  Antigen-specific T cells play an essential role in immunoregulation and
diseases such as cancer. Characterizing the T cell receptor (TCR) sequences
that encode T cell specificity is critical for elucidating the antigenic
determinants of immunological diseases and designing therapeutic remedies.
However, methods of obtaining single-cell TCR sequencing data are labor and
cost intensive, requiring cell sorting and full length single-cell
RNA-sequencing (scRNA-seq). New high-throughput 3' cell-barcoding scRNA-seq
methods can simplify and scale this process; however, they do not routinely
capture TCR sequences during library preparation and sequencing. While 5'
cell-barcoding scRNA-seq methods can be used to examine TCR repertoire at
single-cell resolution, it requires specialized reagents which cannot be
applied to samples previously processed using 3' cell-barcoding methods. Here,
we outline a method for sequencing TCR$\alpha$ and TCR$\beta$ transcripts from
samples already processed using 3' cell-barcoding scRNA-seq platforms, ensuring
TCR recovery at a single-cell resolution. In short, a fraction of the 3'
barcoded whole transcriptome amplification (WTA) product typically used to
generate a massively parallel 3' scRNA-seq library is enriched for TCR
transcripts using biotinylated probes, and further amplified using the same
universal primer sequence from WTA. Primer extension using TCR V-region primers
and targeted PCR amplification results in a 3' barcoded single-cell
CDR3-enriched library that can be sequenced with custom sequencing primers.
Coupled with 3' scRNA-seq of the same WTA, this method enables simultaneous
analysis of single-cell transcriptomes and TCR sequences which can help
interpret inherent heterogeneity among antigen-specific T cells and salient
disease biology. This method can be adapted to enrich other transcripts of
interest from 3' and 5' barcoded WTA libraries.
