Ub-1 Optical Clearing of the Murine Liver v1

We report a urea-amino sugar clearing reagent for the murine liver that rapidly renders the tissue clear with preservation of native architecture, fluorescent proteins and lipophilic dyes. Optical clearing protocols for three-dimensional (3D) imaging, such as confocal or light sheet microscopy, can consist of several steps and solutions, complex apparatuses, or days to weeks for whole-organ clearing. Established protocols that demonstrate efficient clearing can unfortunately quench endogenous proteins, whereas some methods formulated to preserve protein fluorophores can be underwhelming in clearing capability. Many clearing methods have been optimized for neural tissue, with little described for the liver. Our method, a single step modified protocol of the UbasM protocol created by Chen et al., uses Ub-1 to clear the murine liver with only 24 hours incubation and one simple solution. We additionally describe a technique for labeling the murine intrahepatic biliary tree and vasculature. Our methods can benefit investigations of tissue composition and structural relationships in 3D.