Bulk TCR sequencing cost around $500 to $1000 and captures under a million T cells. scRNA Seq costs around $10,000 and captures under ten thousand T cells. The price of sequencing is falling exponentially so my numbers can be out of date
These figures are approximately right. We've been able to bring the cost of single-cell RNA-seq + TCR-seq runs down to $3000 by doing targeted gene expression, which requires less reads. Besides, some newer microfluidics platforms are able to yield more cells, close to 2e4.
I would say that the major limiting factor is the microfluidics platform. Ideally, we would require something that has a yield within the same order of magnitude of bulk methods. To address this limitation, one can e.g. pre-sort activated cells. Otherwise, the number of receptors is typically not enough to be able to observe meaningful statistical patterns.
Parse biosciences and companies have developed methods to perform TCR sequencing without the microfluidics and it will be interesting to see how well it performs. These methods are all based on permeabilizing the cell and keeping it intact instead of encapsulating the in a droplet and then lysing it.
