In situ hybridization of mRNA has long been a standard laboratory practice. Over recent years, the technique has evolved from the laborious sectioning of tissues and treatment with radioactive probes to the easier colorimetric (and occasionally fluorescent) methods now in use. Recent issues of CSH Protocols featured articles detailing in situ hybridization in Xenopus, Drosophila (here as well), and cultured cells.

November’s issue of CSH Protocols provides a full set of instructions for in situ hybridization on mouse embryos, as well as a cutting-edge method for imaging real-time gene expression in living systems with single-transcript resolution.

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The mouse protocols provide instructions for using both sections and whole-mount in situ hybridization.

For sections, there are protocols for preparing glass slides and coverslips, , embedding tissues for sectioning, dewaxing and rehydrating sections, and in situ hybridization with radioactive probes to sections (while a more difficult procedure, this still gives finer resolution and lower background than colorimetric stains).

For whole mounts, instructions are given for embryo and probe preparation, hybridization, washes and histochemistry, followed by imaging and sectioning after hybridization.

For those interested in earlier development, techniques for handling and fixing blastocysts are given as well.

While all of the above are standard procedures in most laboratories, Robert Singer and colleagues bring us a set of new methods that extend our abilities to track transcripts even further, watching them in real time in living cells. Protocols are presented for construct design and system set-up, mammalian cells and yeast. Two protocols for image analysis in these systems are provided here and here.