Tissue Clearing Methods Compatible with HCR™ RNA-ISH

The HCR™ RNA-ISH assay is compatible with a wide range of tissue clearing techniques. Below, we've outlined a categorized list of clearing methods that have been successfully used with the HCR™ platform, along with relevant references for each.

Clearing Methods Compatible Before HCR™ RNA-ISH

• CLARITY: A hydrogel-based method that uses electrophoresis to remove lipids while preserving biomolecules and structure. (Dar et al., 2020) 
• CUBIC: A chemical-based clearing protocol for whole organs and embryos, enabling deep tissue transparency. (Nguyen, 2017)
• iDISCO+: A solvent-based clearing technique optimized for large tissue volumes. (Kramer et al., 2018; Kumar et al., 2021)
• MiPACT: A modified version of PACT developed for microbial identification in tissues. (DePas et al., 2016; Gallego-Hernandez et al., 2020) 
• PACT: A variant of CLARITY that enables effective lipid removal while preserving tissue integrity. (Shah et al., 2016)
• SDS Clearing: A passive clearing method using sodium dodecyl sulfate (SDS) to remove lipids while retaining tissue architecture. (Nicovich et al., 2019; Kim et al., 2020; Mich et al., 2021)
• SHIELD: A stabilization-based clearing technique that protects biomolecules and tissue structure during harsh chemical processing. (Park et al., 2018) 

Clearing Methods Compatible After HCR™ RNA-ISH 

• Ce3D+: A non-toxic, water-based clearing method that uses iohexol and PEG to rapidly match the refractive index of tissue. (Anderson et al., 2020) 
• TDE (2, 2'-Thiodiethanol): A tunable refractive index matching medium that passively clears tissue by reducing light scattering. (Nicovich et al., 2019) 
• SeeDB: A high refractive index clearing protocol based on concentrated fructose solutions. (Kahan et al., 2021) 

Thinking About a Different Clearing Method? 

If you're considering a clearing technique not listed above, we currently do not have user-validated references available. That said, we encourage experimentation and would love to hear how it goes!