23fa Single-Cell Genomics - The C1™ Single-Cell Auto Prep System
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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 Analysis
• 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 with minimal hands on time
• All in one—Comprehensive, automated workflow generates reproducible and reliable results
• Flexible—Supports multiple single cell applications including global transcriptome analysis, targeted gene expression, and miRNA analysis (coming soon)

C1 Single-Cell TaqMan Protocol

Download TaqMan® on the C1 System: A preamplification protocol utilizing TaqMan assays for single-cell gene expression

C1 Single-Cell mRNA Protocol

Learn about the C1 Single-Cell mRNA protocol: A new simplified approach to transcriptome analysis of single cells

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 wins 2012 Good Design Award


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As Awarded by The
Chicago Athenaeum: Museum of Architecture and Design.
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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 gene expression workflow to process 96 single cells across 96 mRNA targets. This new system enables you to rapidly explore unique attributes of individual cells without the technical variability of a standard gene expression workflow.

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

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

Two 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

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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.





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BioMark™ HD System



IFCs & Kits

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
  • Two kits available: gene expression or the new mRNA 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.  


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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 quantity. 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
  • Used in combination with validated scripts to support gene expression or mRNA sequencing
  • 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

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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.


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The 96.96 Dynamic Array™ IFC


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Custom Assays
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

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Software

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 gene expression data. It includes:

  • 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

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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.

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