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Single molecule chromogenic in situ hybridization assay for RNA visualization in fixed cells and tissues.

RNA 2019 May 8
Visualization of gene expression at single RNA molecule level represents a great challenge to both imaging technologies and molecular engineering. Here we show a single molecule chromogenic in situ hybridization (smCISH) assay that enables counting and localizing individual RNA molecules in fixed cells and tissue under bright field microscopy. Our method is based on in situ padlock probe assay directly using RNA as ligation template and rolling circle amplification combined with enzyme catalyzed chromogenic reaction for amplification product visualization. We showed potential applications of our method by detecting gene expression variations in single cells, sub-cellular localization information of expressed genes and gene expression heterogeneity in formalin-fixed, paraffin-embedded tissue sections. This facile and straightforward method can in principle be applied to any types of RNA molecules in different samples.

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