Extended Data Fig. 9: TCR profiling and scRNA-seq of p15E-specific T cells isolated from control and Setdb1 KO LLC tumours.
From: Epigenetic silencing by SETDB1 suppresses tumour intrinsic immunogenicity
a, Unique CDR3 sequences (x-axis) identified from TCR sequencing of flow-sorted p15E-tetramer-positive CD8+ T cells isolated from control LLC tumours. High-confidence CDR3 sequences (n = 377) are highlighted by brackets and identified based on strong statistical enrichment (−log10(P value) > 46 cut-off indicated by dotted line, see Methods) within the p15E-tetramer-positive fraction. b, c, scRNA-seq (5′) of 24,860 lymphoid cells (CD4+CD8+ enrichment) isolated from control (n = 4 untreated, n = 4 ICB-treated) and Setdb1 KO (n = 3 untreated, n = 3 ICB-treated) LLC tumours. b, UMAP plot highlights cell populations identified among CD4+CD8+-enriched lymphoid cells. c, Representative marker genes used to identify and annotate cell clusters in b. d, Representative flow cytometry gating strategy for p15E-tetramer studies. Corresponds to Fig. 4e. *P < 0.05.
