Single-cell Gene Expression

SNP Genotyping

Digital PCR

Automated Target Enrichment for NGS


Biotechnology promises to become the defining technology of the 21st century. Continued development of the industry fundamentally depends on new tools that can deliver miniaturization and integration-just as the integrated circuit gave rise to the computer age.

Today, with MSL™ technology tens of thousands of fluid control valves and interconnected channels are fabricated within miniature devices. We call these devices integrated fluidic circuits (IFCs) because, like their analog in the semiconductor industry, they are networks of discrete pathways and intermediate switches. Instead of electrons, they move molecules of biological samples and reagents in a dazzling variety of patterns.

* IFCs are the core technology in Fluidigm's product portfolio of:


Imagine an experiment where you select the cells and control their environment . Think of the functional questions you can ask if you could simulate their cell state and physiological conditions. You could discover the factors that drive cellular heterogeneity or determine how a rare cell responds to changes in signaling queues. Now stop dreaming and start doing all that and more with the new Polaris™ system. Dose individual cells under strict environmental control, then immediately prepare them for expression analysis via next-generation sequencing. Image and select only the cells you want and improve your sequencing efficiency with unprecedented experimental reproducibility and standardization. And because it all happens on one precisely designed IFC, controlled by an elegant, intuitive touchscreen interface, all you need to think about is what question you'll answer next.

Versatile - Challenge cells in vivo with a variety of parameters, including transcription factors, RNAs, small molecules and more. You determine the number of conditions, dosage, and duration.

Controlled - Keep chosen cells viable in individual environmental chambers for up to 24 hours with precise control of the flow of media, gas, temperature and humidity.

Specific - Test only the cells you want by automatically enriching populations as scarce as 1:100

Simple - Run a complete study from live cell loading to mRNA seq within a single instrument with a touch of your finger.

Please contact us to learn more about the new Polaris System


How would you like to genotype from as little as 5.5 ng total input DNA and get 9,216 data points in under three hours with a single touch of a button? Introducing Juno™, a first-of-its-kind revolution that combines preamplification and SNP genotyping into one automated process. Now researchers in genetic health, agrigenomics, sample identification and more can accurately genotype extremely small and challenging samples with minimal hands-on time. All in a sleek, beautifully designed machine that looks like a work of art. It may not be polite to stare, but no worries. We're doing it too.

Minimal - Get precise data from a starting concentration of as little as 2.5 ng/µL, 5.5 ng total DNA

Easy - Transfer samples and assays, press Start and have complete results within three hours

Flexible - Take advantage of a wide selection of sample and assay configurations without added costs

Intuitive - Enjoy an advanced user interface and modern design that enhances your experience

Please contact us to learn more about the Juno System


A New Approach to Single-Cell Genomics

  • Single-cell precision-greater accuracy to measure differences in gene expression profiles
  • Easy to use-simplified cell isolation and preparation with a streamlined workflow and intuitive interface
  • Fast-cell input-to-data in less than a day
  • All in one-comprehensive, automated workflow generates reproducible and reliable results
  • Flexible-expandable into whole transcriptome and variant discovery

Geneticists and clinical researchers have been looking for a complete workflow that can examine and differentiate single cells and group them according to unique genomes and transcriptomes while minimizing technical noise.

The C1 Single-Cell AutoPrep System takes an entirely new approach, based on innovative microfluidic technology that enables you to rapidly and reliably isolate, process and profile individual cells for genomic analysis. For the first time, you can extract, reverse transcribe, preamplify and ultimately detect and analyze cell activity using just one technology, reducing the variability caused by multi-platform technical errors.

The C1 Single-Cell AutoPrep System enables you to study cell differentiation, measure individual cell responses to specific stimuli, verify critical disease biomarkers, validate RNAi knockdown, and conduct candidate drug screens.

With an optimized protocol, pre-formulated reagent kit, and disposable arrays, you can achieve single-cell accuracy with "load and go" productivity.

NEW! Single-Cell DNA Sequencing with the C1™ Single-Cell Auto Prep System

You can now discover unique cell populations and their genetic signatures within complex samples using the C1 Single-Cell Auto Prep System.

With one method, you can prepare high-quality single-cell genomic DNA template for whole genome, whole exome and targeted sequencing. With whole genome and exome sequencing you can explore the protein-coding or regulatory regions of the genome to comprehensively discover functional and regulatory variants. These methods allow the broadest scope for discovery, ensuring that key mutations are not missed in your initial search. Targeted DNA sequencing is the fastest and most cost-effective approach to screen known loci to profile samples. Using these approaches at the single-cell level provides the most effective methods to rapidly discover and screen mutations responsible for disease onset and progression.


  • Single-cell sensitivity- Discover and detect SNPs, indels and translocations in individual cells
  • One prep, many possibilities- One simple and efficient workflow supports whole genome, whole exome or targeted sequencing directly from a single cell
  • Optimized for superior performance-Achieve uniform chromosomal coverage with low GC bias and error rate, all while saving time and reducing sample input

The C1 Single-Cell DNA Sequencing Workflow

Figure 1. Simplified workflow for single-cell DNA sequencing. The C1 System automates single-cell processing and produces whole genome amplified
template for an easy transition to library preparation and sequencing. Load an enriched cell population into the C1 IFC; the C1 System automatically
performs whole genome amplification (WGA) using optimized chemistry and validated scripts. Harvest the WGA amplicon for whole genome, whole
exome, or targeted sequencing library preparation prior to sequencing. Analyze your data with SINGuLAR Analysis Toolset 3.5.

Learn more on the different Single-Cell DNA Sequencing applications:

Single-Cell Exome Sequencing Workflow

NOW AVAILABLE! Single-Cell Whole genome sequencing Technical Note - download the Technical note and learn how to implement single-cell whole genome sequencing on your C1 today.

View the Infographic:


Please contact us to learn more about the new DNA Sequencing application

on the C1 Single-cell AutoPrep System

mRNA Sequencing application on the C1™ Single-Cell Auto Prep System

The C1 Single-Cell Auto Prep System is a new approach to single-cell genomic applications, including targeted gene expression and the mRNA sequencing protocol for transcriptome analysis of single cells.

mRNA sequencing is a valuable tool to help you study global gene expression patterns in subpopulations of cells. Until now, most methods-like microarrays or many next-generation sequencing protocols-have been impractical for single-cell analysis. They require large numbers of cells, have complex workflows, generate variable results or are too costly to fit within your budget.

The new mRNA Sequencing application on the C1 Single-Cell Auto Prep System changes everything. For the first time you can extract, reverse transcribe, amplify, detect, and analyze cell activity using just one technology. The path less traveled just got a lot easier:


End-to-end workflow for transcriptome analysis of individual cells

Highest throughput

Unprecedented parallel processing of 96 single cells per run


Streamlined sample preparation directly from individual cells with only three hours of hands-on time, and no fragmentation or purification steps

Ultra sensitive

Compatible with single-cell input as little as 10 picograms per reaction

More mappable reads

Over 60% of total reads from single cells are mapped to RefSeq

Full gene analysis

Better read coverage across the entire transcript for better detailed analysis of alternative transcript isoforms and identifica­tion of single nucleotide polymorphisms


One-eighth the cost of other library preparation systems

Compatible with any

Illumina system

Supported on HiSeq, HiScan, GAII, and MiSeq sequencing platforms

More information:

Please contact us to learn more about the mRNA Sequencing application

on the C1 Single-cell AutoPrep System



The BioMark™ HD System provides you with the ability to use a wide variety of sample types, multiple chemistry choices, and an industry leading degree of flexibility. The system offers unparalleled throughput for real-time PCR and digital PCR, integrating thermal cycling and fluorescence detection on Integrated Fluidic Circuits (IFCs).

Integrated Fluidic Circuits significantly improve productivity in life science research by enabling the simultaneous performance of PCR reactions in nanoliter volumes. This is made possible by miniaturizing and integrating liquid handling components on a single microfluidic device. The BioMark HD System consists of a real-time PCR instrument, Dynamic Array™ IFCs for multiplexing the samples and reagents, as well as an IFC loader to load the Dynamic Array IFCs.

Key Applications include:

  • Gene Expression
  • Single Cell Gene Expression
  • SNP Genotyping
  • Copy Number Variation
  • Sample Quantification for Sequencing

The BioMark™ HD System is the newest real-time PCR system developed by Fluidigm. With enhanced productivity, increased reliability, and a smaller footprint, the BioMark HD System gives you everything the original BioMark delivered-and more.

Increase confidence - reproducible results from populations of cells down to a single cellSave time and money - fast PCR-enabled, nanofluidic technology allows you to collect more data points per day at less cost than 384-well systemsExpand your possibilities - ability to use multiple reagents and different sample and assay configurations.

Download the BioMark HD brochure and contact us for more information.


The BioMark™ line of life science products are meeting the challenges of today's high throughput research environment through integrated fluidic circuits known as dynamic arrays and digital arrays. These innovative products allow scientists to practice tried-and-true techniques, such as TaqMan® assays, while realizing a previously unachievable throughput.

The advantages of the BioMark system include:

  • Savings. Researchers save on reagents, pipette tips, time, and on the upkeep of expensive liquid-handling robots.
  • More Data. Far more data are generated compared to microwell chips, and with no pre-spotting required.
  • Throughput. Each 96.96 Dynamic Array is capable of producing 9,216 real-time qPCR data points in the same amount of time as a single 384-well plate, while using just 1/200th the amount of reagents.



Superior Sample Preparation System for Next-Generation Sequencing

The Access Array™ Integrated Fluidic Circuit (IFC) facilitates parallel amplification of 48 unique samples, in effect preparing 48 sequencing libraries, in just a few hours. Every reaction combines both an amplicon tagging and a barcoding (identification) step that enables all 48 amplicons to be multiplexed at the sequencing step. This powerful chemistry simplifies the up-front preparation and maximizes the utility of today's next generation sequencers.

The Fluidigm Access Array System can be used with any PCR-based sample preparation method and with the reagents and primers of your choice. The system includes Access Array IFCs-single-use microfluidic chips-two IFC Controller AXs, and the Stand-Alone Thermal Cycler that easily deliver sample throughput and coverage that scale with laboratory needs.

Learn More Here



The Fluidigm EP1 system for genetic analysis enables high-throughput SNP genotyping and end point digital PCR research through integrated fluidic circuits (IFCs) known as dynamic arrays and digital arrays. These innovative products allow scientists to practice tried-and-true techniques, such as TaqMan® assays, while realizing a previously unachievable throughput.

The advantages of the EP1 system include:

  • Outstanding Data Quality
  • 99%+ Call rates
  • 99.75% Accuracy in SNP genotyping experiments
  • Fast and Easy Workflow
  • 200K+ Genotypes in one day
  • About 100x Fewer pipette steps
  • Cost Effective System
  • About 100x Lower reagent volume requirements
  • About 100x Fewer pipette tips



The Future of Cytometry Today.

Mass cytometry resolves multiple metal probes per cell with minimal signal overlap, maximizing the information obtained from a single sample. With over 100 detector channels and over 30 isotopic probes, mass cytometry provides researchers with an unparalleled ability to phenotypically and functionally profile cells from normal and diseased states.

The Fluidigm line of reagents, instrumentation, and data analysis tools provide all the tools necessary for novel discovery applications using mass cytometry, including

Learn More Here




Push the limits of efficiency using our unique integrated fluidic circuits (IFCs). Learn about the advantages of IFCs for your application.


The Fluidigm Digital Arrays-48.770 and 12.765-provide a practical solution for PCR applications demanding extreme accuracy of copy number.


The Fluidigm Dynamic Arrays-96.96 and 48.48-maximize efficiency for gene-expression analysis and genotyping.


Unleash the power of our unique integrated fluidic circuits (IFCs). Learn about the advantages of using our kits for your application.


The SlingShot™ Kit for sequencing quickly and easily determines the concentration of your DNA library, with absolute accuracy.



If you would like further information on any Fluidigm Genomics products

contact Millennium Science by filling in the form below.

About Fluidigm

Fluidigm develops, manufactures and markets proprietary Integrated Fluidic Circuit (IFC) systems that significantly improve productivity in life science research. Fluidigm IFCs enable the simultaneous performance of thousands of sophisticated biochemical measurements in extremely minute volumes. These "integrated circuits for biology" are made possible by miniaturizing and integrating liquid handling components on a single microfluidic device. Fluidigm systems, consisting of instrumentation, software and chips, increase throughput, decrease costs and enhance sensitivity compared to conventional laboratory systems.

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