PUBLICATION

Mapping a multiplexed zoo of mRNA expression

Authors
Choi, H.M., Calvert, C.R., Husain, N., Huss, D., Barsi, J.C., Deverman, B.E., Hunter, R.C., Kato, M., Lee, S.M., Abelin, A.C., Rosenthal, A.Z., Akbari, O.S., Li, Y., Hay, B.A., Sternberg, P.W., Patterson, P.H., Davidson, E.H., Mazmanian, S.K., Prober, D.A., van de Rijn, M., Leadbetter, J.R., Newman, D.K., Readhead, C., Bronner, M.E., Wold, B., Lansford, R., Sauka-Spengler, T., Fraser, S.E., Pierce, N.A.
ID
ZDB-PUB-161007-14
Date
2016
Source
Development (Cambridge, England)   143: 3632-3637 (Journal)
Registered Authors
Bronner-Fraser, Marianne, Fraser, Scott E., Prober, David, Sauka-Spengler, Tatjana
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
MeSH Terms
  • Animals
  • Drosophila
  • Embryo, Nonmammalian/metabolism
  • Humans
  • In Situ Hybridization/methods*
  • RNA, Messenger/metabolism*
  • Zebrafish
PubMed
27702788 Full text @ Development
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.
Genes / Markers
Figures
Show all Figures
Expression
Phenotype
Mutation and Transgenics
Human Disease / Model Data
Sequence Targeting Reagents
Fish
Antibodies
Orthology
Engineered Foreign Genes
Mapping
Errata and Notes