The first automated solution for single-cell genomics, now capable of even more


The Revolution at Hand

The world’s first automated solution for single-cell genomics research continues to break new ground, now offering more capabilities than ever before. C1 lets you prepare single-cell templates for mRNA sequencing, DNA sequencing, epigenetics or miRNA expression. Now you can conduct large-scale whole transcriptome studies to survey heterogeneity and discover novel cell populations. And with our new single-cell mRNA Seq HT workflow, you can reliably isolate and process up to 800 individual cells per run. Though we know you'll do much more than that.

Learn more about doing bigger, bolder studies with Single-Cell mRNA Seq HT.


Discover differences in heterogeneous populations with single-cell accuracy


Easily isolate and process individual cells with a streamlined workflow and intuitive interface


Minimize hands-on time with an automated cell-to-data workflow


Explore everything from mRNA to epigenetics, or build your own applications with C1 Open App


The innovative C1 system carefully isolates single cells into individual reaction chambers in the exclusive Fluidigm integrated fluidic circuit (IFC). The optically clear IFC lets you automatically stain captured cells and examine them by microscopy for viability, surface markers or reporter genes. After staining, cells are automatically lysed and template is quickly prepared for qPCR or sequencing analysis—all in as little as four hours.


  1. Prime
  2. Capture
  3. Stain
  4. Lyse
  5. Amplify
  6. Harvest


Prime the C1 IFC in preparation for sample transfer.


Insert the IFC into C1 to automatically isolate up to 800 individual cells to separate reaction chambers.


Label each cell and microscopically image the IFC to confirm cell count and viability.


Reinsert the IFC into C1 to lyse each cell for amplification.


Magnify each cell’s genomic content for sequencing or qPCR detection.


Collect product from the C1 outlet.


C1 Support

Explore tutorials and publications, browse frequently asked questions, download technical documents, review training programs and service plans and locate the right IFCs, kits and reagents for your research. Still need help? Reach out to one of our support specialists here


IFCs, Assays and Reagents


Go bigger and bolder—discover novel cell populations or rare cell types with this innovative IFC. Capture and process up to 800 cells per run with on-IFC sample multiplexing and lower library prep costs. Designed to capture cells 10–17 µm in diameter.

Learn more about an important update on our medium cell IFCs used on the C1 system.


Begin exploring cellular heterogeneity with the C1 mRNA Seq IFC. Designed for absolute quantification or full transcript sequencing, our 96-cell IFC gives you access to the whole transcriptome and captures cells 5–25 µm in diameter.

Learn more about an important update on our medium cell IFCs used on the C1 system.


Understand the clonal context of somatic mutations to reveal the true heterogeneity within your sample using the C1 DNA Seq IFC. One integrated workflow lets you isolate and process 96 cells to explore cell lineage at the whole genome, whole exome or targeted loci level. Designed to capture cells 5–25 µm in diameter.

Learn more about an important update on our medium cell IFCs used on the C1 system.

C1 Preamp IFC

The C1 Preamp IFC enables targeted gene expression to verify gene signatures defining a cell population or delve into the miRNA regulating gene expression. Designed to capture cells 5–25 µm in diameter and for use with Biomark systems.

Learn more about an important update on our medium cell IFCs used on the C1 system.

C1 Open App IFC

Create new single-cell applications on the Open App IFC. This innovative IFC is all about flexibility and is designed to capture cells 5–25 µm in diameter.

Learn more about an important update on our medium cell IFCs used on the C1 system.

C1 Reagent Kit

Jump-start your single-cell studies with our ready-to-use reagent kits for mRNA sequencing, DNA sequencing, preamplification and Open App use. Each kit contains the components needed for cell loading, lysis and harvesting.

  1. C1 mRNA Seq HT IFC
  2. C1 mRNA Seq IFC
  3. C1 DNA Seq IFC
  4. C1 Preamp IFC
  5. C1 Open App IFC
  6. C1 Reagent Kit

Related Systems

Access Array

Access Array

Ready your work for the latest in next-generation sequencing by enriching multiple unique targets from a large number of samples on the Access Array™ system.


Callisto Design, optimize and execute multistage, long-term cell culture and model development protocols with just a few taps on the Callisto touchscreen.

Biomark HD

Biomark HD Analyze gene expression with real-time PCR, industry-leading flexibility and consistently high-quality results on the Biomark™ HD system.
  1. Access Array
  2. Callisto
  3. Biomark HD


Script Hub

Script Hub™ is your central source for C1™ methods and applications. Get access to scripts and other applications developed by Fluidigm and the C1 community, including epigenetics, mRNA sequencing, DNA sequencing, cell staining and more.

C1 System Software v2.1.2

The C1 system supports DNA sequencing, mRNA sequencing, targeted gene expression, miRNA analysis and additional applications through the C1 Open App™ IFC (integrated fluidic circuit). Download the C1 system software update and then follow the instructions for updating the C1 system software.

Script Builder Software v2.1.1

C1 Script Builder™ allows you to create innovative single-cell applications to deeply explore cellular heterogeneity and the functional attributes of every cell population. Download the latest version of Script Builder here, then follow the instructions for installation. Note: Script Builder can be used without a license to design custom protocols. A license is required to transform custom protocols into scripts and install them on your C1.

Singular Analysis Toolset Software v3.5.2

An innovative, open-source solution for analyzing and visualizing data, the Singular™ Analysis Toolset offers powerful methods for identifying gene expression and mutation patterns at the single-cell level. Designed for use with Biomark and C1 systems.

  1. Script Hub
  2. C1 System Software v2.1.2
  3. Script Builder Software v2.1.1
  4. Singular Analysis Toolset Software v3.5.2


Clearance 6 in (15 cm) from the rear
Temperature 59–82 °F (15–28 °C) stable
Altitude <8,202 ft (2,500 m)
Site preparation

Refer to the C1 System Site Requirements (PN 100-5201) for more information on operating requirements.

As shipped

Height 30 in (76 cm)
Width 28 in (71 cm)
Depth 39 in (99 cm)
Weight 159 lb (72 kg)


Height 19 in (48 cm)
Width 16 in (41 cm)
Depth 26 (66 cm)
Weight 103 lb (46.7 kg)


Thermal control Peltier-based, 4–99 °C
Max heating rate >4 °C/sec
Max cooling rate >3 °C/sec
IFC compatibility C1 IFCs
Current 9 A (max)
Voltage 100–240 V
Main supply fluctuation Not to exceed ±10% of the nominal supply voltage
Frequency 50/60 Hz