Open-source, high-throughput targeted in situ transcriptomics for developmental and tissue biology.

ABSTRACT: Multiplexed spatial profiling of mRNAs has recently gained traction as a tool to explore the cellular diversity and the architecture of tissues. We propose a sensitive, open-source, simple and flexible method for the generation of in situ expression maps of hundreds of genes. We use direct ligation of padlock probes on mRNAs, coupled with rolling circle amplification and hybridization-based in situ combinatorial barcoding, to achieve high detection efficiency, high-throughput and large multiplexing. We validate the method across a number of species and show its use in combination with orthogonal methods such as antibody staining, highlighting its potential value for developmental and tissue biology studies. Finally, we provide an end-to-end computational workflow that covers the steps of p

SUBMITTER: Lee H 

PROVIDER: S-EPMC11385644 | biostudies-literature | 2024 Aug

REPOSITORIES: biostudies-literature