Journal
CHEM
Volume 4, Issue 6, Pages 1373-1386Publisher
CELL PRESS
DOI: 10.1016/j.chempr.2018.03.003
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Funding
- National Natural Science Foundation of China [21621003, 21235004, 21327806]
- National Key Research and Development Program of China [2016YFA0203101]
- Tsinghua University Initiative Scientific Research Program
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The expression and spatial profile of multiple RNA species at high precision in single cells is key information for understanding cellular behaviors and functions. Fluorescence microscopy is a powerful tool for imaging RNAs, but its multiplexing ability is limited by the number of spectrally distinct fluorophores. Here, we present a DNA-sequence-encoded fluorescence barcoding method, termed sequence-encoded amplicon (SeqEA), enabling highly multiplexed imaging of RNAs in single cells with single-molecule and single-nucleotide resolution. SeqEA exploits a thermodynamically tuning DNA hybridization approach for precisely encoding rolling circle amplicons with discrete fluorescence intensities as fluorescence barcodes, allowing for multiplexed tagging single-molecule RNAs. As a proof of principle, we have demonstrated its ability for simultaneously visualizing nine mRNA species and evaluated the coordination and spatial pattern of breast-cancer-associated oncogene expression. SeqEA provides a single-cell analysis platform for investigating the gene expression network and molecular mechanism of disease development.
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