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

Yang, Bin and Treweek, Jennifer B. and Kulkarni, Rajan P. and Deverman, Benjamin E. and Chen, Chun-Kan and Lubeck, Eric and Shah, Sheel and Cai, Long and Gradinaru, Viviana (2014) Single-Cell Phenotyping within Transparent Intact Tissue through Whole-Body Clearing. Cell, 158 (4). pp. 945-958. ISSN 0092-8674. PMCID PMC4153367.

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[img] MS Excel (Table S2. Reagents for PACT, PARS and RIMS, Related to Figures 1, S1, and S3) - Supplemental Material
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[img] Video (Flash) (Movie S1. PARS GFAP Immunostained Rat Tissue to Visualize Vasculature, Related to Figure S4) - Supplemental Material
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[img] Video (Flash) (Movie S2. Deep-Brain Imaging of Adult Thy1-eYFP Mouse after PARS Clearing, Related to Figure 5B) - Supplemental Material
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[img] Video (Flash) (Movie S3. PARS Cleared and Immunostained Mouse Kidney, Related to Figure 6B) - Supplemental Material
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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.

Item Type:Article
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URLURL TypeDescription Information Information Information Information Information CentralArticle
Deverman, Benjamin E.0000-0002-6223-9303
Lubeck, Eric0000-0002-5457-0258
Cai, Long0000-0002-7154-5361
Gradinaru, Viviana0000-0001-5868-348X
Additional Information:© 2014 Elsevier Inc. Received: May 6, 2014; Received in revised form: July 13, 2014; Accepted: July 15, 2014; Published Online: July 31, 2014. We thank the entire Gradinaru lab for helpful discussions. We also thank Drs. Dianne Newman and David Anderson for helpful discussions and suggestions. We thank Drs. Amir Arbabi and Andrei Faraon for assistance with SEM imaging. We thank Richard Bennett and Erik Cabral for assistance with tumor procurement. We thank Leica Microsystems for acquiring some of the images presented with a Leica TCS SP8 with Leica HC FLUOTAR L 25×/1.00 IMM CORR objective designed for CLARITY imaging. B.D. and V.G. especially wish to acknowledge the contributions of Paul H. Patterson (1943–2014), whose desire to apply tissue clearing to unresolved questions in neuroscience pushed us to further evolve these methods. This work was funded by: the NIH/NINDS New Innovator (NIH IDP20D017782-01); NIH 1R01AG047664-01; Startup funds from the President and Provost of California Institute of Technology and the Biology and Biological Engineering Division of California Institute of Technology; the Beckman Institute of Caltech; the Pew Charitable Trust; the Sidney Kimmel Foundation (to V.G.). And NIH R01HD075605 (to L.C.). V.G. is also supported by: Human Frontiers in Science Program, the Mallinckrodt Foundation, the Gordon and Betty Moore Foundation, the Michael J. Fox Foundation, Caltech-GIST, NIH 1R01NS085910-01, NIH 1R21MH103824-01. C-K.C., S.S., E.L., acknowledge support from the Caltech Biology Division Training grant (NIH/NRSA 5T32GM07616). R.P.K. acknowledges support from NIH/NIAMS (5T32AR058921). J.B.T. acknowledges the Colvin Postdoctoral Fellowship and CALTECH Division of BBE. B.Y. and V.G. have disclosed these methods and findings to the Caltech Office of Technology Transfer (CIT File No.: CIT-6686-P). V.G. is a cofounder of Circuit Therapeutics and holds related IP and stock (less than 5%). At this writing, V.G. receives no research funding, royalties, or consultant fees from any for-profit organization. Author Contribution: B.Y., J.B.T., and V.G. conceived the project. B.Y., J.B.T., R.P.K., B.E.D., C.-K.C., E.L., S.S., L.C., and V.G. planned and executed experiments. B.Y., J.B.T., V.G. made the figures and wrote the paper with input from all other authors. V.G. supervised all aspects of the work.
Funding AgencyGrant Number
Caltech Beckman InstituteUNSPECIFIED
Pew Charitable TrustUNSPECIFIED
Sidney Kimmel FoundationUNSPECIFIED
Human Frontiers Science ProgramUNSPECIFIED
Mallinckrodt FoundationUNSPECIFIED
Gordon and Betty Moore FoundationUNSPECIFIED
Michael J. Fox FoundationUNSPECIFIED
NIH Predoctoral Fellowship5T32GM07616
NIH Predoctoral Fellowship5T32AR058921
Colvin Biology FellowshipUNSPECIFIED
Caltech Division of Biology and Biological Engineering (BBE)UNSPECIFIED
Issue or Number:4
PubMed Central ID:PMC4153367
Record Number:CaltechAUTHORS:20140801-121634734
Persistent URL:
Official Citation:Bin Yang, Jennifer B. Treweek, Rajan P. Kulkarni, Benjamin E. Deverman, Chun-Kan Chen, Eric Lubeck, Sheel Shah, Long Cai, Viviana Gradinaru, Single-Cell Phenotyping within Transparent Intact Tissue through Whole-Body Clearing, Cell, Volume 158, Issue 4, 14 August 2014, Pages 945-958, ISSN 0092-8674, (
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:47811
Deposited By: George Porter
Deposited On:01 Aug 2014 19:50
Last Modified:03 Mar 2020 13:01

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