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

Instrument Specification
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
Incubator Capable of maintaining temperature at 40 ±1°C
Metal heat block For 1.5 mL microcentrifuge tube, placed inside the validated incubator
Temperature validation kit The 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 RNA Fluorochrome label Laser excitation wavelength (nm) Bandpass filter (nm) Fluorescence channel Probe set type
Low Alexa Fluor 647 633, 635 660/20 APC, Alexa Fluor 647, eFluor 660 Type 1
Low Alexa Fluor 568 561 610/20 PE-eFluor 610, Alexa Fluor 568, PE-Texas Red Type 10
Medium-to-high Alexa Fluor 488 488 530/30 FITC, Alexa Fluor 488 Type 4
Medium-to-high Alexa Fluor 750 633, 635 780/60 APC-Cy7, APC-eFluor 780, Alexa Fluor 750 Type 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.

Dye Type Scale Cat. No. Assay ID
AF647 1  40 assays CPF-204 VPNKRHH
AF647 1 100 assays CPF-210 VPNKRHH
AF488 4 40 assays CPF-204 VP9HHYZ
AF488 4 100 assays CPF-210 VP9HHYZ
AF750 6  40 assays CPF-204 VPAAADR
AF750 6 100 assays CPF-210 VPAAADR
AF568 10 40 assays CPF-204 VPCE3XN
AF568 10 100 assays CPF-210 VPCE3XN

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
1 705-1676 orf1ab
2 4356-5607 orf1ab
3 12808-13942 orf1ab
4 20571-21759 orf1ab
5 26646-27763 M
6 28212-29152 ORF8 and N



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

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Not for resale. Super Bright Polymer Dyes are sold under license from Becton, Dickinson and Company.