Can the Stellaris™ method be used for whole mount samples?

The Stellaris method has been successfully employed to examine RNAs in whole-mount zebrafish embryo, C. elegans, and Drosophila as well as in cultured cells, frozen tissue and FFPE (Formalin-fixed Paraffin-embedded) tissue slices 4-20 micrometers in thickness. Visit our Stellaris Citation Center to see all publications citing Stellaris RNA FISH in whole mount applications. Below, you can find examples of publications using Stellaris RNA FISH probes in whole mount samples.  If a whole mount sample is of appropriate thickness, then there is potential for the Stellaris RNA FISH technology to perform well. The Stellaris RNA FISH Probes consist of oligonucleotides on average 20 nucleotides in length, which penetrate tissue better than long DNA probes, or assemblies for indirect detection. In thicker tissue sections, i.e. >20 µm, Stellaris RNA FISH Probes may offer qualitative results sans the ability to effectively count transcripts. Stellaris RNA FISH Probes may not always afford a sufficient signal to visualise transcripts in thick sections.

Oka Y, Sato TN. Whole-mount single molecule FISH method for zebrafish embryo. Scientific Reports. 2015;5:8571. doi:10.1038/srep08571.

Ji N, van Oudenaarden A. Single molecule fluorescent in situ hybridization (smFISH) of C. elegans worms and embryos. Wormbook. 2012;13:1-16 doi: 10.1895/wormbook.1.153.1

Xu H, Sepúlveda LA, Figard L, Sokac AM, Golding I. Combining protein and mRNA quantification to decipher transcriptional regulation. Nature Methods. 2015;12(8):739-42. Doi10.1038/nmeth.3446