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RNA-Chromatin Interactions pp 59–73Cite as

Simultaneous Detection of RNAs and Proteins with Subcellular Resolution

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 2161))

Abstract

We describe the detailed methods of “immunoFISH” to analyze the expression level and the spatial localization of RNA transcripts and proteins on cultured cells and formal-fixed, paraffin-embedded (FFPE) tissue sections. On cultured cells, we detect specific transcripts using the Stellaris fluorescence in situ hybridization (FISH) probes labeled with fluorophores that target multiple regions along the desired transcripts and proteins combining the immunofluorescent staining. On FFPE tissue sections, we use the RNAscope FISH probes, modified branched DNA (bDNA) probes to amplify the RNA signals, followed by immunofluorescent staining for protein detection. The abundance, composition, and spatial distribution are determined by signals from fluorescently labeled proteins and individual transcripts of images acquired using high-resolution fluorescence microscopy.

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References

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Acknowledgments

We thank Dr. Joe Gray (OHSU, USA) for providing his substantial support and conceptual guidance on our immunoFISH research. This work was partially supported by OHSU SOM Faculty Innovation Fund Pilot Program (S.K.).

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Authors and Affiliations

  1. OHSU Center for Spatial Systems Biomedicine, Oregon Health and Sciences University, Portland, OR, USA

    Sunjong Kwon & Koei Chin

  2. Department of Biomedical Engineering, Oregon Health and Sciences University, Portland, OR, USA

    Sunjong Kwon & Koei Chin

  3. Quantitative Imaging Systems, Inc., Pittsburgh, PA, USA

    Michel Nederlof

Authors
  1. Sunjong Kwon
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  2. Koei Chin
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  3. Michel Nederlof
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Corresponding author

Correspondence to Sunjong Kwon .

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Editors and Affiliations

  1. Department for Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark

    Ulf Andersson Vang Ørom

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Kwon, S., Chin, K., Nederlof, M. (2020). Simultaneous Detection of RNAs and Proteins with Subcellular Resolution. In: Ørom, U. (eds) RNA-Chromatin Interactions. Methods in Molecular Biology, vol 2161. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0680-3_6

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  • DOI: https://doi.org/10.1007/978-1-0716-0680-3_6

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-0679-7

  • Online ISBN: 978-1-0716-0680-3

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