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

BioMark™ HD 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.

The reader is equipped with features that enhance throughput and ease-of-use:

• Easy-to-use  acquisition software module to start a chip run in less than one minute.
• Multiplex capability for up to five reporter dyes.
• Computer-controlled chip tray to minimize manual work.
• Integrated barcode scanner to identify each chip type and tracks results.
• Integrated high-speed computer connections.
• Setup and acquisition software that easily interfaces with liquid-handling workstations.

BioMark Reader

IFC Controllers

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

Key advantages

• Automated setup of Dynamic Array and Digital Array IFCs
  
• Significantly fewer liquid handling steps when compared to conventional platforms
• Self-contained and fully integrated design
• Touch screen interface

Dynamic Array™ IFCs

Fluidigm Dynamic Array integrated fluidic circuits (IFCs) deliver a new level of efficiency and throughput for real-time PCR and genotyping applications. Dynamic Array IFCs have an on-chip network of microfluidic channels, chambers and valves that automatically assemble individual PCR reactions, decreasing the number of pipetting steps required by up to 100 fold. Reusable chip formats have also been developed to dramatically decrease costs and increase throughput. The available chip formats are:

• 192.24 - 192 samples x 24 assays (single use)
• FR48.48 – 48 samples x 48 assays (reusable, SNP Genotyping use only)
  
• 48.48 – 48 samples x 48 assays (single use)
  
• 96.96 – 96 samples x 96 assays (single use)

96.96 Dynamic Array IFC

Digital Array™ IFCs

The Fluidigm Digital Array integrated fluidic circuit (IFC) enables users to conduct digital PCR experiments. The digital array partitions a sample, premixed with PCR reagents, into hundreds of individual PCR reactions. This partitioning of the mixture allows the absolute quantification of target sequences. Digital PCR is a novel technique for PCR applications demanding extremely accurate determination of copy number variation.

Using the Fluidigm digital PCR technology, there are just five easy steps from setup to analysis to discovery.  See how it's done. 

48.770 Digital Array IFC

SlingShot™ Kit

The SlingShot™ Sample Quantification Kit offers a novel application of digital PCR for absolute quantification of amplifiable DNA in your library. With the SlingShot kit, you gain the power of digital PCR on Digital Array IFCs for finding the optimal DNA-to-bead ratio for emPCR.

The SlingShot Kit uses digital PCR assays to detect only amplifiable molecules within the sample mixture. This absolute measurement eliminates the need for mass-based calibrators or reference samples. In addition, because of the sensitivity of digital PCR, only minimal sample concentrations are required to achieve quantitative results. The accuracy and sensitivity offered by SlingShot technology allows sequencing of previously undetectable samples while saving time and money.

Key Benefits:

• Obtain absolute measurement of your amplifiable sample
• Eliminate costly titration steps while improving data quality
• Use as little as 1 pg of material

Each bright spot indicates a positive PCR reaction or an amplicon that can be sequenced. By counting the number of positive reactions, the total copy number of amplicons in the samples of interest can be determined.

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 C_t calculation - you can get delta delta C_t 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.

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.

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.

Brochures

• BioMark™ HD System
  
• Analyzing the Gene Expression of Single Cells
• High Sample Throughput SNP Genotyping
  

Specification Sheet

• BioMark HD System
  

Data Sheets

• DELTAgene™ Assays
• SNPtype™ Assays
• SlingShot™ Kit
• 192.24 Dynamic Array™ IFC
  

Application Notes

• The Study Of Copy Number Variations (CNVs) Using the 12.765 Digital Array
• Enabling Loss of Heterozygosity Studies Using Fluidigm Digital Arrays
• Efficient Drug Metabolism Studies using the Fluidigm System
• BioMark Dynamic Array for Single-Cell Gene Expression Analysis
• Comparison of Two Protocols for Single-Cell Gene Expression on Dynamic Arrays
• Fluidigm System for Rapid, Reliable, and Cost Effective Genotyping
• Determining Copy Number Variation (CNV) Using Dynamic Arrays on the BioMark System

Customer Focus

• Scientists Turn Skin Cells into Neurons
• Irv Weissman Lab performs Single-Cell Gene Expression ‘as a Matter of Course’

News

• July 10, 2010
  Leading INRA Facility Reports Robust Genetic Analysis Results from Fluidigm Biomark™ System
  Number One Agricultural Institute in Europe Brings World-leading Integrated Fluidic Circuit Technology to All European Researchers

Featured Publications

• Narsinh, K.H., Sun, N., Sanchez-Freire, V., Lee, A.S., Almeida, P., Hu, S., Jan, T., Wilson, K.D., Leong, D., Rosenberg, J., Yao, M., Robbins, R.C., Wu, J.C. December 15, 2010. Single Cell Transcriptional Profiling Reveals Heterogeneity of Human Induced Pluripotent Stem Cells. Journal of Clinical Investigation
• Menzel, S., Qin, J., Vasavda, N., Thein, S.L., Ramakrishnan, R. September 24, 2010. Experimental Generation of SNP Haplotype Signatures in Patients with Sickle Cell Anaemia. PLoS One
  Download Article
• Petriv, O.I., Kuchenbauer, F., Delaney, A.D., et al. August 11, 2010. Comprehensive microRNA expression profiling of the hematopoietic hierarchy. PNAS
  
  
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Featured Posters                          

• AMN 2011: Digital PCR on Fluidigm's New 200K Digital Array Chips
• PAG 2010: Use of Fluidigm BioMark™ for Genotyping, Gene Expression and 454 Libraries Quantification
• PAG 2010: Use of Fluidigm BioMark for Genotyping, Gene Expression and 454 Libraries Quantification
• ISPD 2010: A Multiplexed Approach for the Detection of Fetal Aneuploidies in Maternal Plasma
  
  
More >

Gene Expression and SNP Genotyping Workflow

• Prime. Prime the Dynamic Array IFC to close the interface valves, preventing premature mixing of samples and assays.
• Transfer. Pipette samples, premixed with master mix, into separate sample inlets and primer-probe sets into separate primer-probe inlets on the frame of the chip.
• Load. Place the Dynamic Array IFC on the IFC Controller, and use the software interface to pressure load the assay components into reaction chambers. Assay components are automatically combined on-chip.
• Run. Place the Dynamic Array IFC on the BioMark System for thermal cycling and end-point or real-time fluorescence detection.
• Analyze. Use the analysis software to view and analyze color-coded allele maps and cluster diagrams for one or more chip runs.

Digital PCR Workflow

• Prime. Prime the Digital Array IFC to prepare it for transferring samples.
• Transfer. Pipette each of the samples, premixed with master mix and primer-probe sets, into separate inlets on the frame of the chip.
• Load. Place the Digital Array IFC on the IFC Controller, and use the software interface to pressure load the assay components into separate panels of reactions.
• Run. Place the Digital Array IFC on the BioMark System for thermal cycling and fluorescence detection.
• Analyze. Use the analysis software to view and analyze amplification curves and color-coded heat maps for one or more chip runs.