Open AccessSCRINSHOT enables spatial mapping of cell states in tissue sections with single-cell resolution
Author(s) -
Alexandros Sountoulidis,
Andreas Liontos,
Hong Phuong Nguyen,
Alexandra B. Firsova,
Athanasios Fysikopoulos,
Xiaoyan Qian,
Werner Seeger,
Erik Sundström,
Mats Nilsson,
Christos Samakovlis
Publication year - 2020
Publication title -
plos biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 4.127
H-Index - 271
eISSN - 1545-7885
pISSN - 1544-9173
DOI - 10.1371/journal.pbio.3000675
Subject(s) - biology , multiplex , cell , single cell analysis , computational biology , in situ hybridization , oligonucleotide , gene expression , microbiology and biotechnology , in situ , gene expression profiling , rna , messenger rna , gene , genetics , physics , meteorology
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 ( S ingle- C ell R esolution IN S itu H ybridization O n T issues), 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.