Questions: Is it possible to detect TCR gamma/delta chains in the V(D)J assay?
Answer: The Single Cell V(D)J Enrichment Kits target constant regions of TCR alpha and beta chains and will not enrich for gamma/delta chains. It is possible that custom primers could be designed to capture these sequences. The User Guide describes the assay scheme and configuration (with oligo sequence info and primer concentrations for target enrichment steps), which can be used for designing a custom assay: https://support.10xgenomics.com/single-cell-vdj/library-prep/doc/user-guide-chromium-single-cell-vdj-reagent-kits-v1-chemistry
Because this is not supported, unfortunately, we cannot provide any further guidance on custom assay development. However, the following two publications successfully used the 5' assay to detect gamma/delta chains:
- Single-cell RNA sequencing identifies shared differentiation paths of mouse thymic innate T cells
- Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells
In principle, the cellranger vdj pipeline (from version 3.0) may be used to assemble and annotate the chains irrespective of the chain type. Note that our annotation algorithms are tuned to work with human and mouse TRA and TRB or IgH and IgL chains. Therefore there may be unforeseen performance issues in annotating the D/G chain types.
Products: Single Cell Immune Profiling