ViewRNA 440μL - FAQs

Here is a list of equipment that would be needed to perform ViewRNA assays:
- Hybridization incubator oven capable of maintaining temperature at 40 ± 1 degrees C (Cat. No. QS0704 or QS0712)
- Humidity chamber (StainTray device, Cat. No. 44-0404)
- Fluorescent microscope with 20X and 40X objectives, appropriate filters, and monochrome camera
- Aspiration system for washing
- ViewRNA Temperature Validation Kit (Cat. No. QV0523)
- Optional cytospin for attaching suspension cells to a slide

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Catalog ViewRNA probe sets can be ordered using a catalog number corresponding to the aliquot size selected:

- Small: 120 µL (Cat. No. VX-06)
- Medium: 440 µL (Cat. No. VX-01)
- Large: 1.44 mL (Cat. No. VX-02)

VX- is used for catalog ViewRNA probe sets and CVX- is used for custom-designed ViewRNA probe sets. To add ViewRNA probe sets to the cart, use the Quick Order portal and add the combination of the catalog number and the associated Assay ID. Alternatively, you may request a quote from your Sales specialist or by contacting Technical Support at cellanalysis.support@thermofisher.com.

Find additional tips, troubleshooting help, and resources within our Cell Analysis Support Center.

ViewRNA probe sets are available in 3 sizes:
- Small: 120 µL
- Medium: 440 µL
- Large: 1.44 mL

ViewRNA probe sets are provided as concentrated stock solutions that need to be diluted in the assay protocol. The dilution factors, as well as the volume per sample vary between assays, based on the type of vessel used. Hence the number of sustained assays will also vary. Cell assays typically require 1:100 dilution while tissue assays can use 1:40 or 1:20 dilution.

If for example, the protocol calls for 1:100 dilution and you purchased the Medium aliquot, this will make 44 mL of the 1X probe set solution: 440 µL x 100 = 44,000 µl.
If using a standard protocol that requires 405 µL of 1X probe set per slide (or sample), the Medium aliquot will sustain 108 assays in total: 44,000 µL/ 405 µL = 108 assays.

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PrimeFlow probe sets can be used for ViewRNA assays and vice versa but note that the 'Type' designation is not equivalent. Please refer to the table below for Type-fluorophore assignments per each assay.



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The design strategy for a ViewRNA probe set involves performing a BLAST of the target gene sequence to identify a unique, non-repetitive region for complete specificity. The target region of a 'standard' ViewRNA probe set is ~800 bp long, helping ensure maximum strength of the probe set. ViewRNA probes are branched DNA probe pairs, called ZZ pairs with each oligo in the pair being ~20 bp long. The left and right ZZ oligos have to align adjacent to each other, otherwise, signal amplification will not occur. This helps ensure the most specific detection. The ViewRNA probe set can consist of anywhere between 1-20 oligo pairs. Even a single oligo pair can help provide resolution down to a single transcript.

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The ViewRNA probe sets come with 12-month warranty, if stored as indicated.

Find additional tips, troubleshooting help, and resources within our Cell Analysis Support Center.

After purchase of a ViewRNA probe set, please reach out to Technical Support at cellanalysis.support@thermofisher.com to obtain the probe set map with full target coverage.

Find additional tips, troubleshooting help, and resources within our Cell Analysis Support Center.

The Custom Branched DNA Probe Set Tool (https://www.thermofisher.com/order/custom-oligo/brancheddna) can be used to search for ViewRNA probe sets for cell or tissue assays.

In the tool, under ''Chemistry'', the ''ViewRNA Tissue'' (VT) option has historically only been set up with Types 1 and 6 probe sets as we used to offer only these two probe sets - the original tissue assays were chromogenic and came with only Type 1 and 6 reagents for amplification and detection. Currently, the tissue fluorescence assays come with Alexa Fluor-conjugated label probes and allow use of probe sets of all 4 Types (1, 4, 6, and 10).

To be able to view all 4 ViewRNA probe set Types in the tool, search using the ''ViewRNA Cell'' (VC) or ''ViewRNA Cell Plus'' (VCP) option, and this will help visualize all Types and associated assay IDs. The assay ID suffix would vary based on the option selected (VT, VC, or VCP). However, as long as the numeral in the middle remains the same, it is the same probe set that is supplied within the vial, and it will be compatible with cell and tissue assays.

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Type 1 and Type 6 ViewRNA assays are recommended for important and low-abundance genes. If performing 1 or 2-plex assays, we recommend assigning Type 1 or Type 6 to the target genes. If performing up to 4 -plex assays, it is best to consider the abundance of individual transcripts and use Type 1and Type 6 for lower abundance genes while reserving Type1, 4,and 10 for higher abundance targets or a positive control (i.e., a house-keeping gene).



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Type refers to the ViewRNA target probe set label used in the individual assays and also indicates compatibility with the amplification reagents provided in assay kits. The ViewRNA target probe sets are available in 4 Types - Type 1, 4, 6, and 10. The same probe set Type can be used across cell and tissue assays.

Tissue chromogenic assays come with Type 1 and Type 6 target probe sets, while cell assays and tissue fluorescence assays are compatible with all 4 Types (1, 4, 6, and 10).

Find additional tips, troubleshooting help, and resources within our Cell Analysis Support Center.

Please use the Custom Branched DNA Probe Set Tool (https://www.thermofisher.com/order/custom-oligo/brancheddna) to order custom ViewRNA probe sets.

Find additional tips, troubleshooting help, and resources within our Cell Analysis Support Center.

Existing ViewRNA probe sets for a target gene can be found here: thermofisher.com/order/genome-database/embeddedSearchForm?searchFormId=quantigene-viewrna-cell-only

Find additional tips, troubleshooting help, and resources within our Cell Analysis Support Center.