Hello folks,
Our lab is just beginning to get in to scRNAseq analysis of some developing T cells in the thymus of TCR-transgenic, Rag-sufficient, TCR alpha-het mice (the cells we sent are sorted CD4 single positive thymocytes, the gating was a bit generous to include the transition population between DP and SP populations, as we are also interested in the various developmental stages). We used 10X genomics scRNAseq and their VDJ clonotype analysis service, 100,000 reads / cell, .
While using their Loupe V(D)J viewer to look at our data, I noticed that certain populations of cells only give sequences of either the alpha or beta chains. I was expecting that all of them would possess both alpha and beta. There are a few possibilities I can think of: 1. some cells are of gamma-delta lineage, so there are no alpha chains, might still have beta chains, so that can explain the beta chain only population; can't explain the alpha chain only population though 2. TCR chain mRNA expression level not high enough 3. I can't remember at the moment...
I'd like to ask if anyone on here had experience analyzing clonotype of developing T cells in the thymus. Would very much appreciate any help!
Thanks! M.
The sequencing of the alpha and beta chains isn't perfect, i.e. there's a significant drop-out rate. The most likely explanation is technical in nature; I recommend reaching out to the 10X Genomics support team as they're quite knowledgeable and reliable and will probably be able to address many questions you may have.