Microarray analysis and RNA-Seq are powerful tools for investigating differential gene expression in animal models of human genetic disease. Often, these models are loss of function mutations introduced by gene targeting or trapping. One difficulty in such experiments, especially where work on congenital malformations is concerned, is that whole embryo or regional dissections will commonly contain cells that do not express the gene of interest. Thus where cell autonomous effects are of primary interest, for example in the case of transcriptional regulators, such experiments will be compromised by dilutional effects and perhaps secondary effects on surrounding, non expressing tissues. Isolation of the relevant expressing lineage can mitigate these effects. Flow cytometry offers one route to cell purification but requires a fluorescent marker, and relatively few fluorescent protein gene reporters are available. FACS-Gal (1) offers the potential to capitalize upon the large existing repository of LacZ trapped ES lines now encompassing approximately 33% of all mouse genes "http://www.genetrap.org/index.html":http://www.genetrap.org/index.html. Moreover, the existence of Cre-reversible traps opens the way to within group comparisons of flow sorted cells, one pool having had expression restored using a tamoxifen activated Cre enzyme (2).