datasetposted on 13.02.2019 by Stephen Daley
Datasets usually provide raw data for analysis. This raw data often comes in spreadsheet form, but can be any collection of data, on which analysis can be performed.
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.
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