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#
# 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_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."
lab_name: "Mark M. Davis"
lab_address: "Stanford University"
submitted_by: "Florian Rubelt"
pub_ids: "PMID:27005435"
subject:
subject_id: TW01A
synthetic: false
species:
id: "NCBITaxon_9606"
value: "Homo sapiens"
sex: female
age_min: 27
age_max: 27
age_unit:
id: UO_0000036
value: year
linked_subjects: TW01B
link_type: twin
sample:
- sample_id: TW01A_B_naive
tissue: PBMC
cell_subset: "Naive B cell"
cell_phenotype: "expression of CD20 and the absence of CD27"
cell_species:
id: "NCBITaxon_9606"
value: "Homo sapiens"
single_cell: false
cell_isolation: FACS
template_class: RNA
pcr_target:
- pcr_target_locus: IGH
sequencing_platform: "Illumina MiSeq"
read_length: "300"
sequencing_files:
file_type: fastq
filename: SRR2905656_R1.fastq.gz
read_direction: forward
paired_filename: SRR2905656_R2.fastq.gz
paired_read_direction: reverse
data_processing:
- data_processing_id: 3059369183532618216-242ac11b-0001-007
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_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."
lab_name: "Mark M. Davis"
lab_address: "Stanford University"
submitted_by: "Florian Rubelt"
pub_ids: "PMID:27005435"
subject:
subject_id: TW01A
synthetic: false
species:
id: "NCBITaxon_9606"
value: "Homo sapiens"
sex: female
age_min: 27
age_max: 27
age_unit:
id: UO_0000036
value: year
linked_subjects: TW01B
link_type: twin
sample:
- sample_id: TW01A_B_memory
tissue: PBMC
cell_subset: "Memory B cell"
cell_phenotype: "expression of CD20 and CD27"
cell_species:
id: "NCBITaxon_9606"
value: "Homo sapiens"
single_cell: false
cell_isolation: FACS
template_class: RNA
pcr_target:
- pcr_target_locus: IGH
sequencing_platform: "Illumina MiSeq"
read_length: "300"
sequencing_files:
file_type: fastq
filename: SRR2905655_R1.fastq.gz
read_direction: forward
paired_filename: SRR2905655_R2.fastq.gz
paired_read_direction: reverse
data_processing:
- data_processing_id: 3059369183532618216-242ac11b-0001-007
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_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."
lab_name: "Mark M. Davis"
lab_address: "Stanford University"
submitted_by: "Florian Rubelt"
pub_ids: "PMID:27005435"
subject:
subject_id: TW01A
synthetic: false
species:
id: "NCBITaxon_9606"
value: "Homo sapiens"
sex: female
age_min: 27
age_max: 27
age_unit:
id: UO_0000036
value: year
linked_subjects: TW01B
link_type: twin
sample:
- sample_id: TW01A_T_naive_CD4
tissue: PBMC
cell_subset: "Naive CD4+ T cell"
cell_phenotype: "expression of CD8 and absence of CD4 and CD45RO"
cell_species:
id: "NCBITaxon_9606"
value: "Homo sapiens"
single_cell: false
cell_isolation: FACS
template_class: RNA
pcr_target:
- pcr_target_locus: TRB
sequencing_platform: "Illumina MiSeq"
read_length: "300"
sequencing_files:
file_type: fastq
filename: SRR2905659_R1.fastq.gz
read_direction: forward
paired_filename: SRR2905659_R2.fastq.gz
paired_read_direction: reverse
data_processing:
- data_processing_id: 651223970338378216-242ac11b-0001-007
analysis_provenance_id: 4625424004665971176-242ac11c-0001-012
|
