Localization of T cell clonotypes using the Visium spatial transcriptomics platform

STAR Protoc. 2022 Jun 10;3(2):101391. doi: 10.1016/j.xpro.2022.101391. eCollection 2022 Jun 17.


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).

Keywords: Immunology; Molecular Biology; Sequence analysis.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Clone Cells
  • Humans
  • T-Lymphocytes*
  • Transcriptome* / genetics