Mapping a multiplexed zoo of mRNA expression

Harry M T Choi, Colby R. Calvert, Naeem Husain, David Huss, Julius C. Barsi, Benjamin E. Deverman, Ryan C. Hunter, Mihoko Kato, S. Melanie Lee, Anna C T Abelin, Adam Z. Rosenthal, Omar S. Akbari, Yuwei Li, Bruce A. Hay, Paul W. Sternberg, Paul H. Patterson, Eric H. Davidson, Sarkis K. Mazmanian, David A. Prober, Matt Van De RijnJared R. Leadbetter, Dianne K. Newman, Carol Readhead, Marianne E. Bronner, Barbara Wold, Rusty Lansford, Tatjana Sauka-Spengler, Scott E. Fraser, Niles A. Pierce

Research output: Contribution to journalArticlepeer-review

108 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)3632-3637
Number of pages6
JournalDevelopment (Cambridge)
Issue number19
StatePublished - Oct 1 2016

Bibliographical note

Funding Information:
This work was funded by the National Institutes of Health (NIH) [5R01EB006192]; the National Science Foundation Molecular Programming Project [NSF-CCF-1317694]; the Gordon and Betty Moore Foundation [GBMF2809]; the Beckman Institute at Caltech (PMTC); the Translational Biomedical Imaging Laboratory at CHLA; the Translational Imaging Center at USC; a Christensen Fellowship at St Catherine’s College, University of Oxford; and by the John Simon Guggenheim Memorial Foundation. Deposited in PMC for release after 12 months.

Publisher Copyright:
© 2016. Published by The Company of Biologists Ltd.


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


Dive into the research topics of 'Mapping a multiplexed zoo of mRNA expression'. Together they form a unique fingerprint.

Cite this