RT Journal Article SR Electronic T1 clampFISH 2.0 enables rapid, scalable amplified RNA detection in situ JF bioRxiv FD Cold Spring Harbor Laboratory SP 2022.03.16.484659 DO 10.1101/2022.03.16.484659 A1 Dardani, Ian A1 Emert, Benjamin L. A1 Goyal, Yogesh A1 Jiang, Connie L. A1 Kaur, Amanpreet A1 Lee, Jasmine A1 Rouhanifard, Sara H. A1 Alicea, Gretchen M. A1 Fane, Mitchell E. A1 Xiao, Min A1 Herlyn, Meenhard A1 Weeraratna, Ashani T. A1 Raj, Arjun YR 2022 UL http://biorxiv.org/content/early/2022/03/17/2022.03.16.484659.abstract AB 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 and exponentially amplify signals from many RNA species at once, while also reducing time and cost compared to the prior clampFISH method. We leverage the increased throughput afforded by multiplexed signal amplification and sequential detection by demonstrating the ability to detect 10 different RNA species in over 1 million cells. We also show that clampFISH 2.0 works in tissue sections. We expect the advantages offered by clampFISH 2.0 will enable many applications in spatial transcriptomics.Competing Interest StatementAR receives patent royalties from LGC/Biosearch Technologies related to Stellaris mRNA FISH products. AR is on the scientific advisory board of Spatial Genomics. ATW is on the Board of Directors at ReGAIN therapeutics. The remaining authors state no conflict of interest.