Single-Cell Phenotyping within Transparent Intact Tissue through Whole-Body Clearing

August 20, 2014

Understanding the structure-function relationships at cellular, circuit, and organ-wide scale requires 3D anatomical and phenotypical maps, currently unavailable for many organs across species. At the root of this knowledge gap is the absence of a method that enables whole-organ imaging. Herein, we present techniques for tissue clearing in which whole organs and bodies are rendered macromolecule-permeable and optically transparent, thereby exposing their cellular structure with intact connectivity. We describe PACT (passive clarity technique), a protocol for passive tissue clearing and immunostaining of intact organs; RIMS (refractive index matching solution), a mounting media for imaging thick tissue; and PARS (perfusion-assisted agent release in situ), a method for whole-body clearing and immunolabeling. We show that in rodents PACT, RIMS, and PARS are compatible with endogenous-fluorescence, immunohistochemistry, RNA single-molecule FISH, long-term storage, and microscopy with cellular and subcellular resolution. These methods are applicable for high-resolution, high-content mapping and phenotyping of normal and pathological elements within intact organs and bodies.

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Yang B, Treweek JB, Kulkarni RP, Deverman BE, Chen C-K, Lubeck E, Shah S, Cai L, and Gradinaru V:
Single-Cell Phenotyping within Transparent Intact Tissue through Whole-Body Clearing

Cell 158 (4): 945–58 (2014); doi: dx.doi.org/10.1016/j.cell.2014.07.017

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