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Cell. 2016 Feb 11;164(4):792-804. doi: 10.1016/j.cell.2016.01.038.

Multiplexed Intact-Tissue Transcriptional Analysis at Cellular Resolution.

Author information

1
Department of Bioengineering, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA.
2
Department of Bioengineering, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA; Department of Psychiatry and Behavioral Sciences, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA.
3
Department of Bioengineering, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA; Department of Psychiatry and Behavioral Sciences, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA. Electronic address: deissero@stanford.edu.

Abstract

In recently developed approaches for high-resolution imaging within intact tissue, molecular characterization over large volumes has been largely restricted to labeling of proteins. But volumetric nucleic acid labeling may represent a far greater scientific and clinical opportunity, enabling detection of not only diverse coding RNA variants but also non-coding RNAs. Moreover, scaling immunohistochemical detection to large tissue volumes has limitations due to high cost, limited renewability/availability, and restricted multiplexing capability of antibody labels. With the goal of versatile, high-content, and scalable molecular phenotyping of intact tissues, we developed a method using carbodiimide-based chemistry to stably retain RNAs in clarified tissue, coupled with amplification tools for multiplexed detection. The resulting technology enables robust measurement of activity-dependent transcriptional signatures, cell-identity markers, and diverse non-coding RNAs in rodent and human tissue volumes. The growing set of validated probes is deposited in an online resource for nucleating related developments from across the scientific community.

PMID:
26871636
PMCID:
PMC4775740
DOI:
10.1016/j.cell.2016.01.038
[Indexed for MEDLINE]
Free PMC Article

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