Combining genotypes and T cell receptor distributions to infer genetic loci determining V(D)J recombination probabilities: validation cohort meta data and parsed TCR repertoire data
Authors/Creators
- 1. Department of Immunology, St. Jude Children's Research Hospital; Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center
- 2. Department of Immunology, St. Jude Children's Research Hospital
- 3. Centro Nacional de Diagnóstico y Referencia, Ministry of Health, Nicaragua; Sustainable Sciences Institute, Managua, Nicaragua
- 4. Department of Epidemiology, University of Michigan
Description
Meta data corresponding the the validation cohort for the paper, "Combining genotypes and T cell receptor distributions to infer genetic loci determining V(D)J recombination probabilities" by Magdalena L Russell, Aisha Souquette, David M Levine, Stefan A Schattgen, E Kaitlynn Allen, Guillermina Kuan, Noah Simon, Angel Balmaseda, Aubree Gordon, Paul G Thomas, Frederick A Matsen IV, and Philip Bradley. These meta data include:
(1) SNP genotypes for the two SNPs which overlap with the discovery cohort
- (nicaragua_snp_genotypes_ints.tsv) -- SNP genotypes as integers
- (nicaragua_snp_genotypes_strings.tsv) -- SNP genotypes as allele strings
(2) the ancestry PCs for each individual in the validation cohort (nicaragua_snp_ancestry_PCA.tsv)
(3) a file including IMGT genes and sequences used for parsing TCRB repertoire data (human_vj_allele_cdr3_nucseqs.tsv)
(4) a file including IMGT genes used for parsing TCRA repertoire data (human_vj_alleles_alpha.tsv)
(5) Parsed TCRA repertoire data (nicaragua_parsed_TCRA.tgz)
(6) Parsed TCRB repertoire data (nicaragua_parsed_TCRB.tgz)
Corresponding raw validation cohort TCR repertoire data is available here: https://www. ncbi.nlm.nih.gov/bioproject/PRJNA762269 (The BioProject database, accession number: PRJNA762269)
Software tools designed to work with these data are available here: https://github.com/phbradley/tcr-gwas
Files
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