Barcoded complementary DNA libraries (WTA products) including TCRα and TCRβ transcripts, in addition to other transcripts (top). Fragmentation and selective amplification of cDNA results in the sequencing library used for transcriptomic sequencing, and analyzed via 3′ gene mapping as previously described18. TCR enrichment of the same cDNA library through affinity capture with biotinylated oligonucleotides results in amplified products enriched in TCRα and TCRβ transcripts. The sequencing library is made by primer extension with V-region primer sets, followed by PCR amplification using the UPS2 handles (bottom). The CDR3 region is sequenced using Illumina MiSeq with custom sequencing primers, and merged with the transcriptomic data on the basis of single-cell barcodes (BC).