Which fluorescent dye should I choose for my Stellaris RNA FISH probe set?

Selection of the fluorescent dye for your Stellaris RNA FISH probe set should be chosen to best match the specifications of the available band-pass filters sets on the microscope you will be using. Visit our Stellaris Dyes and Modifications page for specific recommendations and considerations for each of our dyes. To learn more about how to align the dye spectra with your filters, check out our blog here (Imaging Stellaris Assays: Get to Know Your Microscope). It is equally important to consider the autofluorescence of the sample types you plan to study. Autofluorescence in tissue samples is more pronounced in the green wavelengths. Fluorescein, as an example, absorbs around 450 nm and emits around 520 nm. It is easier to discern true signal from autofluorescence if longer wavelength fluorophores, such as Quasar™ 570, 670, or CAL Fluor™ Red 610 dyes, which emit in the red or far-red, are used instead. Additionally, be mindful that if you plan on using a transgenic cell line that may be expressing a fluorescent protein like GFP or tdTomato, you want to choose a fluorophore with a different fluorescence maximum. We recommend that you use Chroma’s online dye and filter selection software to help you choose.