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Development. 2016 Oct 1;143(19):3632-3637.

Mapping a multiplexed zoo of mRNA expression.

Author information

1
Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
2
Department of Radiology, Children's Hospital Los Angeles, CA 90027, USA Department of Radiology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.
3
Division of Engineering & Applied Science, California Institute of Technology, Pasadena, CA 91125, USA.
4
Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.
5
Department of Pathology, Stanford University Medical School, Stanford, CA 94305, USA.
6
Radcliffe Department of Medicine, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
7
Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA Department of Biomedical Engineering, University of Southern California, Los Angeles, CA 90089, USA.
8
Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA Division of Engineering & Applied Science, California Institute of Technology, Pasadena, CA 91125, USA niles@caltech.edu.

Abstract

In situ hybridization methods are used across the biological sciences to map mRNA expression within intact specimens. Multiplexed experiments, in which multiple target mRNAs are mapped in a single sample, are essential for studying regulatory interactions, but remain cumbersome in most model organisms. Programmable in situ amplifiers based on the mechanism of hybridization chain reaction (HCR) overcome this longstanding challenge by operating independently within a sample, enabling multiplexed experiments to be performed with an experimental timeline independent of the number of target mRNAs. To assist biologists working across a broad spectrum of organisms, we demonstrate multiplexed in situ HCR in diverse imaging settings: bacteria, whole-mount nematode larvae, whole-mount fruit fly embryos, whole-mount sea urchin embryos, whole-mount zebrafish larvae, whole-mount chicken embryos, whole-mount mouse embryos and formalin-fixed paraffin-embedded human tissue sections. In addition to straightforward multiplexing, in situ HCR enables deep sample penetration, high contrast and subcellular resolution, providing an incisive tool for the study of interlaced and overlapping expression patterns, with implications for research communities across the biological sciences.

KEYWORDS:

Bacteria, Whole-mount embryos and larvae; Deep sample penetration; High contrast; Hybridization chain reaction (HCR); In situ amplification; In situ hybridization; Multiplexing; Subcellular resolution; Tissue sections

PMID:
27702788
PMCID:
PMC5087610
DOI:
10.1242/dev.140137
[Indexed for MEDLINE]
Free PMC Article

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