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. Reflected in over 100 published studies, the breadth of C1 applications empowers users to survey cell diversity, identify rare cell types and characterize cellular functions, all on the same single-cell biology platform. Investigate tissue heterogeneity with transcript end counting. Use T cell receptor sequencing and other full-length mRNA-seq protocols to recognize isoform- and receptor-specific expression. Examine gene-specific and microRNA expression. Perform epigenetic analysis and identify genomic variants. The C1 system delivers power and flexibility to support you all along your path to discovery.

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 applications for analyzing DNA, RNA and chromatin, or build your own applications with Script Hub


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, viability or phenotype.


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


Magnify each cell’s RNA or DNA 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.


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.

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.


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.

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, this innovative IFC can be used with the extensive library of C1 applications available through Script Hub™.

C1 Reagent Kits

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

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

Related Systems

Biomark HD

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


Polaris Seamlessly integrate cell biology and molecular analysis at the single-cell level. Within one workflow Polaris™ processes single cells for mRNA sequencing applications.
  1. Biomark HD
  2. Polaris


C1 mRNA Seq HT Demultiplex Script

The C1™ mRNA Sequencing High Throughput Demultiplexer Perl script application programming interface (API) allows automatic demultiplexing of individual single-cell samples from each column using the cell barcodes on the R1 reads. The API also automatically separates the large FASTQ file generated from each column pool into 40 pairs. This enables your C1 medium-cell HT IFC data to be preprocessed in a more efficient way.

C1 System Software

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

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, 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 system.

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.

Singular Analysis Toolset Software

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 Biomarkand C1 systems.

  1. C1 mRNA Seq HT Demultiplex Script
  2. C1 System Software
  3. Script Builder Software
  4. Script Hub
  5. Singular Analysis Toolset Software