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Update repertoire example for R
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@bussec
bussec committed Feb 21, 2024
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Showing 1 changed file with 124 additions and 28 deletions.
152 changes: 124 additions & 28 deletions lang/R/inst/extdata/repertoire-example.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -11,15 +11,37 @@ Repertoire:
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, [email protected], 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
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:
keywords_study:
- "contains_ig"
- "contains_tr"
subject:
Expand All @@ -28,14 +50,19 @@ Repertoire:
species:
id: "NCBITaxon_9606"
label: "Homo sapiens"
sex: F
sex: female
age_min: 27
age_max: 27
age_unit:
id: UO_0000036
label: year
age_event: null
ancestry_population: null
ancestry_population:
id: null
label: null
location_birth:
id: null
label: null
ethnicity: null
race: null
strain_name: null
Expand Down Expand Up @@ -77,21 +104,26 @@ Repertoire:
reverse_pcr_primer_target_location: null
sequencing_platform: "Illumina MiSeq"
sequencing_files:
sequencing_data_id: SRR2905656
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_time_point_relative_unit:
id: null
label: null
collection_time_point_reference: null
collection_location:
id: null
label: null
biomaterial_provider: null
cell_number: null
cells_per_reaction: null
Expand Down Expand Up @@ -134,13 +166,35 @@ Repertoire:
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, [email protected], 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
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"
Expand All @@ -151,14 +205,19 @@ Repertoire:
species:
id: "NCBITaxon_9606"
label: "Homo sapiens"
sex: F
sex: female
age_min: 27
age_max: 27
age_unit:
id: UO_0000036
label: year
age_event: null
ancestry_population: null
ancestry_population:
id: null
label: null
location_birth:
id: null
label: null
ethnicity: null
race: null
strain_name: null
Expand Down Expand Up @@ -200,21 +259,26 @@ Repertoire:
reverse_pcr_primer_target_location: null
sequencing_platform: "Illumina MiSeq"
sequencing_files:
sequencing_data_id: SRR2905655
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:
id: null
label: null
collection_time_point_reference: null
collection_location:
id: null
label: null
biomaterial_provider: null
cell_number: null
cells_per_reaction: null
Expand Down Expand Up @@ -257,13 +321,35 @@ Repertoire:
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, [email protected], 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
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"
Expand All @@ -274,14 +360,19 @@ Repertoire:
species:
id: "NCBITaxon_9606"
label: "Homo sapiens"
sex: F
sex: female
age_min: 27
age_max: 27
age_unit:
id: UO_0000036
label: year
age_event: null
ancestry_population: null
ancestry_population:
id: null
label: null
location_birth:
id: null
label: null
ethnicity: null
race: null
strain_name: null
Expand Down Expand Up @@ -323,21 +414,26 @@ Repertoire:
reverse_pcr_primer_target_location: null
sequencing_platform: "Illumina MiSeq"
sequencing_files:
sequencing_data_id: SRR2905659
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
collection_location:
id: null
label: null
biomaterial_provider: null
cell_number: null
cells_per_reaction: null
Expand Down

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