{
"@context": "/terms/",
"@id": "/analysis-sets/IGVFDS7239LNZO/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7239LNZO",
"aliases": [
"charles-gersbach:cd8-tcells-analysis-set-rna-seq-cas-ko-gata3"
],
"assay_titles": [
"RNA-seq"
],
"audit": {
"WARNING": [
{
"category": "missing age",
"detail": "Primary cell [IGVFSM9627TJZO](/primary-cells/IGVFSM9627TJZO/) is missing `upper_bound_age`, `lower_bound_age`, and `age_units`. Tissues, primary cells, and whole organisms are expected to specify a lower bound age, upper bound age, and age units.",
"level": 40,
"level_name": "WARNING",
"name": "audit_biosample_age",
"path": "/primary-cells/IGVFSM9627TJZO/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM7117ATUZ](/primary-cells/IGVFSM7117ATUZ/) is missing `upper_bound_age`, `lower_bound_age`, and `age_units`. Tissues, primary cells, and whole organisms are expected to specify a lower bound age, upper bound age, and age units.",
"level": 40,
"level_name": "WARNING",
"name": "audit_biosample_age",
"path": "/primary-cells/IGVFSM7117ATUZ/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM0383IKGE](/primary-cells/IGVFSM0383IKGE/) is missing `upper_bound_age`, `lower_bound_age`, and `age_units`. Tissues, primary cells, and whole organisms are expected to specify a lower bound age, upper bound age, and age units.",
"level": 40,
"level_name": "WARNING",
"name": "audit_biosample_age",
"path": "/primary-cells/IGVFSM0383IKGE/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM0829UPAR](/primary-cells/IGVFSM0829UPAR/) is missing `upper_bound_age`, `lower_bound_age`, and `age_units`. Tissues, primary cells, and whole organisms are expected to specify a lower bound age, upper bound age, and age units.",
"level": 40,
"level_name": "WARNING",
"name": "audit_biosample_age",
"path": "/primary-cells/IGVFSM0829UPAR/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM6537MPGY](/primary-cells/IGVFSM6537MPGY/) is missing `upper_bound_age`, `lower_bound_age`, and `age_units`. Tissues, primary cells, and whole organisms are expected to specify a lower bound age, upper bound age, and age units.",
"level": 40,
"level_name": "WARNING",
"name": "audit_biosample_age",
"path": "/primary-cells/IGVFSM6537MPGY/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM1498WFCO](/primary-cells/IGVFSM1498WFCO/) is missing `upper_bound_age`, `lower_bound_age`, and `age_units`. Tissues, primary cells, and whole organisms are expected to specify a lower bound age, upper bound age, and age units.",
"level": 40,
"level_name": "WARNING",
"name": "audit_biosample_age",
"path": "/primary-cells/IGVFSM1498WFCO/"
}
]
},
"award": {
"@id": "/awards/HG012053/",
"component": "functional characterization",
"contact_pi": {
"@id": "/users/5d329c0e-3ea9-49bf-9bb9-844a53a882c0/",
"title": "Charles Gersbach"
},
"title": "High-Throughput Functional Annotation of Gene Regulatory Elements and Variants Critical to Complex Cellular Phenotypes"
},
"control_for": [],
"creation_timestamp": "2024-09-05T18:22:00.698633+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO7589UJKG/",
"accession": "IGVFDO7589UJKG",
"aliases": [
"charles-gersbach:cd8-tcells-donor-13"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO4048LCOU/",
"accession": "IGVFDO4048LCOU",
"aliases": [
"charles-gersbach:cd8-tcells-donor-14"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO8565PQXZ/",
"accession": "IGVFDO8565PQXZ",
"aliases": [
"charles-gersbach:cd8-tcells-donor-12"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "principal analysis",
"files": [
{
"@id": "/tabular-files/IGVFFI4884FITS/",
"accession": "IGVFFI4884FITS",
"aliases": [
"charles-gersbach:cd8-tcells-deseq2-results-rna-seq-cas-ko-gata3"
],
"assembly": "GRCh38",
"content_type": "fold change over control",
"creation_timestamp": "2024-09-05T20:42:36.340015+00:00",
"file_format": "tsv",
"file_size": 885107,
"href": "/tabular-files/IGVFFI4884FITS/@@download/IGVFFI4884FITS.tsv.gz",
"s3_uri": "s3://igvf-files/2024/09/05/db32df51-95ea-4c1d-b845-f404666530f6/IGVFFI4884FITS.tsv.gz",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/T7C_GATA3_KO_RNA-seq.simple.txt.gz",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI2071KQLY/",
"accession": "IGVFFI2071KQLY",
"aliases": [
"charles-gersbach:cd8-tcells-counts-rna-seq-cas-ko-gata3"
],
"assembly": "GRCh38",
"content_type": "transcript quantifications",
"creation_timestamp": "2024-09-20T18:41:05.638649+00:00",
"file_format": "tsv",
"file_size": 546886,
"href": "/tabular-files/IGVFFI2071KQLY/@@download/IGVFFI2071KQLY.tsv.gz",
"s3_uri": "s3://igvf-files/2024/09/20/2d39440c-8f23-4a84-a1f0-18ca72d144bc/IGVFFI2071KQLY.tsv.gz",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/cd8.rnaseq.pSM73.nt_gata3.star2.featurecounts.counts.txt.gz",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/analysis-sets/IGVFDS0006MFFD/",
"accession": "IGVFDS0006MFFD",
"aliases": [
"charles-gersbach:cd8-tcells-intermediate-analysis-rna-seq-cas-ko-gata3"
],
"file_set_type": "intermediate analysis"
},
{
"@id": "/analysis-sets/IGVFDS6924DJJC/",
"accession": "IGVFDS6924DJJC",
"aliases": [
"charles-gersbach:cd8-tcells-intermediate-analysis-rna-seq-cas-ko-nt"
],
"file_set_type": "intermediate analysis"
}
],
"input_for": [],
"lab": {
"@id": "/labs/charles-gersbach/",
"title": "Charles Gersbach, Duke"
},
"protocols": [],
"publications": [
{
"@id": "/publications/6cc80a53-4ca1-4bd4-9942-f0f335b7ec20/",
"publication_identifiers": [
"PMID:37945901",
"doi:10.1038/s41588-023-01554-0",
"PMCID:PMC10703699"
]
}
],
"release_timestamp": "2024-10-25T04:18:35.350952+00:00",
"sample_summary": "CD8-positive, alpha-beta memory T cell primary cell, modified with CRISPR modifications, transfected with a guide library",
"samples": [
{
"@id": "/primary-cells/IGVFSM9627TJZO/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9627TJZO",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-cas9-ko-gata3-rep1"
],
"classifications": [
"primary cell"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS2398ZXBQ/"
],
"modifications": [
{
"@id": "/crispr-modifications/9fef21f2-9727-4a97-a5a7-c590a637c101/",
"modality": "knockout"
}
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000909/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "CD8-positive, alpha-beta memory T cell",
"term_name": "CD8-positive, alpha-beta memory T cell"
}
],
"status": "released",
"summary": "CD8-positive, alpha-beta memory T cell, Homo sapiens modified with CRISPRko Sp-Cas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM7117ATUZ/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7117ATUZ",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-cas9-ko-gata3-rep3"
],
"classifications": [
"primary cell"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS2398ZXBQ/"
],
"modifications": [
{
"@id": "/crispr-modifications/9fef21f2-9727-4a97-a5a7-c590a637c101/",
"modality": "knockout"
}
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000909/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "CD8-positive, alpha-beta memory T cell",
"term_name": "CD8-positive, alpha-beta memory T cell"
}
],
"status": "released",
"summary": "CD8-positive, alpha-beta memory T cell, Homo sapiens modified with CRISPRko Sp-Cas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM0829UPAR/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0829UPAR",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-cas9-ko-gata3-rep2"
],
"classifications": [
"primary cell"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS2398ZXBQ/"
],
"modifications": [
{
"@id": "/crispr-modifications/9fef21f2-9727-4a97-a5a7-c590a637c101/",
"modality": "knockout"
}
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000909/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "CD8-positive, alpha-beta memory T cell",
"term_name": "CD8-positive, alpha-beta memory T cell"
}
],
"status": "released",
"summary": "CD8-positive, alpha-beta memory T cell, Homo sapiens modified with CRISPRko Sp-Cas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM1498WFCO/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1498WFCO",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-cas9-ko-nt-rep2"
],
"classifications": [
"primary cell"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS9830PJVQ/"
],
"modifications": [
{
"@id": "/crispr-modifications/9fef21f2-9727-4a97-a5a7-c590a637c101/",
"modality": "knockout"
}
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000909/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "CD8-positive, alpha-beta memory T cell",
"term_name": "CD8-positive, alpha-beta memory T cell"
}
],
"status": "released",
"summary": "CD8-positive, alpha-beta memory T cell, Homo sapiens modified with CRISPRko Sp-Cas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM6537MPGY/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6537MPGY",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-cas9-ko-nt-rep1"
],
"classifications": [
"primary cell"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS9830PJVQ/"
],
"modifications": [
{
"@id": "/crispr-modifications/9fef21f2-9727-4a97-a5a7-c590a637c101/",
"modality": "knockout"
}
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000909/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "CD8-positive, alpha-beta memory T cell",
"term_name": "CD8-positive, alpha-beta memory T cell"
}
],
"status": "released",
"summary": "CD8-positive, alpha-beta memory T cell, Homo sapiens modified with CRISPRko Sp-Cas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM0383IKGE/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0383IKGE",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-cas9-ko-nt-rep3"
],
"classifications": [
"primary cell"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS9830PJVQ/"
],
"modifications": [
{
"@id": "/crispr-modifications/9fef21f2-9727-4a97-a5a7-c590a637c101/",
"modality": "knockout"
}
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000909/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "CD8-positive, alpha-beta memory T cell",
"term_name": "CD8-positive, alpha-beta memory T cell"
}
],
"status": "released",
"summary": "CD8-positive, alpha-beta memory T cell, Homo sapiens modified with CRISPRko Sp-Cas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
}
],
"schema_version": "9",
"status": "released",
"submitted_by": {
"@id": "/users/29f5f78d-ac90-421e-90c6-a90e1dc407a7/",
"title": "Alejandro Barrera"
},
"submitted_files_timestamp": "2024-09-05T20:42:36.340015+00:00",
"summary": "knockout RNA-seq: fold change over control, transcript quantifications",
"uuid": "88683a11-57fd-4f64-b2ff-4a7c3324e13c",
"workflows": [
{
"@id": "/workflows/IGVFWF6270QWBB/",
"accession": "IGVFWF6270QWBB",
"name": "Gersbach GGR RNA-seq Pipeline"
}
]
}