RNA Detection By Flow Cytometry

Detecting RNA Targets by Flow Cytometry

Invitrogen PrimeFlow RNA Assay expands the capability of flow cytometry to measure RNA. Combine PrimeFlow with immunolabeling of both cell-surface and intracellular proteins using fluorophore-conjugated antibodies. Researchers now can reveal the dynamics of RNA transcription together with protein expression patterns in single cell resolutions

Find PrimeFlow probes for your target–including SARS-CoV-2

Ready to start the PrimeFlow RNA Assay? Check what you’ll need

Principle behind the PrimeFlow RNA assay

Principle of the PrimeFlow RNA Assay
In the PrimeFlow RNA Assay, target-specific probe sets hybridize to the target RNA transcript. Signal amplification is achieved through specific hybridization of adjacent oligonucleotide pairs to bDNA structures, formed by preamplifiers, amplifiers, and fluorescently labeled probes, resulting in excellent specificity, low background, and high signal-to-noise ratios.

Featured PrimeFlow Assay applications

Featured PrimeFlow applications

Evaluate virus RNA in infected cells

Featured PrimeFlow applications

Detect microRNA

Featured PrimeFlow applications

Probe mRNA when no antibody exists to detect the protein

Not finding the application you're looking for? Let us know what you need

Ordering information

Follow the five steps below to begin your PrimeFlow RNA Assay

Flow cytometer


  • Blue (488 nm)
  • Yellow-green (561 nm)
  • Red (633 nm)

Filter sets:

  • FITC: 530/20
  • PE-eFluor-610: 610/20
  • APC: 660/20
  • APC-eFluor 780 (APC-Cyanine7): 780/60
IncubatorCapable of maintaining temperature at 40 ±1°C
Metal heat blockFor 1.5 mL microcentrifuge tube, placed inside the validated incubator
Temperature validation kitThe Invitrogen ViewRNA Temperature Validation Kit uses a calibrated thermometer to verify the incubator temperature

Optional: Is your target microRNA? This buffer helps ensure you get improved signal and better sensitivity for miRNA.

Optional: Will the assay be processed in a 96-well plate?

  • Four types of probe sets are currently available for RNA detection 
  • Select different types of probe set depending on the RNA expression level 
  • For multiplex analysis with immunolabeling of both cell-surface and intracellular proteins, find fluorophore-conjugated antibodies
Expression level of target RNAFluorochrome labelLaser excitation wavelength (nm)Bandpass filter (nm)Fluorescence channelProbe set type
LowAlexa Fluor 647633, 635660/20APC, Alexa Fluor 647, eFluor 660Type 1
LowAlexa Fluor 568561610/20PE-eFluor 610, Alexa Fluor 568, PE-Texas RedType 10
Medium-to-highAlexa Fluor 488488530/30FITC, Alexa Fluor 488Type 4
Medium-to-highAlexa Fluor 750633, 635780/60APC-Cy7, APC-eFluor 780, Alexa Fluor 750Type 6

Search for available (in stock) probe sets

Not finding what you're looking for? Go to Custom Branched DNA Probe Set Tool

  • Positive control—use positive control probe sets in every experiment to ensure proper assay performance: RPL13a for human leukocytes and β-actin (ACTB) for mouse tissues; for specific cell types and other recommended genes, refer to Appendix 5 in the product manual of the PrimeFlow RNA Assay Kit
  • Negative control—such as samples with the target specific probe omitted, or samples labeled with a probe against a target not expressed in the cells of interest (e.g., dapB, a bacterial gene); highly recommended

Search probes used for positive and negative controls in probe search tool in Step 4.

Do you need SARS-CoV-2 probes?

Use the step-by-step ordering information above to order your kit and probes, including controls. In step 4, if you need SARS-CoV-2 probes, see the table below, and follow the ‘How to order SARS-CoV-2 probes’ instructions provided.

DyeTypeScaleCat. No.Assay ID
AF6471 40 assaysCPF-204VPNKRHH
AF6471100 assaysCPF-210VPNKRHH
AF488440 assaysCPF-204VP9HHYZ
AF4884100 assaysCPF-210VP9HHYZ
AF7506 40 assaysCPF-204VPAAADR
AF7506100 assaysCPF-210VPAAADR
AF5681040 assaysCPF-204VPCE3XN
AF56810100 assaysCPF-210VPCE3XN

PrimeFlow probe sets were designed using the NCBI strain and sequence from Accession Number LC521925, and cover multiple regions of the viral transcript. Find in the table below the binding sites and transcript region for the probe sets included in the assay. If you need a custom probe designed for a specific RNA region, use the Custom Branched DNA Probe Set Tool.

 Position (5' to 3')Region
628212-29152ORF8 and N



Fluorophore and reagent selection guide for flow cytometry

Download Flow Cytometry Protocols Handbook

Spectral Flow Cytometry Fundamentals


Invitrogen eBioscience Resources—Selection guides, Best Protocols, product performance and more.

Intracellular Staining for Flow Cytometry How-To Video—for detecting cytokines and intranuclear markers.

Flow Cytometry Learning Center—Access flow cytometry educational resources for better experiment planning and execution.

Flow Cytometry Panel Builder—Design your flow cytometry panel with this online tool for a simplified, customizable experience to fit your needs.

5 Steps Resources


Flow Cytometry Support Center—Find technical support recommendations for your flow cytometry workflows, including tips for experimental setup and in-depth troubleshooting help.

Flow Cytometry Panel Design Support—Work with one of our technical sales specialists to discuss your experimental needs and guide you through the process.

Flow Cytometry Protocols

Flow Cytometry Application Notes and Posters

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For Research Use Only. Not for use in diagnostic procedures.