Map

Automatic cluster calling.

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Digital PCR Analysis
The Fluidigm Digital PCR software includes features for digital PCR.

  • Multiplex capability—Up to four reporter dyes can be used per reaction, allowing you to quantitate up to four targets per sample in each reaction
  • Copy number variation—The software will automatically apply statistical correction and determine the ratio of your targets of interest
  • End-point analysis—Allows you to use end-point image for analysis, greatly increasing the throughput of the system

Heat Map and Call/No-Call Map
The software automatically counts and reports the number of positives for each reporter dye.

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Fluidigm-BioMark – Tutorials