PUBLICATION

Multidimensional quantitative analysis of mRNA expression within intact vertebrate embryos

Authors
Trivedi, V., Choi, H.M.T., Fraser, S.E., Pierce, N.A.
ID
ZDB-PUB-180330-11
Date
2018
Source
Development (Cambridge, England)   145(1): (Journal)
Registered Authors
Fraser, Scott E.
Keywords
Multiplexed in situ hybridization, Quantitative in situ hybridization, Read-in, Read-out
MeSH Terms
  • Animals
  • Embryo, Nonmammalian
  • Gene Expression Profiling/methods*
  • Gene Expression Regulation, Developmental/physiology*
  • In Situ Hybridization/methods*
  • Nucleic Acid Amplification Techniques/methods*
  • RNA, Messenger/biosynthesis*
  • Zebrafish/embryology*
PubMed
29311262 Full text @ Development
Abstract
For decades, in situ hybridization methods have been essential tools for studies of vertebrate development and disease, as they enable qualitative analyses of mRNA expression in an anatomical context. Quantitative mRNA analyses typically sacrifice the anatomy, relying on embryo microdissection, dissociation, cell sorting and/or homogenization. Here, we eliminate the trade-off between quantitation and anatomical context, using quantitative in situ hybridization chain reaction (qHCR) to perform accurate and precise relative quantitation of mRNA expression with subcellular resolution within whole-mount vertebrate embryos. Gene expression can be queried in two directions: read-out from anatomical space to expression space reveals co-expression relationships in selected regions of the specimen; conversely, read-in from multidimensional expression space to anatomical space reveals those anatomical locations in which selected gene co-expression relationships occur. As we demonstrate by examining gene circuits underlying somitogenesis, quantitative read-out and read-in analyses provide the strengths of flow cytometry expression analyses, but by preserving subcellular anatomical context, they enable bi-directional queries that open a new era for in situ hybridization.
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