Localization of T cell clonotypes using the Visium spatial transcriptomics platform
William Henry Hudson, Lisa Sudmeier
Abstract
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).
Topics & Concepts
TranscriptomeBiologyRepertoireComputational biologyCellT cellT-cell receptorCell biologyGeneGeneticsGene expressionImmune systemAcousticsPhysicsSingle-cell and spatial transcriptomicsT-cell and B-cell ImmunologyCAR-T cell therapy research