ClampFISH 2.0 enables rapid, scalable amplified RNA detection in situ

• Published in: Nature methods Vol. 19; no. 11; pp. 1403 - 1410
• Main Authors: Dardani, Ian, Emert, Benjamin L., Goyal, Yogesh, Jiang, Connie L., Kaur, Amanpreet, Lee, Jasmine, Rouhanifard, Sara H., Alicea, Gretchen M., Fane, Mitchell E., Xiao, Min, Herlyn, Meenhard, Weeraratna, Ashani T., Raj, Arjun
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01-11-2022; Nature Publishing Group
• Subjects: 631/1647/1888/1890; 631/1647/2017/1947; 631/61/191/2018; Amplification; Bioengineering; Bioinformatics; Biological Microscopy; Biological Techniques; Biomedical and Life Sciences; Biomedical Engineering/Biotechnology; Costs; Design; Enzymes; Gene expression; Hybridization; Labeling; Life Sciences; Medicine; Methods; Molecular biology; Multiplexing; Proteomics; Ribonucleic acid; RNA; RNA - genetics; Transcriptome; Transcriptomics
• ISSN: 1548-7091; 1548-7105
• DOI: 10.1038/s41592-022-01653-6

RNA labeling in situ has enormous potential to visualize transcripts and quantify their levels in single cells, but it remains challenging to produce high levels of signal while also enabling multiplexed detection of multiple RNA species simultaneously. Here, we describe clampFISH 2.0, a method that uses an inverted padlock design to efficiently detect many RNA species and exponentially amplify their signals at once, while also reducing the time and cost compared with the prior clampFISH method. We leverage the increased throughput afforded by multiplexed signal amplification and sequential detection to detect 10 different RNA species in more than 1 million cells. We also show that clampFISH 2.0 works in tissue sections. We expect that the advantages offered by clampFISH 2.0 will enable many applications in spatial transcriptomics.
ClampFISH 2.0 enables highly specific multiplexed signal amplification in RNA FISH. The approach was used to detect 10 RNA species that ranged in abundance in more than 1 million cells and is also applicable to tissue sections.