To whom it may concern,
I hope this email finds you well.
I am writing because I am using the ImmGenData() from celldex to annotate my cells. There are some subtypes such as T cells (T.DP, T.DP69-, T.DP69+, T.DPbl, and T.DPsm) in the label.fine. The terms look confusing to me. Would you mind explaining the difference to me? Thank you.
BW,
Marcus
Very sorry about the tardy reply.
The nomenclature for cell-types in ImmGen data is somewhat codified, but also varies a little.
- The first one or two letter(s) before the first dot refer to the lineage (T or B lymphocytes, DC for dendritic cells).
- Characters after the first dot refer to the specific subpopulation within this lineage, which can be more or less extensive are refined, using “field jargon” that isn’t always clear. So “DP refers to CD4+CD8+ double-positive cells in the thymus. Either as a whole (“T.DP”) or as subsets thereof (like CD69+ or CD69- fractions, which denote cells that have received, or not TCR activation signals and are on their way to positive selection). This section also encodes a possible experimental treatment (but the longer description is where this should be more intelligible)
- One or two characters after the last dot indicate the organ from which the sample was obtained, using constant nomenclature.
The T.DP seems to include all the other subtypes but they are all exclusively aligned to a single cell so they shouldnt have any overlaps. What exactly the T.DP would be?