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C1™ Single-Cell Auto Prep System
A New Approach to Single-Cell Genomics

Key Applications:
Gene Expression, Single-Cell Gene Expression, Single-Cell mRNA Sequencing Analysis, Single-Cell DNA Sequencing

Single cell precision—Greater accuracy lets you measure differences in gene expression profiles
Easy to use—Simplify cell isolation and preparation with a streamlined workflow and intuitive interface
Fast—Cell input-to-data with minimal hands on time
All in one—Comprehensive, automated workflow generates reproducible and reliable results
Flexible—Supports multiple single-cell applications, allowing you to run global transcriptome analysis, targeted gene expression, miRNA analysis, and whole genome amplification for DNA sequencing

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 Auto Prep 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, amplify, and ultimately detect and analyze cell activity using just one technology, reducing the variability caused by multi-platform technical errors.

The C1 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 IFCs, you can achieve single-cell accuracy with “load and go” productivity.

C1 Single Cell Auto Prep System, for single cell isolation and single cell analysis
• C1 System Technology Video
• C1 System Workflow Video
• Winner 2012 Good Design Award

Winner of the IBO Gold
Design Award 2013

 Awarded by The Chicago
Athenaeum: Museum of
Architecture and Design

New workflow enhancements:

New The Single-Cell Preparation Guide

Achieve high quality data with every run. The Single-Cell Preparation Guide compiles the most robust prep methods for the C1™ System into one guide. Download it here >>

Streamline your analysis

The SINGuLAR™ Analysis Toolset 3.5 is an intuitive, easy-to-use tool to analyze Fluidigm Single-Cell DNA sequencing, Gene Expression, miRNA Profiling, and mRNA sequencing data sets. Based on the popular statistical programming language, R, you can quickly and easily analyze, visualize and compare transcriptional or variant profiles. You can use an automated analysis command and advanced functions to perform unbiased hierarchical clustering and principal component analysis (PCA), ANOVA, and much more.

Get Started >>

The C1™ Single-Cell Auto Prep System is the world’s first commercially available, automated single-cell isolation and preparation system for genomic analysis. The C1 System provides an easy and highly reproducible workflow to process 96 single cells for DNA or RNA analysis. This new system enables you to rapidly explore unique attributes of individual cells without the technical variability of manual single-cell workflows.

The C1 Single Cell Auto Prep System consists of:
  • C1 Single-Cell Auto Prep System—Breakthrough, bench top automation of the isolation, lysis, and preamplification of single cells

  • C1 Single-Cell Auto Prep Array IFC—Proprietary integrated fluidic circuit that facilitates capture and highly paralleled preparation of 96 individual cells

  • C1 Single-Cell Auto Prep Reagent Kit—Pre-formulated reagent kit to support cell suspension, lysis, and purification


See how the C1 Single-Cell Auto Prep System can help you to go from discovery to validation using just one technology.

Three Innovative Systems, One Powerful Workflow

C1 Single-Cell Auto Prep System

Simple “plug and play” workflow to reproducibly prepare 96 single cells in about 1 hour.

  • Capture cells—batches of cells are loaded in a single pipetting step and rapidly separated into 96 individual chambers for preparation
  • Verify—quality control checkpoint to verify the number of captured cells and distinguish live and dead cells preserves your data integrity
  • Lyse—rapid direct cell lysis method that saves time and cost without RNA purification
  • Reverse transcribe and preamplify—cDNA synthesis and preamplification occur on the same sample without reagent mixing and sample transfer
  • Harvest—the multiplex preamplification products are harvested, and transferred to the BioMark™ HD System for quantitative PCR analysis or to library preparation for next generation sequencing


C1 Single-Cell Auto Prep System

BioMark™ HD System

Unparalleled throughput for real-time PCR experiments that complements the C1 System.

  • Quantitative PCR—Amplified products from the C1 System are diluted and pipetted into the Dynamic Array IFC, then loaded and thermal cycled on the BioMark HD System.  Quantitative PCR analysis can be used for differential gene expression or to quantitate the relative amount of cDNA library prior to mRNA Sequencing. 
  • Analyze—use the Fluidigm Real-Time PCR Analysis Software to view and analyze real-time data including delta Ct, delta delta Ct, and fold change calculations

The C1 Single-Cell AutoPrep System coupled with the BioMark HD System streamlines gene expression analysis seamlessly and efficiently to support up to 96 individual cells across 96 transcripts. The C1 Single-Cell AutoPrep System dramatically increases productivity to further accelerate expression profiling studies.


BioMark HD System

Access Array™ System

The first high-throughput target enrichment system designed to work with all next-generation sequencing platforms.

  • Single-cell target enrichment—compatible with the C1 system for single-cell DNA sequencing
  • Analyze—Use D3™ Assay Design to build custom panels for your target loci. Interrogate up to 480 targets per single cell.


Access Array System

C1™  Single-Cell Auto Prep Reagent Kit

Ready-to-use Reagents
  • Kits contain buffers and wash solutions
  • Ready for automated capture, lysis, dilution, and harvest
  • Use in the C1™ Single-Cell Auto Prep System
  • Three kits available: gene expression, mRNA sequencing, or the new DNA sequencing kit

Reagent mixing is not required, minimizing tube mix-ups and providing a convenient automated method for single-cell processing. Reagents for reverse transcription and preamplification must be purchased separately.  


C1™ Single-Cell Auto Prep Reagent Kit

C1™ Single-Cell Auto Prep IFC

Enable the Fluidigm easy single-cell gene expression and single-cell mRNA sequencing workflow

Using integrated thermal and pneumatic control at nanoliter scale, all steps of the workflow, from capture to preamplification, can be contained and completed reproducibly within the AutoPrep IFC without intervention. No reagent mixing, transfer or addition is required. It is easy to load, requires minimal hands-on time, reduces the risk of carryover contamination, and provides highly reliable data quality. Learn more about the C1™ Single-Cell Auto Prep IFC.

  • Specifically captures and prepares cells for genomic analysis
  • Newest microfluidic circuit design
  • Easy to load samples and reagents
  • Optimized to isolate cells by cell size:
    • 5-10 micron new: for small cells such as stem cells and WBC
    • 10-17 micron: for medium cells such as iPS, progenitor cells, neurons, and others
    • 17-25 micron: for large cells such as fibroblasts, keratinocytes, cardiomyocytes, smooth muscle cells, and others


C1™ Single Cell Auto Prep IFC

Dynamic Array™ IFC

Match with Fluidigm integrated fluidic circuit (IFC) technology

  • Sensitive, high-throughput, simple tool for quantitative analysis
  • The 96.96 Dynamic Array IFC of mRNA from single cells
  • Compatible with DELTAgene™ or TaqMan® Gene Expression assays

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 by up to 100-fold.


The 96.96 Dynamic Array IFC

DELTAgene™ Assays

Take full advantage of your C1™ Single-Cell Auto Prep System

  • High quality—sensitivity and linearity similar to probe-based assays
  • MIQE compliant—assay primer sequences provided
  • Cost savings—low startup and running costs

Flexible groups of biologically-related genes are available for your specific requirements; there is no need to use fixed content. Simply provide us with your genes of interest (via RefSeq IDs) and the target species. All assays are ready to use via Fluidigm standard protocols.

Cq difference between 1, 10 and 100 cells easily distinguished

C1™ Single-Cell Auto Prep System OS 2.0 Upgrade

The latest operating system upgrade for the C1™ Single-Cell Auto Prep System OS 2.0 supports DNA sequencing, mRNA sequencing, targeted gene expression, miRNA Analysis, and our new Open App IFC.

Download the OS 2.0 upgrade >


The SINGuLAR™ Analysis Toolset

The SINGuLAR™ Analysis Toolset is a powerful analysis tool based on the programming language R, for analyzing and visualizing single-cell DNA sequencing and gene expression data. It includes:

  • Identify and evaluate novel mutations — Perform Fisher’s Exact test and display Manhattan plots to select for significant variants
  • Compare gene expression levels — Convert Ct values to Log2 gene expression using LoD method to assign unexpressed genes
  • Sort and filter function — Sort by gene expression and rapidly exclude low variance genes
  • Scalable computing — Process individual or multiple data sets in parallel
  • Multivariant analysis — Analyze data in hierarchical clustering or PCA to compare factors
  • Visualization tools — View data in violin plot, scatter plot, or heat map to rapidly identify major
    classes of individual cells

Download the scripts and sample data >


Visualization Tools - Violin Plot
Results are easily viewed in multiple plots or map views.

Real-Time PCR Analysis

Intuitive and easy to use

  • Standard curve view—easily calculate the standard curve by identifying dilution samples
  • Delta Ct calculation—get delta delta Ct in just three easy steps
  • Automated threshold setting—automatically determine the ideal threshold setting for each chip run

An automatic curve quality score quickly and efficiently sorts through the real-time PCR curves
and excludes those that do not meet your criteria. The Fluidigm software features include pipetting
templates, easy import/export functionality, predefined experiment layouts, and a selection of
data viewing options.

Table and Amplification Curve Views

Results may be easily viewed in table format.