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 healthy human B-cells pre- and post-flu vaccination, available on our Support Website, show this reduced clonotype diversity as a result of vaccine response. This is reflected in the higher frequency of the top clonotype in the post-vaccination data as opposed to pre-vaccination. These datasets are available at:
- https://support.10xgenomics.com/single-cell-vdj/datasets/5.0.0/sc5p_v2_hs_B_prevax_10k_5gex_B
- https://support.10xgenomics.com/single-cell-vdj/datasets/5.0.0/sc5p_v2_hs_B_postvax_10k_5gex_B
Products: VDJ