Whole mount in situ hybridization of E8.5 To E11.5 mouse embryos

Qiaozhi Wei, Nancy R. Manley, Brian G. Condie

Research output: Contribution to journalArticlepeer-review

12 Scopus citations


Whole mount in situ hybridization is a very informative approach for defining gene expression patterns in embryos. The in situ hybridization procedures are lengthy and technically demanding with multiple important steps that collectively contribute to the quality of the final result. This protocol describes in detail several key quality control steps for optimizing probe labeling and performance. Overall, our protocol provides a detailed description of the critical steps necessary to reproducibly obtain high quality results. First, we describe the generation of digoxygenin (DIG) labeled RNA probes via in vitro transcription of DNA templates generated by PCR. We describe three critical quality control assays to determine the amount, integrity and specific activity of the DIG-labeled probes. These steps are important for generating a probe of sufficient sensitivity to detect endogenous mRNAs in a whole mouse embryo. In addition, we describe methods for the fixation and storage ofE8.5-E11.5 day old mouse embryos for in situ hybridization. Then, we describe detailed methods for limited proteinase K digestion of there hydrated embryos followed by the details of the hybridization conditions, post-hybridization washes and RNase treatment to remove non-specific probe hybridization. An AP-conjugated antibody is used to visualize the labeled probe and reveal the expression pattern of the endogenous transcript. Representative results are shown from successful experiments and typical suboptimal experiments.

Original languageEnglish (US)
Article numbere2797
JournalJournal of Visualized Experiments
Issue number56
StatePublished - Oct 2011
Externally publishedYes


  • Developmental biology
  • Gene expression
  • Hybridization
  • In situ
  • In vitro
  • Issue 56
  • Mouse embryo
  • Riboprobe
  • Transcription
  • Transcriptome
  • Transcripts
  • mRNA

ASJC Scopus subject areas

  • Neuroscience(all)
  • Chemical Engineering(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)


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