Single-cell phenotyping within transparent intact tissue through whole-body clearing

Bin Yang, Jennifer B. Treweek, Rajan P. Kulkarni, Benjamin E. Deverman, Chun Kan Chen, Eric Lubeck, Sheel Shah, Long Cai, Viviana Gradinaru

Research output: Contribution to journalArticlepeer-review

730 Scopus citations

Abstract

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.

Original languageEnglish
Pages (from-to)945-958
Number of pages14
JournalCell
Volume158
Issue number4
DOIs
StatePublished - Aug 14 2014

Fingerprint

Dive into the research topics of 'Single-cell phenotyping within transparent intact tissue through whole-body clearing'. Together they form a unique fingerprint.

Cite this