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The majority of organic solvent clearing procedures has a simple two step mechanism in common:
The organic solvent clearing leads to very transparent samples and is perfectly suited for dense tissue like tumors, adult tissue, or highly myelinated brain. The majority of immuno-histochemical staining is well conserved.
The most common operating principle of water-based clearing protocols is by depolymerization. By splitting large structures like lipid bilayers into small micelles of different sizes, the opacity is remarkably reduced. Urea can be used as depolimerization agent as with CUBIC clearing. A SDS buffer and an advanced electrophoresis protocol are used for CLARITY clearing.
The clearing protocols differ in complexity and in the degree of translucency that can be achieved. By depolymerization, the entire structure of a sample can be debilitated while the fluorescence of proteins like GFP is well preserved.
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Hama, H. et al. (2011) Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain. Nat. Neurosci. 14(11):1481-8
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Murray, E et al. (2015) Simple, scalable proteomic imaging for high-dimensional profiling of intact systems. Cell 163(6):1500-14
Pan, C et al. (2016): Shrinkage-mediated imaging of entire organs and organisms using uDISCO. Nat Methods 13(10):859-67
Renier, N et al. (2014) iDISCO: A Simple, Rapid Method to Immunolabel Large Tissue Samples for Volume Imaging. Cell 159(4):896-910
Schwarz, MK et al. (2015) Fluorescent-Protein Stabilization and High-Resolution Imaging of Cleared, Intact Mouse Brains. PLoS One 10(5):e0124650
Susaki, EA et al. (2015) Advanced CUBIC protocols for whole-brain and whole-body clearing and imaging. Nat Protoc 10(11):1709-27
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Yang, B et al. (2014) Single-cell phenotyping within transparent intact tissue through whole-body clearing. Cell 158(4):945-958
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