Design, Labeling, and Application of Probes for RNA smFISH

Ewa Piskadlo; Bastian Th Eichenberger; Luca Giorgetti; Jeffrey A Chao

doi:10.1007/978-1-0716-2521-7_10

Design, Labeling, and Application of Probes for RNA smFISH

Methods Mol Biol. 2022:2537:173-183. doi: 10.1007/978-1-0716-2521-7_10.

Authors

Ewa Piskadlo¹, Bastian Th Eichenberger^{1

2}, Luca Giorgetti¹, Jeffrey A Chao³

Affiliations

¹ Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
² University of Basel, Basel, Switzerland.
³ Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland. jeffrey.chao@fmi.ch.

PMID: 35895264
DOI: 10.1007/978-1-0716-2521-7_10

Abstract

Visualization of single mRNA molecules in fixed cells can be achieved using single molecule fluorescent in situ hybridization (smFISH). This approach enables accurate quantification of mRNA numbers and localization at a single-cell level. To ensure reliable results using smFISH, it is critical to use fluorescent probes that are highly specific to their RNA target. To facilitate probe design, we have created anglerFISH, a user-friendly command-line based pipeline. In this chapter, we present how to perform a smFISH experiment using user-designed and labeled probes.

Keywords: Command line interface (CLI); FISH probe design; Fluorescence labeling of oligonucleotides; Nextflow workflow; Single-molecule fluorescence in situ hybridization (smFISH).

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Fluorescent Dyes*
In Situ Hybridization, Fluorescence / methods
Nanotechnology
Oligonucleotide Probes / genetics
RNA* / genetics
RNA, Messenger / genetics

Substances

Fluorescent Dyes
Oligonucleotide Probes
RNA, Messenger
RNA