Fig. 3: Single-nuclei analysis of lymph node biopsy by 5’ Slide-tags.
From: A clonally expanded nodal T-cell population diagnosed as T-cell lymphoma after CAR-T therapy
a UMAP embedding of Slide-tags 5’ snRNA-seq transcriptome profiles, colored by cell type assignment. b Spatial mapping of snRNA-seq profiles, split by cell type. c T-cell gene expression program average usage scores. d Volcano plot of differentially expressed genes in the CD4+ CD8+ T cell population compared with all other T cells using a two-sided Wilcoxon rank-sum test with adjustment for multiple testing using the Bonferroni correction. Select genes are highlighted. e Size of beta chain clonotypes by T-cell population. Each color represents a different clonotype. The two beta chain sequences belonging to the most expanded clonotype are written in white text. f Module scoring of viral reactivity transcriptional signature by T-cell population. g Spatial neighborhood enrichment heatmap where Z scores denote the magnitude of enrichment or depletion between a given center cell type and neighbor cell type. Z scores are capped at 9 and −9 for visualization purposes.
