Site Specific Recombinases (SSRs): Cre & Other Genetic Reporters
While the Rosa26-lox-stop-lox-lacZ (R26-LSL-lacZ, or R26R) mouse originally developed by the Soriano lab is an amazing resource, beta-galactosidase has its own caveats and limitations (maturation time, perdurance, the necessity of colorimetric staining/no live reporting, tetramers needed for enzymatic activity, etc). Additionally, the level of lacZ expression depends on the endogenous activity of the native Rosa promoter. This can lead to under-reporting a Cre allele's activity, or missing the contribution of a cell population (the same can be said for the early Rosa-LSL-EYFP reporter allele).
Newer reporters often incorporate an exogenous, powerful promoter (such as CAGGs). A particular favorite reporter allele of the lab is the Rosa26-mTmG variant developed by the Luo lab at Stanford, which has CAGGs driving tdTomato expression in every cell, until Cre-mediated recombination occurs (which removes the tdTomato cassette), bringing an EGFP cDNA cassette immediately distal to the CAGGs promoter. This is schematized on the right, with a representative vibratome section of an E14.5 Tbx5-CreER/+ mouse heart following a pulse of tamoxifen during cardiac crescent formation.
Critically, the choice of lineage reporter will absolutely influence what you see, and what you don't. Choosing a lineage reporter carefully, and interpreting the results accordingly, is paramount in these experiments.