Bulk T cell receptor (TCR) sequencing of naive mouse T cells from the thymus of CCR4-knockout and wild-type mice The mice have a fixed beta-chain in the TCR that keeps half of the protein constant. This reduces the possible number of TCR sequences that can be found because only some TCR alpha-chains can pair with the fixed beta-chain.
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DE_source_functions.R and vdj_gene_comparison_functions.R contain functions that I use for all of my differential expression and TCR analyses.
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Finding differences in V gene and J gene usage in the TCRs of wild-type and CCR4-knockout mouse is done using comparing_VJuCDR3_normalized_gene_usage.qmd
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comparing_aa_comp_bw_WT_CCR4KO.qmd compares amino acid composition by position between WT & CCR4KO TCRs (See images below.)
Amino acid usage by position for each cell type and genotype
Maximum difference in amino acid proportion between CCR4KO and wild-type mice shows that some positions are more variable, even across TCRs of different lengths.
