vdjdb-db
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antigenomics
PMID:18025130
One point of uncertainty: whether they actually used the two different epitopes (KK10 and KK10-L6M) for the tetramer (pentamer) sorting, or just the KK10. I cannot make it out from the methods or the main text, although common sense says both were used. http://jem.rupress.org/content/204/12/2813
That indicates which virus epitope is present in the subjects, and I indeed took that as evidence that they also used these two different epitopes in their pentamer-sort. That is how I put it in the table. But they never actually say that explicitly. Leave it like this?
But the sort was performed using tetramers, not pentamers, as the methods and table says. They used pentamers for mixed lymphocyte reactions: they incubated dendritic cells with these pentamers and used them for some sort of reaction with PBMC (doesn't make much sense to me as you usually mature DCs with a peptide, not peptide conjugated with MHC).
It seems most likely that they used just the KK10 tetramer for Table 1, and both KK10 WT and mutant KK10 for Figure 2 (two clones there). They say that the KK10 mut results in a different repertoire, but they specify only KK10WT in the title. So better set those from the Table 1 to KK10.
In the methods they mix up tetramers and pentamers when describing the sorting of the T cells: Sorting of tetramer+ HIV-1–specific CD8+ T cell populations.
Fresh or frozen PBMC samples were stained with PE-labeled MHC class I pentamers refolded with epitopic HIV-1 peptides (ProImmune) and fluorophore-labeled CD8+ antibodies, followed by decontamination with 1:100 dilution of fixation solution A (Caltag). Tetramer+ CD8+ cells were sorted on a FACS Aria cell sorter (BD Biosciences) at 70 pounds per square inch. The purity of sorted cell populations was consistently >98%.
I'll change it to tetramers I guess.
2016-12-14 17:57 GMT+01:00 Mikhail Shugay [email protected]:
Ok. But the sort was performed using tetramers, not pentamers, as the methods and table says. They used pentamers for mixed lymphocyte reactions: they incubated dendritic cells with these pentamers and used them for some sort of reaction with PBMC (doesn't make much sense to me as you usually mature DCs with a peptide, not peptide conjugated with MHC). It seems most likely that they used just the KK10 tetramer for Table 1, and both KK10 WT and mutant KK10 for Figure 2 (two clones there).
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