Rather than working with an entire genome, our lab focuses on the genomic sequences of individual B Cell Receptors and T Cell Receptors. By using the 10X Genomics platform to multiplex our samples, we can process thousands of cells at once; and by taking full advantage of the incredible degree of specialization those receptors naturally display, we can tease out genomic data as clearly as if we'd handled each cell alone.
During the setup phase of each sequencing run, we chemically bind unique "barcodes" to each of the viral peptides we want to assay. When we later incubate those peptides with B or T cells, those barcodes become name-tags, personalized for every single cell based on its viral reactivity. From there on, each barcode stays matched to its peptide, even after the cells themselves have been lysed.
By barcoding each multimer before it's bound to any cells, we can use the unique sequence of those barcodes to tell individual target cells apart after sequencing. We also record the sequences of each TCR and BCR while we're going. That means we know which T or B cell recognized which antigen--and how.
Pools of DNA-tagged peptide:HLA multimer probes are used to stain a T cell sample. This results in a physical co-localization of both the internal cellular mRNAs and the cell-surface multimer barcodes. Microfluidic partitioning allows these sequences to be associated with cell-barcodes indicating their origin and evaluated by sequencing.