PT - JOURNAL ARTICLE AU - Dardani, Ian AU - Emert, Benjamin L. AU - Goyal, Yogesh AU - Jiang, Connie L. AU - Kaur, Amanpreet AU - Lee, Jasmine AU - Rouhanifard, Sara H. AU - Alicea, Gretchen M. AU - Fane, Mitchell E. AU - Xiao, Min AU - Herlyn, Meenhard AU - Weeraratna, Ashani T. AU - Raj, Arjun TI - clampFISH 2.0 enables rapid, scalable amplified RNA detection <em>in situ</em> AID - 10.1101/2022.03.16.484659 DP - 2022 Jan 01 TA - bioRxiv PG - 2022.03.16.484659 4099 - http://biorxiv.org/content/early/2022/03/17/2022.03.16.484659.short 4100 - http://biorxiv.org/content/early/2022/03/17/2022.03.16.484659.full 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.