Home » Applications » Single-Cell Genomics » Single-Cell Gene Expression
Single-Cell Gene Expression
Individual cells can differ by cell state, size, protein
level and expressed mRNA transcripts, even within
a homogeneous cell population. Therefore, assuming
that every cell in your sample behaves exactly
the same is a dangerous gamble; taking averages
of pooled cells can mask the dramatic variations in
gene expression.

The Fluidigm Single-Cell Gene Expression Workflow combines our innovative C1™ Single-Cell Auto Prep System with the BioMark™ HD System to illuminate these differences, enabling you to profile up to 96 single cells for the expression of up to 96 genes in just a few hours, using standard reagents and easy-to-use single cell analysis tools.
Single Cell Gene Expression Heat Map by SINGuLAR

It provides an easy-to-use workflow and flexible assay configuration.  With an automated workflow, ready-to-use reagents, and optimized IFCs, you can eliminate tedious pipetting steps and sample mixing to achieve  “load and go” productivity.

Single Cell Gene Expression workflow using the C1 System and BioMark HD

•    Single-cell resolution—Identify previously unrecognized subpopulations
•    Easy to use—“Load and go” automation means there’s no mixing or adding reagent
•    Flexible assay format—Compatible with DELTAgene™ Assays or TaqMan® Gene Expression Assays  
•    Highly sensitive—Use picograms of starting material to screen against hundreds of genes
•    High throughput—Explore 96 single cells across 96 assays in a single run
•    Cost effective—Generate more data per dollar using nanoliter-scale reaction volumes
•    Reliable—Get consistent and reproducible data with every run

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 >>


Single-Cell Gene Expression
Fluidigm provides scientists with a practical means to rapidly achieve new insights from single-cell analysis. The Fluidigm BioMark™ System and Dynamic Array™ IFCs enable hundreds of individual cells to be tested for the expression of hundreds of genes in a few hours. The Fluidigm open platform allows scientists to use off-the-shelf reagents and standard analysis tools. Fluidigm Dynamic Array IFCs provide an easy-to-use workflow and flexible assay configuration (just as with microwell plates, but without the tedious liquid-transfer steps).

Key Features:
•    High Sample Throughput—Screen up to 96 single cells across 96 assays in one Dynamic Array IFC.
•    Produce More Results Faster—Produce 9,216 data points in just four hours with one Dynamic Array IFC and one technician.
•    Assay Flexibility—Practice tried-and-true techniques such as TaqMan assays or other assays you already have in your lab.

Fluidigm DELTAgene Assays are high-quality, rapid turnaround, custom qPCR gene expression assays. They permit you to take full advantage of your BioMark System with minimal experiment setup time and validated protocols that provide quality results.

Learn more about other single-cell genomic applications

•    Single-Cell Genomics
•    Single-Cell mRNA Sequencing
•    Single-Cell MicroRNA Expression Profiling
•    Single-Cell DNA Sequencing




C1 Single-Cell Auto Prep System

Measure individual cell responses to specific stimuli, verify critical disease biomarkers, validate RNAi knockdown, and conduct candidate drug screens.


BioMark™ HD System

Streamlines workflow for applications demanding sensitivity and dynamic range, at extremely high throughput.



C1™ Single-Cell Auto Prep Array IFC for PreAmp

Capture and prepare cells for genomic analysis


Dynamic Array™ IFCs

Maximize efficiency for Gene Expression Analysis. Options: 96.96, 48.48, FLEXsix



C1 Single-Cell Auto Prep Reagent Kit for PreAmp (under Chips & Kits tab)

Pre-formulated reagents for cell load, wash, lysis, and harvest


Specification Sheet

Data Sheet


Technical Notes

Application Notes





   More >

Featured Posters

ISSCR 2013:

ASCB 2012:

ISSCR 2012:

   More >