ProbeDealer

This page includes resources published in our paper titled “ProbeDealer is a convenient tool for designing probes for highly multiplexed fluorescence in situ hybridization”. Reference: Mengwei Hu*, Bing Yang*, Yubao Cheng, Jonathan S.D. Radda, Yanbo Chen, Miao Liu & Siyuan Wang,¬†Scientific Reports, Volume 10, Number 22031, (2020). *Co-first authors. (Link).

Right click each link and use “Save link as” to download the following files as needed:
ProbeDealer package 
Human database (NEW updated to Gencode v37)
Mouse database (NEW updated to Gencode vM26)
Drosophila melanogaster database (NEW)
Honey bee transcriptome database (NEW)
Example target files
ProbeDealer user manual (Please follow the user manual to install a compatible BLAST version.)
Instruction for ordering dye-labeled secondary probes and primers

Note: Besides probe design for multiplexed FISH experiments, ProbeDealer can be used to design FISH probes targeting individual RNA species for conventional single-molecule RNA FISH (smRNA FISH). This functionality may offer a cheaper alternative to commercial options of custom-target smRNA FISH. An instruction for how to use ProbeDealer for conventional smRNA FISH probe design is included here:
Instruction for using ProbeDealer for conventional smRNA FISH