HCR-FISH on mouse brain sections v1

This protocol provides a starting point for localization and visualization of RNAs in mouse brain tissue, using hybridization chain reaction (HCR)-amplified RNA-FISH (HCR-FISH). This can be useful for marking cell types of interest or investigating the effect of experimental manipulations on RNA expression. This protocol is compatible with multiple downstream analysis processes, including microscopy and laser capture microdissection, and can be used with free-floating tissue or tissue that has already been mounted onto a slide (but be sure to choose the option that is best suited for your downstream application). This protocol can also be combined with immunohistochemical (IHC) detection of proteins in mouse brain tissue (e.g. https://www.protocols.io/view/immunohistochemistry-ihc-on-mouse-brain-slices-5qpvokmq7l4o/v1). If combining HCR-FISH and IHC, brief fixation of slices in 4% PFA after HCR-FISH may help in preserving HCR-FISH signal.