Wirasinha.CDD.2019.txt.zip

The file contains mouse T cell receptor (TCR) sequences collected by multiplex PCR amplification of cDNA molecules followed by Illumina sequencing. Sequences were aligned to the mouse genome using MIGEC software (see doi: 10.1038/nmeth.2960 for details). Except for the header row, each row contains information about a unique TCR nucleotide sequence. Columns 1-11 contain output from MIGEC software. Columns 12-16 contain information about sample origin, detailed as follows: column 12 "sample_id" is an identifier for the sample of origin; column 13 "chain" specifies the TCR chain ("a" = alpha, "b" = beta); column 14 "genotype" specifies the transgene status of donor mouse ("wt" or "bcl2" to indicate the absence or presence of BCL2-tg expression, respectively); column 15 "tcr_b" specifies the TCR beta chain status of donor mouse ("poly" = C57BL/6 inbred mouse strain); column 16 "mouse" is an identifier of the donor mouse; column 17 "organ" specifies organ of origin (thymus, "gut" = small intestine and spleen); column 18 "subset" specifies the T cell subset of origin ("t_p" = pre-selection thymocytes; "t_1" = Type A IELp; "t_1b" = Type B IELp; "t_r" = thymic T-reg; "t_4" = CD4+ T-conv thymocytes; "t_8" = CD8+ T-conv thymocytes; "g8a" = small intestinal CD8aa+ intraepithelial lymphocytes; "s_r" = splenic T-reg; "s_4" = splenic CD4+ naive T cells and "s_8" = splenic CD8+ naive T cells); column 19 is identical to column 18 except that column 19 shows whether the T-reg sample of origin was a CD25+ ("t_u" and "s_u") or CD25– ("t_d" and "s_d") fraction of a thymic or splenic T-reg population.