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MarioniLab / GammaDeltaTcells2018

Code for the gamma delta T cell project with Maike De La Roche, Hung-Chang Chen and Celia Martinez
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Preference of TCRdelta usage #4

Closed chenhc720 closed 6 years ago

chenhc720 commented 6 years ago

Each Vg chain subsets (Vg1, Vg4 and Vg6) have distinct preferences in their coupling with different TCRdelta chain (Vd: Vsegment of TCRdelta chain). We would like to investigate whether this coupling preference of each Vg chain subsets with specific Vd chain is changed by aging. The results indicate possible clonal expansion from specific Vg/Vd cell subsets.

A table for the nomenclature of TCRdelta chains is enclosed in the shared dropbox folder.

We can also look into the preferential coupling in terms of J segment usage of TCRd chain if time allows.

This analysis can be done using CalcSegmentUsage function of VDJtools.

nilseling commented 6 years ago

I added the figure summarising delta chain usage to the "Figures" folder and the xlsx files containing the clone fractions to the Results/Clones/TRD folder

chenhc720 commented 6 years ago

The plots look beautiful as always! But the table for Vg4_Th1 is missing.

nilseling commented 6 years ago

Sorry, that's fixed now