Abstract
Mosaic analysis with double markers (MADM) mouse models closely mimic the clonal origin of human cancers by generating sporadic, GFP-labeled cancer-initiating cells. Traditional clonal analysis pipelines are labor intensive, hindering throughput and disrupting the 3D architecture. Here, we present a protocol that integrates tissue clearing and light-sheet imaging to analyze pre-malignant clones in whole-mount MADM-labeled tissues. We describe steps for generating mosaic-labeled cancer mouse models, tissue harvesting, fixation, and clearing. We then detail procedures for light-sheet imaging and clonal size analysis. For complete details on the use and execution of this protocol, please refer to Zeng et al.1,2.