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FlowRNA Probe Sets

Choose from Thousands of Target-Specific Probe Sets

Selection of a Probe Set to detect RNA using the PrimeFlow® RNA or QuantiGene® FlowRNA Assays is virtually unlimited. Each synthesized set of target probes typically spans 1000 bases (1 kb) of a target RNA. There are exceptions when the targeted RNA requires a smaller region or is expressed at low levels.

A Probe Set type is determined by its tag, a specific DNA sequence that generates a highly specific interaction with its own PreAmplifier, Amplifier and Label Probe. Three Probe Set types are currently available (Type 1, Type 4 and Type 6). When detecting more than one RNA target in a single cell, each Probe Set must be a unique type to differentiate its’ signal from the other Probe Sets. This is similar to cells labeled with multiple conjugated antibodies. Detection requires signals to be captured in individual channels on the flow cytometer using specific laser and filter set configurations (see table below).

Probe Set Type selection for Prime FlowRNA and QuantiGene FlowRNA assays should use the following criteria:

  • Select Type 1 (Alexa Fluor® 647) when using one probe set in an assay to obtain the brightest signal. Select Type 6 (Alexa Fluor® 750) when adding a second probe set and finally Type 4 (Alexa Fluor® 488) is recommended for the third probe set.
  • When multiplexing RNA targets, do not use Probe Sets of the same Type.

Currently, up to three compatible fluorochrome-labeled amplification “tree” structures allow simultaneous measurement of up to three different RNA targets. For each RNA target, a unique probe set type must be selected in order to detect it independently of the others.

FlowRNA Probe Set Type Specifications

Probe Set Type

Fluorochrome Label

Excitation Wavelength(max)

Emission Wavelength (max)

Laser Excitation Wavelength

Bandpass Filter Recommendation

Type 1

Alexa Fluor® 647

647 nm

668 nm

632-640 nm


Type 4

Alexa Fluor® 488

488 nm

519 nm

488 nm


Type 6

Alexa Fluor® 750

749 nm

775 nm

632-640 nm


Probe set volume requirements can be determined by the number of assays required.

  • 120 µL = ~ 24 assays
  • 600 µL = ~ 100 assays
  • Larger sizes can be made available.

Over 3000 sequences used in microarray or sequencing assays are currently in stock, and other RNA targets including most mRNA or noncoding RNA sequences can be designed and manufactured for use in the FlowRNA assay in five business days or less.

Available (In Stock) RNA Probe Sets

FlowRNA Probe Sets are designed for unrivaled, ultra-sensitive and specific detection of RNA by in situ hybridization. Multiplexing up to three RNA transcripts is possible by running different target-specific Probe Set types. A searchable database of available Probe Sets is listed below. For any gene or target you cannot locate in the Probe Set database, a custom probe set can be requested.

"By Request" or Custom RNA Probe Sets

Probe sets for RNA sequences currently not available or to novel RNA targets will be designed and synthesized. Custom probes are only available in 100 test sizes and can range in price ($385-500 USD) depending upon the number of number of probe sets in its design. Simply provide the sequence information and any details on special design requirements on the order form. Custom probe set design and shipment is typically complete in five business days or less.

All targets are designed to be specific unless otherwise requested; if there are issues with achieving specificity for highly homologous targets, our probe design team will contact you with available options. All multi-transcript targets are designed to pick up all transcripts unless otherwise requested.

Probe Set Selection

All available Probe Set Types will be listed here in a searchable table (under development). Search capabilities will allow one to selectively identify a Probe Set by species of interest, accession number, gene name or symbol. A sample view can be seen here. For now, current stock probe sets are listed in this downloadable PDF.

Sample of Available Probe Sets
Type Species Symbol Gene Name Accession Cat. No.
Type 4 Human GHRL Ghrelin precursor NM-016362 VA4-10928
Type 1 Humab KRT17 Keratin 17 NM-000422 VA1-10904
Type 1 Human TRPV1 transient receptor potential cation channel, subfamily V, member 1 NM_018727 VA1-10885
Type 1 Mouse Nr5a2 nuclear receptor subfamily 5, group A, member 2 NM_030676 VB1-10935
Type 1 Human SCN9A sodium channel, voltage-gated, type IX, alpha subunit NM_002977 VA1-10939
Type 6 Human PRR11 Proline rich 11 NM_018304 VA6-10914
Type 4 Human HoxD1-D3-ncRNA HoxD1-D3-ncRNA BC030713 VA4-10920
Type 1 Mouse Fah fumarylacetoacetate hydrolase NM_010176 VB1-10953
Type 4 Human HoxD4-D8-ncRNA HoxD4-D8-ncRNA BC047605 VA4-10919