Fig. 3
Validation of antigen–receptor assembly. a Number of cells assigned productive TCRα and TCRβ chains for Jurkat cells (n = 1463) or productive heavy and light chains for Ramos cells (n = 2000). Only receptor chains expressing the reference V and J gene combinations of Jurkat (TRA: TRAV8-4, TRAJ3; TRB: TRBV12-3, and TRBJ1-2) or Ramos (IGH: VH4-34, IGHJ6; IGL: IGLV2-14, and IGLJ2) were assigned. NR no receptor. b CDR3 accuracy measured by the number of Jurkat cells with assigned TRA or TRB sequences that directly match the reference Jurkat CDR3 nucleotide sequences (Supplementary Fig. 2a). ‘Non-productive’ refers to a cell with a CDR3 sequence that is out-of-frame or contains stop-codons. ‘Non-reference’ refers to a cell with a productive CDR3 sequence that does not match the reference. Only cells with Jurkat reference V and J gene combinations were analysed. c Recovery of TCR and BCR chains as a function of sequencing depth. Subsampling was performed on exactly 200 Jurkat cells and 200 Ramos cells with >1000 nanopore reads and assigned paired receptor chains. For Ramos, cells with the most common IGH and IGL CDR3 sequence were pre-selected as the reference sequence (Supplementary Fig. 2a). Subsampling was performed at the indicated read depths on the X-axis. d Accuracy of the assembled CDR3 sequence as a function of sequencing depth, as described in c. The percentage of cells with a CDR3 sequence that matched the reference CDR3 sequence was measured at each subsampling depth
