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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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QC of TCRgamma repertoire #3

Closed chenhc720 closed 6 years ago

chenhc720 commented 6 years ago

As MIXCR picked up unexpected TCRgamma chains from each purified cell populations (Vg1, Vg4 and Vg6), quality controls looking into (i) the proportion of actual TCRgamma chain of each cell population and (ii) the proportion of contaminating TCRgamma chains in each purified cell populations are crucial. Especially, a significant proportion (~30%) of TCRgamma clones was aligned to Vg3 chain in the purified Vg1 cell populations. This is likely due to the fact that Vg1 and Vg3 chains share the same sequence at their CDR3 region.

It would be great to plot the proportion of all Vg chains picked up by MIXCR from each data sets and make sure the purity of isolated cell populations (according to their Vg chain expression) is good and/or at acceptable level. The results of young and old mice should be plotted together in the same figure for direct comparison and to confirm no bias existing between young and old groups for the comparison of their TCR repertoires.

All repertoire analyses for Vg1 cells should be performed looking into both Vg1 and Vg3 repertoires. The comparison between Vg1 and Vg3 repertoires would allow us to understand the quality of alignment of CDR3 sequences by MIXCR.

nilseling commented 6 years ago

I added these plots as figure "GammaChainUsage_qualityControl" to the Figures folder and corresponding xlsx files to the folder Results/Clones/TRG.