title: Mapping a multiplexed zoo of mRNA expression.
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.
authors.affiliation: Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
authors.forename: Harry M T
authors.initials: HM
authors.lastname: Choi
authors.affiliation: Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
authors.forename: Colby R
authors.initials: CR
authors.lastname: Calvert
authors.affiliation: Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
authors.forename: Naeem
authors.initials: N
authors.lastname: Husain
authors.affiliation: 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.
authors.forename: David
authors.initials: D
authors.lastname: Huss
authors.affiliation: Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
authors.forename: Julius C
authors.initials: JC
authors.lastname: Barsi
authors.affiliation: Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
authors.forename: Benjamin E
authors.initials: BE
authors.lastname: Deverman
authors.affiliation: Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
authors.forename: Ryan C
authors.initials: RC
authors.lastname: Hunter
authors.affiliation: Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
authors.forename: Mihoko
authors.initials: M
authors.lastname: Kato
authors.affiliation: Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
authors.forename: S Melanie
authors.initials: SM
authors.lastname: Lee
authors.affiliation: Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
authors.forename: Anna C T
authors.initials: AC
authors.lastname: Abelin
authors.affiliation: Division of Engineering & Applied Science, California Institute of Technology, Pasadena, CA 91125, USA.
authors.forename: Adam Z
authors.initials: AZ
authors.lastname: Rosenthal
authors.affiliation: Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
authors.forename: Omar S
authors.initials: OS
authors.lastname: Akbari
authors.affiliation: 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.
authors.forename: Yuwei
authors.initials: Y
authors.lastname: Li
authors.affiliation: Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
authors.forename: Bruce A
authors.initials: BA
authors.lastname: Hay
authors.affiliation: Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
authors.forename: Paul W
authors.initials: PW
authors.lastname: Sternberg
authors.affiliation: Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
authors.forename: Paul H
authors.initials: PH
authors.lastname: Patterson
authors.affiliation: Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
authors.forename: Eric H
authors.initials: EH
authors.lastname: Davidson
authors.affiliation: Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
authors.forename: Sarkis K
authors.initials: SK
authors.lastname: Mazmanian
authors.affiliation: Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
authors.forename: David A
authors.initials: DA
authors.lastname: Prober
authors.affiliation: Department of Pathology, Stanford University Medical School, Stanford, CA 94305, USA.
authors.forename: Matt
authors.initials: M
authors.lastname: van de Rijn
authors.affiliation: Division of Engineering & Applied Science, California Institute of Technology, Pasadena, CA 91125, USA.
authors.forename: Jared R
authors.initials: JR
authors.lastname: Leadbetter
authors.affiliation: Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
authors.forename: Dianne K
authors.initials: DK
authors.lastname: Newman
authors.affiliation: 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.
authors.forename: Carol
authors.initials: C
authors.lastname: Readhead
authors.affiliation: Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
authors.forename: Marianne E
authors.initials: ME
authors.lastname: Bronner
authors.affiliation: Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
authors.forename: Barbara
authors.initials: B
authors.lastname: Wold
authors.affiliation: 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.
authors.forename: Rusty
authors.initials: R
authors.lastname: Lansford
authors.affiliation: Radcliffe Department of Medicine, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
authors.forename: Tatjana
authors.initials: T
authors.lastname: Sauka-Spengler
authors.affiliation: 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.
authors.forename: Scott E
authors.initials: SE
authors.lastname: Fraser
authors.affiliation: 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.
authors.forename: Niles A
authors.identifier: 0000-0003-2367-4406
authors.initials: NA
authors.lastname: Pierce
mesh_terms: D000818:Animals; D004330:Drosophila; D004625:Embryo, Nonmammalian / Q000378:metabolism; D006801:Humans; D017403:In Situ Hybridization / Q000379:methods*; D012333:RNA, Messenger / Q000378:metabolism*; D015027:Zebrafish
chemical_list: D012333:RNA, Messenger
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