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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_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."
study_contact: "Mark M. Davis, mmdavis@stanford.edu, ORCID:0000-0001-6868-657X"
inclusion_exclusion_criteria: null
lab_name: "Mark M. Davis"
lab_address: "Stanford University"
submitted_by: "Florian Rubelt"
pub_ids: "PMID:27005435"
collected_by: null
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
age_max: 27
age_unit:
id: UO_0000036
label: year
age_event: null
ancestry_population: 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:
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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
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collection_time_point_relative: null
collection_time_point_relative_unit:
id: null
label: null
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biomaterial_provider: null
cell_number: null
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cell_storage: false
cell_quality: null
cell_processing_protocol: null
template_quality: null
template_amount: null
template_amount_unit:
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label: 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
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sequencing_kit: null
data_processing:
- data_processing_id: 3059369183532618216-242ac11b-0001-007
primary_annotation: true
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quality_thresholds: null
primer_match_cutoffs: null
collapsing_method: null
data_processing_protocols: null
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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."
study_contact: "Mark M. Davis, mmdavis@stanford.edu, ORCID:0000-0001-6868-657X"
inclusion_exclusion_criteria: null
lab_name: "Mark M. Davis"
lab_address: "Stanford University"
submitted_by: "Florian Rubelt"
pub_ids: "PMID:27005435"
collected_by: null
grants: null
keywords_study:
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subject:
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synthetic: false
species:
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label: "Homo sapiens"
sex: female
age_min: 27
age_max: 27
age_unit:
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strain_name: null
linked_subjects: TW01B
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diagnosis:
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disease_diagnosis:
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label: null
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immunogen: null
intervention: null
medical_history: null
sample:
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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:
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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_time_point_relative_unit:
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biomaterial_provider: null
cell_number: null
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template_quality: null
template_amount: null
template_amount_unit:
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label: null
library_generation_method: "RT(oligo-dT)+PCR"
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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
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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."
study_contact: "Mark M. Davis, mmdavis@stanford.edu, ORCID:0000-0001-6868-657X"
inclusion_exclusion_criteria: null
lab_name: "Mark M. Davis"
lab_address: "Stanford University"
submitted_by: "Florian Rubelt"
pub_ids: "PMID:27005435"
collected_by: null
grants: null
keywords_study:
- "contains_ig"
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subject:
subject_id: TW01A
synthetic: false
species:
id: "NCBITaxon_9606"
label: "Homo sapiens"
sex: female
age_min: 27
age_max: 27
age_unit:
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label: year
age_event: null
ancestry_population: null
ethnicity: null
race: null
strain_name: null
linked_subjects: TW01B
link_type: twin
diagnosis:
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disease_diagnosis:
id: null
label: null
disease_length: null
disease_stage: null
prior_therapies: null
immunogen: null
intervention: null
medical_history: null
sample:
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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_time_point_relative_unit:
id: null
label: null
collection_time_point_reference: null
biomaterial_provider: null
cell_number: null
cells_per_reaction: null
cell_storage: false
cell_quality: null
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template_quality: null
template_amount: null
template_amount_unit:
id: null
label: null
library_generation_method: "RT(oligo-dT)+PCR"
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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
|
