
ALT Spatial transcriptomics–based method to map B cell and T cell receptors. Targeted capture of antigen receptor sequences from spatial transcriptomics gene expression libraries resolves full-length receptor distribution alongside tissue anatomy and whole transcriptome in human tissue sections. Spatial VDJ uncovers B and T cell clonal dynamics, including linking clones to tumor-associated gene expression, pairing receptor chains, and reconstructing spatial B cell lineage trajectories.

ALT Clonal eviction of autoreactive CD8 thymocytes signaled to undergo negative selection. (A) CD4 versus CD8α expression on TCRhi thymocytes from HYcd4 male and female mice (left) and expression of various proteins in the indicated thymocyte subsets (single-color histograms). (C) To identify cells exiting the thymus, thymocytes were harvested 5 min after in vivo i.v. injection of phycoerythrin (PE)–conjugated anti-CD5 mAb. Thymocytes that bound the injected anti-CD5 mAb were referred to as CD5(i.v.)+ cells. (D) CD4 versus CD8 profiles of HY-specific T3.70+ peripheral T cells in HYcd4 male and female mice. Only negatively selecting male mice contained peripheral CD4/8dull HY-specific T cells.
























