SCRINSHOT enables spatial mapping of cell states in tissue sections with single-cell resolution.
IF: 9.593
Cited by: 11


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.


Gene Expression

MeSH terms

Cell Line
Fluorescent Dyes
In Situ Hybridization
Nucleic Acid Amplification Techniques
Nucleic Acid Hybridization
RNA, Messenger
Single-Cell Analysis


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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