ProbeDealer is a convenient tool for designing probes for highly multiplexed fluorescence in situ hybridization

Mengwei Hu,Bing Yang,Jonathan S D Radda,Siyuan Wang,Miao Liu,Yubao Cheng,Yanbo Chen

doi:10.1038/s41598-020-76439-x

Abstract

Fluorescence in situ hybridization (FISH) is a powerful method to visualize the spatial positions of specific genomic loci and RNA species. Recent technological advances have leveraged FISH to visualize these features in a highly multiplexed manner. Notable examples include chromatin tracing, RNA multiplexed error-robust FISH (MERFISH), multiplexed imaging of nucleome architectures (MINA), and sequential single-molecule RNA FISH. However, one obstacle to the broad adoption of these methods is the complexity of the multiplexed FISH probe design. In this paper, we introduce an easy-to-use, versatile, and all-in-one application called ProbeDealer to design probes for a variety of multiplexed FISH techniques and their combinations. ProbeDealer offers a one-stop shop for multiplexed FISH design needs of the research community.

Highlights

Fluorescence in situ hybridization (FISH) is a powerful method to visualize the spatial positions of specific genomic loci and RNA species
A library of oligonucleotide probes termed primary probes targeting all genomic loci or RNA species of interest are simultaneously hybridized to the targets
To generate primary probes from target sequences, ProbeDealer utilizes the following algorithm implemented in MATLAB: Each target sequence is scanned with a sliding window with customizable length

Summary

Introduction

Fluorescence in situ hybridization (FISH) is a powerful method to visualize the spatial positions of specific genomic loci and RNA species. We introduce ProbeDealer, an easy-to-use application that facilitates probe design for chromatin tracing, RNA MERFISH and sequential single-molecule RNA FISH of individual transcript species.

Results

Conclusion