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Hybridization chain reaction enables a unified approach to multiplexed, quantitative, high-resolution immunohistochemistry and in situ hybridization

Schwarzkopf, Maayan and Liu, Mike C. and Schulte, Samuel J. and Ives, Rachel and Husain, N. and Choi, Harry M. T. and Pierce, Niles A. (2021) Hybridization chain reaction enables a unified approach to multiplexed, quantitative, high-resolution immunohistochemistry and in situ hybridization. . (Unpublished) https://resolver.caltech.edu/CaltechAUTHORS:20210604-111535359

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Abstract

RNA in situ hybridization (RNA-ISH) based on the mechanism of hybridization chain reaction (HCR) enables multiplexed, quantitative, high-resolution RNA imaging in highly autofluorescent samples including whole-mount vertebrate embryos, thick brain slices, and formalin-fixed paraffin-embedded (FFPE) tissue sections. Here, we extend the benefits of 1-step, multiplexed, quantitative, isothermal, enzyme-free HCR signal amplification to immunohistochemistry (IHC), enabling accurate and precise protein relative quantitation with subcellular resolution in an anatomical context. More-over, we provide a unified framework for simultaneous quantitative protein and RNA imaging with 1-step HCR signal amplification performed for all target proteins and RNAs simultaneously.


Item Type:Report or Paper (Discussion Paper)
Related URLs:
URLURL TypeDescription
https://doi.org/10.1101/2021.06.02.446311DOIDiscussion Paper
ORCID:
AuthorORCID
Schwarzkopf, Maayan0000-0001-8128-1059
Liu, Mike C.0000-0002-2539-3459
Schulte, Samuel J.0000-0001-9982-6504
Ives, Rachel0000-0001-8221-5133
Husain, N.0000-0003-4962-7237
Choi, Harry M. T.0000-0002-1530-0773
Pierce, Niles A.0000-0003-2367-4406
Additional Information:The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. We thank F. Chen for discussions, M.E. Bronner for reading a draft of the manuscript, and the following resources within the Beckman Institute at Caltech: A. Collazo of the Biological Imaging Facility for assistance with imaging, G. Shin of Molecular Technologies for providing HCR reagents, and the Zebrafish Facility for providing zebrafish embryos. This work was funded by the National Institutes of Health (NIBIB R01EB006192, NIGMS R44GM140796), by DARPA (HR0011-17-2-0008; the findings are those of the authors and should not be interpreted as representing the official views or policies of the U.S. Government), and by the Beckman Institute at Caltech (Programmable Molecular Technology Center, PMTC). Author contributions. Conceptualization: N.A.P.; Methodology: M.S., M.C.L., S.J.S., N.H., H.M.T.C., N.A.P.; Validation: M.S., S.J.S., R.I.; Investigation: M.S., M.C.L, S.J.S., R.I., N.H.; Writing - original draft: N.A.P.; Writing - review & editing: all; Visualization: M.S., R.I., S.J.S.; Supervision: M.C.L., H.M.T.C., and N.A.P.; Project administration: H.M.T.C. and N.A.P.; Funding acquisition: H.M.T.C. and N.A.P. The authors declare competing financial interests in the form of patents, pending patent applications, and the startup company Molecular Instruments, Inc.
Funders:
Funding AgencyGrant Number
NIHR01EB006192
NIHR44GM140796
Defense Advanced Research Projects Agency (DARPA)HR0011-17-2-0008
Subject Keywords:Immunofluorescence (IF), RNA fluorescence in situ hybridization (RNA-FISH), qHCR imaging, formalin-fixed paraffin-embedded (FFPE) mouse brain and human breast tissue sections, whole-mount zebrafish embryos
Record Number:CaltechAUTHORS:20210604-111535359
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20210604-111535359
Official Citation:Hybridization chain reaction enables a unified approach to multiplexed, quantitative, high-resolution immunohistochemistry and in situ hybridization Maayan Schwarzkopf, Mike C. Liu, Samuel J. Schulte, Rachel Ives, N. Husain, Harry M.T. Choi, Niles A. Pierce bioRxiv 2021.06.02.446311; doi: https://doi.org/10.1101/2021.06.02.446311
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:109386
Collection:CaltechAUTHORS
Deposited By: George Porter
Deposited On:07 Jun 2021 14:42
Last Modified:07 Jun 2021 14:42

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