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

By Bin Yang, Jennifer B. Treweek, Rajan P. Kulkarni, Benjamin E. Deverman, Chun-Kan Chen, Eric Lubeck, Sheel Shah, Long Cai, Viviana Gradinaru. Cell, 2014

895 citations recorded by the source corpus.

SUMMARY 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, a protocol for passive tissue clearing and immunostaining of intact organs; RIMS, a refractive index matching media for imaging thick tissue; and PARS, 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.

Subfields: Biophysics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/0afab54265d2ad6f77a0d6fb1af3e4129a80c3a0

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Citations in the corpus

Clarifying Tissue Clearing (2015, neutral): “The CLARITY andPACT/PARSmethods attempt to address these issuesby first embedding the tissue in hydrogel (Chunget al., 2013; Tomer et al., 2014; Yang et al., 2014).”
The Human Cell Atlas (2017, background): “…at cellular or sub-cellular resolution (Angelo et al., 2014; Chen et al., 2015a; Giesen et al., 2014; Hama et al., 2011; Susaki et al., 2014; Yang et al., 2014); various aspects of chromatin state (Buenrostro et al., 2015; Cusanovich et al., 2015; Farlik et al., 2015; Guo et al., 2013;…”
iDISCO: a simple, rapid method to immunolabel large tissue samples for volume imaging. (2014, neutral): “…to the development of several important new clearing methods: ScaleA2 (Hama et al., 2011), 3DISCO (Ertürk et al., 2012a, 2012b, 2014), ClearT2 (Kuwajima et al., 2013), SeeDB (Ke et al., 2013), CLARITY (Chung et al., 2013; Tomer et al., 2014; Yang et al., 2014), and CUBIC (Susaki et al., 2014).”