Localization of T cell clonotypes using the Visium spatial transcriptomics platform

Abstract

Summary: We present a protocol to localize T cell receptor clones using the Visium spatial transcriptomics platform. This approach permits simultaneous localization of both gene expression and T cell clonotypes in situ within tissue sections. T cell receptor sequences identified by this protocol are readily recapitulated by single-cell sequencing. This technique enables detailed studies of the spatial organization of the human T cell repertoire, such as the localization of infiltrating T cell clones within the tumor microenvironment.For complete details on the use and execution of this protocol, please refer to Sudmeier et al. (2022). : Publisher's note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

Keywords

• Sequence analysis
• Immunology
• Molecular Biology