Hybridisation Chain Reaction (HCR) probe designer for Drosophila transcripts

Fluorescent RNA in situ hybridisation (FISH) allows quantification and localisation of RNA transcripts by visualising individual RNA molecules in single cells. Hybridisation Chain Reaction (HCR) is a popular and open FISH method with detection signal amplification that builds upon the development of catalytic DNA hairpins for highly amplified and multiplexed RNA imaging. While the third generation of the protocol is very well developed, the limited availability of HCR probe designer tools remains a key constraint. Here, we present an open-source HCR probe designer tool for Drosophila transcripts, providing a complete pipeline from cDNA sequence to probe selection and initiator attachment. The resulting oligonucleotides can be synthesised at low cost in 96-well plate formats, and our generalised algorithm can be easily adapted to other species.