{
"@context": "/terms/",
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],
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"WARNING": [
{
"category": "missing age",
"detail": "Primary cell [IGVFSM0066TACG](/primary-cells/IGVFSM0066TACG/) 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,
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"name": "audit_biosample_age",
"path": "/primary-cells/IGVFSM0066TACG/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM4716FORO](/primary-cells/IGVFSM4716FORO/) 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,
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"name": "audit_biosample_age",
"path": "/primary-cells/IGVFSM4716FORO/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM0293OVAT](/primary-cells/IGVFSM0293OVAT/) 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,
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"path": "/primary-cells/IGVFSM0293OVAT/"
}
]
},
"award": {
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"title": "High-Throughput Functional Annotation of Gene Regulatory Elements and Variants Critical to Complex Cellular Phenotypes"
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"status": "released",
"taxa": "Homo sapiens"
},
{
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"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO1522NSLA/",
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],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "intermediate analysis",
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"file_format": "bam",
"file_size": 1822140938,
"href": "/alignment-files/IGVFFI3376UGYD/@@download/IGVFFI3376UGYD.bam",
"s3_uri": "s3://igvf-files/2024/10/14/20b0392e-7259-4c74-bdfe-94e3b27c8ff3/IGVFFI3376UGYD.bam",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/SCM-70-rep3.masked.dups_marked.bam",
"upload_status": "validated"
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{
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"accession": "IGVFFI2179DDWP",
"aliases": [
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"creation_timestamp": "2024-10-14T21:13:07.002700+00:00",
"file_format": "bam",
"file_size": 1959503002,
"href": "/alignment-files/IGVFFI2179DDWP/@@download/IGVFFI2179DDWP.bam",
"s3_uri": "s3://igvf-files/2024/10/14/aba55832-5efb-4dfe-b324-aa8df7068855/IGVFFI2179DDWP.bam",
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"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
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"accession": "IGVFDS1619VKNB",
"aliases": [
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},
{
"@id": "/measurement-sets/IGVFDS2737CQNK/",
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"aliases": [
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{
"@id": "/measurement-sets/IGVFDS5292QYYE/",
"accession": "IGVFDS5292QYYE",
"aliases": [
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],
"file_set_type": "experimental data"
}
],
"input_for": [
"/analysis-sets/IGVFDS2302NLIO/"
],
"lab": {
"@id": "/labs/charles-gersbach/",
"title": "Charles Gersbach, Duke"
},
"protocols": [
"https://www.protocols.io/view/atac-seq-primary-human-t-cells-overexpressing-batf-c5pfy5jn"
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"publications": [
{
"@id": "/publications/6cc80a53-4ca1-4bd4-9942-f0f335b7ec20/",
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"doi:10.1038/s41588-023-01554-0",
"PMCID:PMC10703699"
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"release_timestamp": "2024-10-29T17:33:35.681219+00:00",
"sample_summary": "CD8-positive, alpha-beta memory T cell primary cell, transfected with a expression vector library",
"samples": [
{
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"construct_library_sets": [
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"sample_terms": [
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"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 transduced (lentivirus) with a expression vector library",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM0066TACG/",
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"Sample",
"Item"
],
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"aliases": [
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"sample_terms": [
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"@type": [
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"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 transduced (lentivirus) with a expression vector library",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM4716FORO/",
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"Sample",
"Item"
],
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"aliases": [
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"classifications": [
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"construct_library_sets": [
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"sample_terms": [
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"@type": [
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"status": "released",
"summary": "CD8-positive, alpha-beta memory T cell",
"term_name": "CD8-positive, alpha-beta memory T cell"
}
],
"status": "released",
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}
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"title": "Alejandro Barrera"
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"summary": "ATAC-seq: alignments",
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"name": "Gersbach GGR ATAC-seq Pipeline"
}
]
}