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, the C1™ system employs our innovative microfluidic technology to rapidly and reliably isolate, process and prepare individual cells for genome and transcriptome analysis. With just one instrument, you can isolate cells, stain them and prepare template for sequencing or qPCR. Though we’re sure you'll do much more than that.


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


Get DNA and mRNA seq, targeted gene expression and miRNA template with one platform



The innovative C1 system carefully isolates single cells into individual reaction chambers in Fluidigm's exclusive 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 96 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.


IFCs, Assays and Reagents


Achieve highly reliable and reproducible data from individual cells with our latest microfluidic IFCs, designed to capture cells from 5 to 25 µm. Created specifically for C1™ systems.

C1 Reagent Kit

Automate your single-cell research with our ready-to-use reagent solutions for DNA sequencing, mRNA sequencing and targeted gene expression.

  1. C1 IFCs
  2. C1 Reagent Kit

Related Systems

Biomark HD

Biomark HD Analyze single-cell gene expression with real-time PCR, industry-leading flexibility and consistently high-quality results on the Biomark™ HD system.

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.
  1. Biomark HD
  2. Access Array


Singular Analysis Toolset

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.

Singular Practice Sets v3.5.2

Practice your Singular software skills with this set of sample scripts. Validate your technique before you commit valuable resources.

C1 System Software v2.0

The latest system software upgrade for C1 supports IFC for Open App in addition to DNA sequencing, mRNA sequencing, targeted gene expression and miRNA analysis.

  1. Singular Analysis Toolset
  2. Singular Practice Sets v3.5.2
  3. C1 System Software v2.0


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 (99cm)
Weight 159 lb (72 kg)


Height 19 in (48 cm)
Width 16 in (41 cm)
Depth 26 (66cm)
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