Introduction

This webinar will explain tissue clearing, how it functions, and the three main methods for making tissues transparent. Moreover, the advantages and limitations of various tissue cleansing methods.

  1. PEGASOS version 1：Polyethylene glycol(PEG) Associated Solvent System

    • Jing, Dian, et al. “Tissue clearing of both hard and soft tissue organs with the PEGASOS method.” Cell research 28.8 (2018): 803-818. [PDF | DOI Link]

  2. TESOS system:

    • Yi, Yating, et al. “Mapping of individual sensory nerve axons from digits to spinal cord with the Transparent Embedding Solvent System.” bioRxiv (2021). [PDF | DOI Link]

CUBIC

  • The alcoholic amines in CUBIC can effectively remove the heme pigments within the sample hemoglobin and myoglobin, which can further reduce the light scattering and absorption and increase the transparency effect.
    • Matsumoto, Katsuhiko, et al. “Advanced CUBIC tissue clearing for whole-organ cell profiling.” Nature protocols 14.12 (2019): 3506-3537. [PDF | DOI Link]
  • CUBIC-HL：CUBIC-HL is capable of degreasing and decolorizing samples, with N-butyldiethanolamine and 1,3-bis(diaminomethyl)cyclohexane as the main components.

DISCO

  1. uDISCO
  2. FDISCO

CLARITY

  1. Chung, Kwanghun, et al. “Structural and molecular interrogation of intact biological systems.” Nature 497.7449 (2013): 332-337. [PDF | DOI Link]

SHIELD

  • P3PE： SHIELD started from protein conformation protection and selected P3PE from hundreds of chemical reagents. Its epoxidation of tissues makes it show very excellent performance in tissue fluorescence protection, endogenous protein and RNA structure protection, and reduction of autofluorescence, so SHIELD method completely abandoned the original acrylamide fixation and chose P3PE as fixative, and also abandoned the step of acrylamide gel embedding, and the fixed samples do not need embedding and can be directly subjected to SDS transparency.

HYBRiD

  1. Nudell, Victoria, et al. “HYBRiD: hydrogel-reinforced DISCO for clearing mammalian bodies.” Nature Methods 19.4 (2022): 479-485. [HYBRiD Protocol | PDF | PMID: 35347322 | DOI Link]

Expansion Microscopy

  1. Expansion Revealing (ExR)
    • Sarkar D, Kang J, Wassie A T, et al. Revealing nanostructures in brain tissue via protein decrowding by iterative expansion microscopy[J]. Nature Biomedical Engineering, 2022: 1-17 [[PDF] | PMID: 36038771 | DOI Link]
  2. X10 ExM: The resolution of X10 is ~25 nm
    • Truckenbrodt, S. et al. X10 expansion microscopy enables 25-nm resolution on conventional microscopes. EMBO Rep 19, e45836 (2018) [[PDF] | PMID: 29987134 | DOI Link]

Ref labs

  1. Ali Erturk Lab, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH)
  2. Edward Boyden Lab, Synthetic Neurobiology Group, MIT
  3. Hiroki R Ueda Lab, Quantitative Biology Center, RIKEN
  4. Kwanghun Chung Lab, MIT
  5. Ye Li Lab, The Scripps Research Institute
  6. Hu Zhao Lab, CIBR

Vendor company

  1. Sigma-Aldrich: Sigma-Aldrich is an American chemical, life science, and biotechnology company that is owned by the German chemical conglomerate Merck Group. Sigma-Aldrich was created in 1975 by the merger of Sigma Chemical Company and Aldrich Chemical Company.
  2. Aladdin, 阿拉丁： This company covers reagents and R & D materials in high-end chemistry, life sciences, analytical chromatography and materials science.

Ref labs

  1. Ali Erturk Lab, MIT
  2. Edward Boyden Lab, MIT
  3. Hiroki R Ueda Lab, RIKEN
  4. Ye Li Lab, The Scripps Research Institute
  5. Hu Zhao Lab, CIBR

Reference

  1. Vieites-Prado, Alba, and Nicolas Renier. “Tissue clearing and 3D imaging in developmental biology.” Development 148.18 (2021): dev199369. [PDF | DOI Link]