SCRINSHOT enables spatial mapping of cell states in tissue sections with single-cell resolution
| Autor: | Sountoulidis, Alexandros, Liontos, Andreas, Nguyen, Hong Phuong, Firsova, Alexandra B., Fysikopoulos, Athanasios, Qian, Xiaoyan, Seeger, Werner, Sundström, Erik, Nilsson, Mats, Samakovlis, Christos |
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| Rok vydání: | 2020 |
| Předmět: |
Lung Development
QH301-705.5 Organogenesis Respiratory System Oligonucleotides Molecular Probe Techniques Gene Expression Research and Analysis Methods Biochemistry Epithelium Cell Line Ligases Mice Sequencing techniques Genetics Medicine and Health Sciences Animals Humans RNA Messenger Biology (General) Molecular Biology Techniques Molecular Biology In Situ Hybridization Fluorescent Dyes Methods and Resources Nucleic Acid Hybridization Biology and Life Sciences Proteins RNA sequencing Probe Hybridization Enzymes Trachea Biological Tissue Enzymology RNA RNA hybridization Single-Cell Analysis Anatomy Nucleic Acid Amplification Techniques Organism Development Developmental Biology |
| Zdroj: | PLoS Biology PLoS Biology, Vol 18, Iss 11, p e3000675 (2020) |
| ISSN: | 1545-7885 |
| Popis: | Changes in cell identities and positions underlie tissue development and disease progression. Although single-cell mRNA sequencing (scRNA-Seq) methods rapidly generate extensive lists of cell states, spatially resolved single-cell mapping presents a challenging task. We developed SCRINSHOT (Single-Cell Resolution IN Situ Hybridization On Tissues), a sensitive, multiplex RNA mapping approach. Direct hybridization of padlock probes on mRNA is followed by circularization with SplintR ligase and rolling circle amplification (RCA) of the hybridized padlock probes. Sequential detection of RCA-products using fluorophore-labeled oligonucleotides profiles thousands of cells in tissue sections. We evaluated SCRINSHOT specificity and sensitivity on murine and human organs. SCRINSHOT quantification of marker gene expression shows high correlation with published scRNA-Seq data over a broad range of gene expression levels. We demonstrate the utility of SCRINSHOT by mapping the locations of abundant and rare cell types along the murine airways. The amenability, multiplexity, and quantitative qualities of SCRINSHOT facilitate single-cell mRNA profiling of cell-state alterations in tissues under a variety of native and experimental conditions. This study presents SCRINSHOT, an amenable, multiplex RNA-mapping method, applicable to a wide variety of tissue types and conditions. It can function quantitatively across a broad range of expression levels and detect even rare cell types, facilitating the creation of digital tissue maps with single-cell resolution. |
| Databáze: | OpenAIRE |
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