Single-molecule RNA in situ hybridization (smFISH) and immunofluorescence (IF) in the Drosophila egg chamber

Livia V. Bayer, Mona Batish, Stephen K. Formel, Diana P. Bratu

Research output: Contribution to journalArticlepeer-review

18 Scopus citations


Detection of nucleic acids in whole tissues has become key in our understanding of gene expression during development. In situ hybridization (ISH) has been an invaluable technique in the making of numerous discoveries. Most recently, the technical advance of using short, fluorescently labeled probes has allowed for the detection of single-mRNA molecules. Thus, quantification of RNA levels in single cells or even within subcellular regions is now possible without RNA isolation. In combination with the immunofluorescence (IF) technique, visualization of nucleic acids and associating proteins is achieved with higher resolution than ever before using light microscopy. Here we describe the steps implemented to achieve the visualization of individual messenger RNAs (mRNA) using single-molecule FISH (smFISH) probes, as well as detection of mRNA/protein (mRNP) complexes via smFISH in combination with IF.

Original languageEnglish (US)
Pages (from-to)125-136
Number of pages12
JournalMethods in Molecular Biology
StatePublished - 2015

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Genetics


  • Drosophila melanogaster
  • Egg chambers
  • Immunofl uorescence
  • MRNA
  • MRNP
  • Oogenesis
  • SmFISH
  • Stellaris™ probe


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