#
# Example metadata
#

Repertoire:
  - repertoire_id: 1841923116114776551-242ac11c-0001-012
    study:
      study_id: PRJNA300878
      study_title: "Homo sapiens B and T cell repertoire - MZ twins"
      study_type:
        id: null
        label: null
      study_description: "The adaptive immune system's capability to protect the body requires a highly diverse lymphocyte antigen receptor repertoire. However, the influence of individual genetic and epigenetic differences on these repertoires is not typically measured. By leveraging the unique characteristics of B, CD4+ T, and CD8+ T lymphocyte subsets isolated from monozygotic twins, we have quantified the impact of heritable factors on both the V(D)J recombination process and thymic selection in the case of T cell receptors, and show that the repertoires of both naive and antigen experienced cells are subject to biases resulting from differences in recombination. We show that biases in V(D)J usage, as well as biased N/P additions, contribute to significant variation in the CDR3 region. Moreover, we show that the relative usage of V and J gene segments is chromosomally biased, with approximately 1.5 times as many rearrangements originating from a single chromosome. These data refine our understanding of the heritable mechanisms affecting the repertoire, and show that biases are evident on a chromosome-wide level."
      inclusion_exclusion_criteria: null
      contributors:
        - contributor_id: "1"
          name: "Florian Rubelt"
          orcid_id:
            id: null
            label: null
          affiliation:
            id: "ROR:00f54p054"
            label: "Stanford University"
          affiliation_department: "Department of Microbiology and Immunology, Stanford University School of Medicine"
          contributions:
            - role: "investigation"
              degree: null
            - role: "data curation"
              degree: null
        - contributor_id: "2"
          name: "Mark M. Davis"
          orcid_id:
            id: "ORCID:0000-0001-6868-657X"
            label: "Mark Davis"
          affiliation:
            id: "ROR:00f54p054"
            label: "Stanford University"
          affiliation_department: "Department of Microbiology and Immunology, Stanford University School of Medicine"
          contributions:
            - role: "supervision"
              degree: null
      pub_ids: ["PMID:27005435"]
      grants: null
      keywords_study:
        - "contains_ig"
        - "contains_tr"
    subject:
      subject_id: TW01A
      synthetic: false
      species:
        id: "NCBITAXON:9606"
        label: "Homo sapiens"
      sex: female
      age:
        min: 27
        max: 27
        unit:
          id: UO:0000036
          label: year
      age_event: null
      ancestry_population:
        id: null
        label: null
      location_birth:
        id: null
        label: null
      ethnicity: null
      race: null
      strain_name: null
      linked_subjects: TW01B
      link_type: twin
      diagnosis:
        - study_group_description: null
          disease_diagnosis:
            id: null
            label: null
          disease_length: null
          disease_stage: null
          prior_therapies: null
          immunogen: null
          intervention: null
          medical_history: null

    sample:
      - sample_id: TW01A_B_naive
        sample_processing_id: null
        sample_type: "peripheral venous puncture"
        tissue:
          id: "UBERON:0000178"
          label: "blood"
        tissue_processing: "Ficoll gradient"
        cell_subset:
          id: "CL:0000788"
          label: "naive B cell"
        cell_phenotype: "expression of CD20 and the absence of CD27"
        cell_species:
          id: "NCBITAXON:9606"
          label: "Homo sapiens"
        single_cell: false
        cell_isolation: FACS
        template_class: RNA
        pcr_target:
          - pcr_target_locus: IGH
            forward_pcr_primer_target_location: null
            reverse_pcr_primer_target_location: null
        sequencing_platform: "Illumina MiSeq"
        sequencing_files:
          sequencing_data_id: SRA:SRR2905656
          file_type: fastq
          filename: SRR2905656_R1.fastq.gz
          read_direction: forward
          read_length: 300
          paired_filename: SRR2905656_R2.fastq.gz
          paired_read_direction: reverse
          paired_read_length: 300
          index_filename: SRR2905656_R3.fastq.gz
          index_length: 8
        anatomic_site: null
        disease_state_sample: null
        collection_time_point_relative: null
        collection_location:
          id: null
          label: null
        biomaterial_provider: null
        cell_number: null
        cells_per_reaction: null
        cell_storage: false
        cell_quality: null
        cell_processing_protocol: null
        template_quality: null
        template_amount: null
        library_generation_method: "RT(oligo-dT)+PCR"
        library_generation_protocol: null
        library_generation_kit_version: null
        complete_sequences: "partial"
        physical_linkage: "none"
        sequencing_run_id: null
        total_reads_passing_qc_filter: null
        sequencing_facility: null
        sequencing_run_date: null
        sequencing_kit: null
    data_processing:
      - data_processing_id: 3059369183532618216-242ac11b-0001-007
        primary_annotation: true
        software_versions: null
        paired_reads_assembly: null
        quality_thresholds: null
        primer_match_cutoffs: null
        collapsing_method: null
        data_processing_protocols: null
        data_processing_files: null
        germline_database: null
        analysis_provenance_id: 6623294219256599016-242ac11c-0001-012

  - repertoire_id: 1602908186092376551-242ac11c-0001-012
    study:
      study_id: PRJNA300878
      study_title: "Homo sapiens B and T cell repertoire - MZ twins"
      study_type:
        id: null
        label: null
      study_description: "The adaptive immune system's capability to protect the body requires a highly diverse lymphocyte antigen receptor repertoire. However, the influence of individual genetic and epigenetic differences on these repertoires is not typically measured. By leveraging the unique characteristics of B, CD4+ T, and CD8+ T lymphocyte subsets isolated from monozygotic twins, we have quantified the impact of heritable factors on both the V(D)J recombination process and thymic selection in the case of T cell receptors, and show that the repertoires of both naive and antigen experienced cells are subject to biases resulting from differences in recombination. We show that biases in V(D)J usage, as well as biased N/P additions, contribute to significant variation in the CDR3 region. Moreover, we show that the relative usage of V and J gene segments is chromosomally biased, with approximately 1.5 times as many rearrangements originating from a single chromosome. These data refine our understanding of the heritable mechanisms affecting the repertoire, and show that biases are evident on a chromosome-wide level."
      inclusion_exclusion_criteria: null
      contributors:
        - contributor_id: "1"
          name: "Florian Rubelt"
          orcid_id:
            id: null
            label: null
          affiliation:
            id: "ROR:00f54p054"
            label: "Stanford University"
          affiliation_department: "Department of Microbiology and Immunology, Stanford University School of Medicine"
          contributions:
            - role: "investigation"
              degree: null
            - role: "data curation"
              degree: null
        - contributor_id: "2"
          name: "Mark M. Davis"
          orcid_id:
            id: "ORCID:0000-0001-6868-657X"
            label: "Mark Davis"
          affiliation:
            id: "ROR:00f54p054"
            label: "Stanford University"
          affiliation_department: "Department of Microbiology and Immunology, Stanford University School of Medicine"
          contributions:
            - role: "supervision"
              degree: null
      pub_ids: ["PMID:27005435"]
      grants: null
      keywords_study:
        - "contains_ig"
        - "contains_tr"
    subject:
      subject_id: TW01A
      synthetic: false
      species:
        id: "NCBITAXON:9606"
        label: "Homo sapiens"
      sex: female
      age:
        min: 27
        max: 27
        unit:
          id: UO:0000036
          label: year
      age_event: null
      ancestry_population:
        id: null
        label: null
      location_birth:
        id: null
        label: null
      ethnicity: null
      race: null
      strain_name: null
      linked_subjects: TW01B
      link_type: twin
      diagnosis:
        - study_group_description: null
          disease_diagnosis:
            id: null
            label: null
          disease_length: null
          disease_stage: null
          prior_therapies: null
          immunogen: null
          intervention: null
          medical_history: null

    sample:
      - sample_id: TW01A_B_memory
        sample_processing_id: null
        sample_type: "peripheral venous puncture"
        tissue:
          id: "UBERON:0000178"
          label: "blood"
        tissue_processing: "Ficoll gradient"
        cell_subset:
          id: "CL:0000787"
          label: "memory B cell"
        cell_phenotype: "expression of CD20 and CD27"
        cell_species:
          id: "NCBITAXON:9606"
          label: "Homo sapiens"
        single_cell: false
        cell_isolation: FACS
        template_class: RNA
        pcr_target:
          - pcr_target_locus: IGH
            forward_pcr_primer_target_location: null
            reverse_pcr_primer_target_location: null
        sequencing_platform: "Illumina MiSeq"
        sequencing_files:
          sequencing_data_id: SRA:SRR2905655
          file_type: fastq
          filename: SRR2905655_R1.fastq.gz
          read_direction: forward
          read_length: 300
          paired_filename: SRR2905655_R2.fastq.gz
          paired_read_direction: reverse
          paired_read_length: 300
          index_filename: SRR2905655_R3.fastq.gz
          index_length: 8
        anatomic_site: null
        disease_state_sample: null
        collection_time_point_relative: null
        collection_location:
          id: null
          label: null
        biomaterial_provider: null
        cell_number: null
        cells_per_reaction: null
        cell_storage: false
        cell_quality: null
        cell_processing_protocol: null
        template_quality: null
        template_amount: null
        library_generation_method: "RT(oligo-dT)+PCR"
        library_generation_protocol: null
        library_generation_kit_version: null
        complete_sequences: "partial"
        physical_linkage: "none"
        sequencing_run_id: null
        total_reads_passing_qc_filter: null
        sequencing_facility: null
        sequencing_run_date: null
        sequencing_kit: null
    data_processing:
      - data_processing_id: 3059369183532618216-242ac11b-0001-007
        primary_annotation: true
        software_versions: null
        paired_reads_assembly: null
        quality_thresholds: null
        primer_match_cutoffs: null
        collapsing_method: null
        data_processing_protocols: null
        data_processing_files: null
        germline_database: null
        analysis_provenance_id: 6623294219256599016-242ac11c-0001-012

  - repertoire_id: 2366080924918616551-242ac11c-0001-012
    study:
      study_id: PRJNA300878
      study_title: "Homo sapiens B and T cell repertoire - MZ twins"
      study_type:
        id: null
        label: null
      study_description: "The adaptive immune system's capability to protect the body requires a highly diverse lymphocyte antigen receptor repertoire. However, the influence of individual genetic and epigenetic differences on these repertoires is not typically measured. By leveraging the unique characteristics of B, CD4+ T, and CD8+ T lymphocyte subsets isolated from monozygotic twins, we have quantified the impact of heritable factors on both the V(D)J recombination process and thymic selection in the case of T cell receptors, and show that the repertoires of both naive and antigen experienced cells are subject to biases resulting from differences in recombination. We show that biases in V(D)J usage, as well as biased N/P additions, contribute to significant variation in the CDR3 region. Moreover, we show that the relative usage of V and J gene segments is chromosomally biased, with approximately 1.5 times as many rearrangements originating from a single chromosome. These data refine our understanding of the heritable mechanisms affecting the repertoire, and show that biases are evident on a chromosome-wide level."
      inclusion_exclusion_criteria: null
      contributors:
        - contributor_id: "1"
          name: "Florian Rubelt"
          orcid_id:
            id: null
            label: null
          affiliation:
            id: "ROR:00f54p054"
            label: "Stanford University"
          affiliation_department: "Department of Microbiology and Immunology, Stanford University School of Medicine"
          contributions:
            - role: "investigation"
              degree: null
            - role: "data curation"
              degree: null
        - contributor_id: "2"
          name: "Mark M. Davis"
          orcid_id:
            id: "ORCID:0000-0001-6868-657X"
            label: "Mark Davis"
          affiliation:
            id: "ROR:00f54p054"
            label: "Stanford University"
          affiliation_department: "Department of Microbiology and Immunology, Stanford University School of Medicine"
          contributions:
            - role: "supervision"
              degree: null
      pub_ids: ["PMID:27005435"]
      grants: null
      keywords_study:
        - "contains_ig"
        - "contains_tr"
    subject:
      subject_id: TW01A
      synthetic: false
      species:
        id: "NCBITAXON:9606"
        label: "Homo sapiens"
      sex: female
      age:
        min: 27
        max: 27
        unit:
          id: UO:0000036
          label: year
      age_event: null
      ancestry_population:
        id: null
        label: null
      location_birth:
        id: null
        label: null
      ethnicity: null
      race: null
      strain_name: null
      linked_subjects: TW01B
      link_type: twin
      diagnosis:
        - study_group_description: null
          disease_diagnosis:
            id: null
            label: null
          disease_length: null
          disease_stage: null
          prior_therapies: null
          immunogen: null
          intervention: null
          medical_history: null

    sample:
      - sample_id: TW01A_T_naive_CD4
        sample_processing_id: null
        sample_type: "peripheral venous puncture"
        tissue:
          id: "UBERON:0000178"
          label: "blood"
        tissue_processing: "Ficoll gradient"
        cell_subset:
          id: "CL:0000895"
          label: "naive thymus-derived CD4-positive, alpha-beta T cell"
        cell_phenotype: "expression of CD8 and absence of CD4 and CD45RO"
        cell_species:
          id: "NCBITAXON:9606"
          label: "Homo sapiens"
        single_cell: false
        cell_isolation: FACS
        template_class: RNA
        pcr_target:
          - pcr_target_locus: TRB
            forward_pcr_primer_target_location: null
            reverse_pcr_primer_target_location: null
        sequencing_platform: "Illumina MiSeq"
        sequencing_files:
          sequencing_data_id: SRA:SRR2905659
          file_type: fastq
          filename: SRR2905659_R1.fastq.gz
          read_direction: forward
          read_length: 300
          paired_filename: SRR2905659_R2.fastq.gz
          paired_read_direction: reverse
          paired_read_length: 300
          index_filename: SRR2905659_R3.fastq.gz
          index_length: 8
        anatomic_site: null
        disease_state_sample: null
        collection_time_point_relative: null
        collection_location:
          id: null
          label: null
        biomaterial_provider: null
        cell_number: null
        cells_per_reaction: null
        cell_storage: false
        cell_quality: null
        cell_processing_protocol: null
        template_quality: null
        template_amount: null
        library_generation_method: "RT(oligo-dT)+PCR"
        library_generation_protocol: null
        library_generation_kit_version: null
        complete_sequences: "partial"
        physical_linkage: "none"
        sequencing_run_id: null
        total_reads_passing_qc_filter: null
        sequencing_facility: null
        sequencing_run_date: null
        sequencing_kit: null
    data_processing:
      - data_processing_id: 651223970338378216-242ac11b-0001-007
        primary_annotation: true
        software_versions: null
        paired_reads_assembly: null
        quality_thresholds: null
        primer_match_cutoffs: null
        collapsing_method: null
        data_processing_protocols: null
        data_processing_files: null
        germline_database: null
        analysis_provenance_id: 4625424004665971176-242ac11c-0001-012
