Figure 3. Expression analysis of two different genes using whole-mount smFISH protocol.

(a) Filtered and threshold applied single plane confocal images of the indicated tissues of embryos subjected to the whole-mount smFISH protocol showing the co-localization of two genes (kdrl and gapdh, olig2 and neurog1) in the same single cells (outlined by white lines). (b) Filtered and threshold applied single plane images of brain (2dpf) of embryos subjected to the whole-mount smFISH protocol showing individual cells (outlined by while lines) that express one ubiquitously expressed gene (gapdh, sdha), but not cell type-specific (endothelial cell-specific) genes (fli1a, kdrl). In both (a) and (b), shown are confocal images taken with intact whole-mount embryos, except the panels labeled as “brain” that are taken with the head tissue separated from the rest of the body.