2 files

TCRseq dataset for an NFKB2 allelic series in mice

posted on 11.03.2020, 04:24 by Stephen DaleyStephen Daley
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 12-17 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 genotype of the donor mouse ("wt" = Nfkb2+/+; "ndg" = Nfkb2+/D865G; "ngg" = Nfkb2D865G/D865G; "lym" = Nfkb2+/Lym1; "xdr" = Nfkb2xdr/xdr; "aire" = Aire–/–); column 15 "mouse" is an identifier of the donor mouse; column 16 "organ" specifies organ of origin (thymus or spleen); column 17 "subset" specifies the T cell subset of origin ("t_1" = Type A IELp; "t_4" = CD4+ T-conv thymocytes; "t_8" = CD8+ T-conv thymocytes; "s_r" = splenic T-reg; "s_4" = splenic CD4+ naive T cells and "s_8" = splenic CD8+ naive T cells). The file called "TCRseq_data_summary_by_sample.xlsx" is a summary, which describes the numbers of unique sequences, cysteine index positive sequences and hydrophobic index positive sequences for each of the 296 samples reported in the accompanying paper by Wirasinha et al.


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