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Development
2016 Oct 01;14319:3632-3637. doi: 10.1242/dev.140137.
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Mapping a multiplexed zoo of mRNA expression.
Choi HM
,
Calvert CR
,
Husain N
,
Huss D
,
Barsi JC
,
Deverman BE
,
Hunter RC
,
Kato M
,
Lee SM
,
Abelin AC
,
Rosenthal AZ
,
Akbari OS
,
Li Y
,
Hay BA
,
Sternberg PW
,
Patterson PH
,
Davidson EH
,
Mazmanian SK
,
Prober DA
,
van de Rijn M
,
Leadbetter JR
,
Newman DK
,
Readhead C
,
Bronner ME
,
Wold B
,
Lansford R
,
Sauka-Spengler T
,
Fraser SE
,
Pierce NA
.
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.
Acloque,
In situ hybridization analysis of chick embryos in whole-mount and tissue sections.
2008, Pubmed
Acloque,
In situ hybridization analysis of chick embryos in whole-mount and tissue sections.
2008,
Pubmed
Barroso-Chinea,
Detection of two different mRNAs in a single section by dual in situ hybridization: a comparison between colorimetric and fluorescent detection.
2007,
Pubmed
Capodieci,
Gene expression profiling in single cells within tissue.
2005,
Pubmed
Chan,
Method for multiplex cellular detection of mRNAs using quantum dot fluorescent in situ hybridization.
2005,
Pubmed
Chen,
Nanoscale imaging of RNA with expansion microscopy.
2016,
Pubmed
Chen,
Optical imaging. Expansion microscopy.
2015,
Pubmed
Choi,
Programmable in situ amplification for multiplexed imaging of mRNA expression.
2010,
Pubmed
Choi,
Next-generation in situ hybridization chain reaction: higher gain, lower cost, greater durability.
2014,
Pubmed
Clay,
Multiplex fluorescent in situ hybridization in zebrafish embryos using tyramide signal amplification.
2005,
Pubmed
Cox,
Detection of mrnas in sea urchin embryos by in situ hybridization using asymmetric RNA probes.
1984,
Pubmed
,
Echinobase
Denkers,
FISHing for chick genes: Triple-label whole-mount fluorescence in situ hybridization detects simultaneous and overlapping gene expression in avian embryos.
2004,
Pubmed
Dirks,
Triggered amplification by hybridization chain reaction.
2004,
Pubmed
Femino,
Visualization of single RNA transcripts in situ.
1998,
Pubmed
Gall,
Formation and detection of RNA-DNA hybrid molecules in cytological preparations.
1969,
Pubmed
Harland,
In situ hybridization: an improved whole-mount method for Xenopus embryos.
1991,
Pubmed
Huss,
Combinatorial analysis of mRNA expression patterns in mouse embryos using hybridization chain reaction.
2015,
Pubmed
Jung,
Diagnostic applications of nucleic acid circuits.
2014,
Pubmed
Kerstens,
A novel in situ hybridization signal amplification method based on the deposition of biotinylated tyramine.
1995,
Pubmed
Kislauskis,
Isoform-specific 3'-untranslated sequences sort alpha-cardiac and beta-cytoplasmic actin messenger RNAs to different cytoplasmic compartments.
1993,
Pubmed
Kosman,
Multiplex detection of RNA expression in Drosophila embryos.
2004,
Pubmed
Larsson,
In situ genotyping individual DNA molecules by target-primed rolling-circle amplification of padlock probes.
2004,
Pubmed
Larsson,
In situ detection and genotyping of individual mRNA molecules.
2010,
Pubmed
Lehmann,
In situ hybridization to RNA.
1994,
Pubmed
Levsky,
Single-cell gene expression profiling.
2002,
Pubmed
McLennan,
Neural crest migration is driven by a few trailblazer cells with a unique molecular signature narrowly confined to the invasive front.
2015,
Pubmed
Nieto,
In situ hybridization analysis of chick embryos in whole mount and tissue sections.
1996,
Pubmed
Nikolakakis,
Use of Hybridization Chain Reaction-Fluorescent In Situ Hybridization To Track Gene Expression by Both Partners during Initiation of Symbiosis.
2015,
Pubmed
Pernthaler,
Fluorescence in situ hybridization and catalyzed reporter deposition for the identification of marine bacteria.
2002,
Pubmed
Piette,
An optimized procedure for whole-mount in situ hybridization on mouse embryos and embryoid bodies.
2008,
Pubmed
Player,
Single-copy gene detection using branched DNA (bDNA) in situ hybridization.
2001,
Pubmed
Raj,
Imaging individual mRNA molecules using multiple singly labeled probes.
2008,
Pubmed
Rosen,
Whole-mount in situ hybridization in the mouse embryo: gene expression in three dimensions.
1993,
Pubmed
Rosenthal,
Localizing transcripts to single cells suggests an important role of uncultured deltaproteobacteria in the termite gut hydrogen economy.
2013,
Pubmed
Ruf-Zamojski,
Spatio-Temporal Differences in Dystrophin Dynamics at mRNA and Protein Levels Revealed by a Novel FlipTrap Line.
2015,
Pubmed
Shah,
Single-molecule RNA detection at depth by hybridization chain reaction and tissue hydrogel embedding and clearing.
2016,
Pubmed
Sylwestrak,
Multiplexed Intact-Tissue Transcriptional Analysis at Cellular Resolution.
2016,
Pubmed
Tautz,
A non-radioactive in situ hybridization method for the localization of specific RNAs in Drosophila embryos reveals translational control of the segmentation gene hunchback.
1989,
Pubmed
Thisse,
High-resolution in situ hybridization to whole-mount zebrafish embryos.
2008,
Pubmed
Thisse,
Spatial and temporal expression of the zebrafish genome by large-scale in situ hybridization screening.
2004,
Pubmed
Wallner,
Optimizing fluorescent in situ hybridization with rRNA-targeted oligonucleotide probes for flow cytometric identification of microorganisms.
1993,
Pubmed
Wang,
From cascaded catalytic nucleic acids to enzyme-DNA nanostructures: controlling reactivity, sensing, logic operations, and assembly of complex structures.
2014,
Pubmed
Wang,
RNAscope: a novel in situ RNA analysis platform for formalin-fixed, paraffin-embedded tissues.
2012,
Pubmed
Weiszmann,
Determination of gene expression patterns using high-throughput RNA in situ hybridization to whole-mount Drosophila embryos.
2009,
Pubmed
Wiedorn,
Comparison of in-situ hybridization, direct and indirect in-situ PCR as well as tyramide signal amplification for the detection of HPV.
1999,
Pubmed
Yamaguchi,
In situ DNA-hybridization chain reaction (HCR): a facilitated in situ HCR system for the detection of environmental microorganisms.
2015,
Pubmed
Zhang,
DNA-mediated homogeneous binding assays for nucleic acids and proteins.
2013,
Pubmed
Zhou,
Two-color, rolling-circle amplification on antibody microarrays for sensitive, multiplexed serum-protein measurements.
2004,
Pubmed
