Stellaris RNA FISH (fluorescence in situ hybridisation) is a RNA visualisation method that allows for simultaneous detection, localization, and quantification of individual RNA molecules at the cellular level in fixed samples using fluorescence microscopy. A set of Stellaris RNA FISH Probes is comprised of a pool of up to 48 unique probes, each labeled with a fluorophore, that collectively bind along an RNA target transcript to produce a diffraction limited spot.

The Stellaris RNA FISH technology follows a simple protocol, does not need exotic reagents and is platform-independent. It can offer same-day results and is versatile in terms of sample type, species and application. Stellaris RNA FISH probes can be labeled with several different dyes to allow for simultaneous detection of different RNA targets in multiplexed experiments. The Stellaris RNA FISH technology enables scientists to visualise gene expression through direct detection without isolation, purification or amplification.

The large number of probes in a Stellaris RNA FISH assay ensures both high sensitivity and specificity. The inherent redundancies of this direct detection method minimize the possibility of false negative and false positive signals. Positive signals are identified from the combined localized fluorescence of multiple probes. Off-target binding of single probes generates only weak and diffuse fluorescence, which falls well below the threshold for detection of the targeted mRNAs. The short probe lengths are able to easily penetrate the cellular matrix for efficient hybridization.

Stellaris RNA FISH probes are available in a wide variety of fluorophores in the visible spectrum, including LGC, Biosearch Technologies’ CAL Fluor™ and Quasar™ dyes and can be used in a multiplex assay. The dye choices in a multiplex assay are largely determined by the filters available on the imaging platform, but it is certainly possible to design an assay including a DAPI nuclear stain and three Stellaris RNA FISH probe sets labeled with reporter dyes with minimal spectral overlap. See our Stellaris Dyes and Modifications page for detailed information on all our available dyes and modifications as well as a multiplexing guide.

Multiplex assays can be used to identify a correlation in expression levels between multiple genes, compare a control probe set of known expression to the expression of a target, or simply save time over running the many separate assays. Our ShipReady Probe Sets are assays designed to detect well-known, previously validated targets and have been wet bench tested for success as positive controls. The ShipReady probe sets are convenient and affordable. Our DesignReady Probe Sets are made to order and take the guess work out of designing your own Stellaris assay. We have a catalogue of over 4,000 professionally designed assays for many common species and model organisms. These have undergone an additional level of bioinformatics analysis to ensure specificity.

Stellaris RNA FISH can also be combined with existing technologies such as qPCR, DNA FISH, IHC (immunohistochemistry), IF (immunofluorescence) and western blotting to provide complementary information.