Question: Why are there only a few V(D)J dominant clonotypes in my sample?
Answer: The Single Cell V(D)J assay profiles full-length (5’ UTR to constant region) paired T-Cell Receptor (TCR) transcripts or Immunoglobulin (Ig) transcripts in single cells.
If the cell population is clonal or selected to recognize specific peptide antigens, the detected TRA/B chains or Ig chains may be shared across many cells. This observation is biological and is indicative of the reduced clonotype diversity of the sample.
Datasets generated from EBV-selected T Cells or a B-lymphoblastoid cell line, available on our Support Website, show this reduced clonotype diversity. This is reflected in the 'Paired Clonotype Diversity' metric reported by Cell Ranger, which is quite low. These datasets are available at: