{
"@context": "/terms/",
"@id": "/analysis-sets/IGVFDS3609QWUZ/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3609QWUZ",
"aliases": [
"charles-gersbach:cd8-tcells-intermediate-set-atac-seq-chronic-activation-gfp"
],
"assay_titles": [
"ATAC-seq"
],
"audit": {
"WARNING": [
{
"category": "missing age",
"detail": "Primary cell [IGVFSM3805WZUU](/primary-cells/IGVFSM3805WZUU/) 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/IGVFSM3805WZUU/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM6508DFUL](/primary-cells/IGVFSM6508DFUL/) 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/IGVFSM6508DFUL/"
}
]
},
"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": "2024-10-17T19:49:49.223558+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO9588OERW/",
"accession": "IGVFDO9588OERW",
"aliases": [
"charles-gersbach:cd8-tcells-donor-9"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO1522NSLA/",
"accession": "IGVFDO1522NSLA",
"aliases": [
"charles-gersbach:cd8-tcells-donor-10"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "intermediate analysis",
"files": [
{
"@id": "/alignment-files/IGVFFI4926QIFF/",
"accession": "IGVFFI4926QIFF",
"aliases": [
"charles-gersbach:cd8-tcells-atac-seq-chronic-activation-gfp-bam-rep1"
],
"assembly": "GRCh38",
"content_type": "alignments",
"creation_timestamp": "2024-10-14T21:06:40.648784+00:00",
"file_format": "bam",
"file_size": 1529837023,
"href": "/alignment-files/IGVFFI4926QIFF/@@download/IGVFFI4926QIFF.bam",
"s3_uri": "s3://igvf-files/2024/10/14/5a560ef4-79c5-4256-88f8-0a39f3c458f0/IGVFFI4926QIFF.bam",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/SCM-C69-rep1.masked.dups_marked.bam",
"upload_status": "validated"
},
{
"@id": "/alignment-files/IGVFFI5684XZYN/",
"accession": "IGVFFI5684XZYN",
"aliases": [
"charles-gersbach:cd8-tcells-atac-seq-chronic-activation-gfp-bam-rep2"
],
"assembly": "GRCh38",
"content_type": "alignments",
"creation_timestamp": "2024-10-14T21:07:35.491147+00:00",
"file_format": "bam",
"file_size": 1605239609,
"href": "/alignment-files/IGVFFI5684XZYN/@@download/IGVFFI5684XZYN.bam",
"s3_uri": "s3://igvf-files/2024/10/14/64b29a7d-551a-465a-a4db-d7356e98ae75/IGVFFI5684XZYN.bam",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/SCM-C69-rep2.masked.dups_marked.bam",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/measurement-sets/IGVFDS3810SJRN/",
"accession": "IGVFDS3810SJRN",
"aliases": [
"charles-gersbach:cd8-tcells-atac-seq-chronic-activation-gfp-rep1"
],
"file_set_type": "experimental data"
},
{
"@id": "/measurement-sets/IGVFDS9111EVGC/",
"accession": "IGVFDS9111EVGC",
"aliases": [
"charles-gersbach:cd8-tcells-atac-seq-chronic-activation-gfp-rep2"
],
"file_set_type": "experimental data"
}
],
"input_for": [
"/analysis-sets/IGVFDS6344XBAV/"
],
"lab": {
"@id": "/labs/charles-gersbach/",
"title": "Charles Gersbach, Duke"
},
"protocols": [
"https://www.protocols.io/view/atac-seq-primary-human-t-cells-overexpressing-batf-c5pfy5jn"
],
"publications": [
{
"@id": "/publications/6cc80a53-4ca1-4bd4-9942-f0f335b7ec20/",
"publication_identifiers": [
"PMID:37945901",
"doi:10.1038/s41588-023-01554-0",
"PMCID:PMC10703699"
]
}
],
"release_timestamp": "2024-10-29T17:33:33.495662+00:00",
"sample_summary": "CD8-positive, alpha-beta memory T cell primary cell, transfected with a expression vector library",
"samples": [
{
"@id": "/primary-cells/IGVFSM3805WZUU/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3805WZUU",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-chronic-activation-gfp-rep2"
],
"classifications": [
"primary cell"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS5584SPIV/"
],
"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 transduced (lentivirus) with a expression vector library",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM6508DFUL/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6508DFUL",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-chronic-activation-gfp-rep1"
],
"classifications": [
"primary cell"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS5584SPIV/"
],
"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 transduced (lentivirus) with a expression vector library",
"taxa": "Homo sapiens"
}
],
"schema_version": "9",
"status": "released",
"submitted_by": {
"@id": "/users/29f5f78d-ac90-421e-90c6-a90e1dc407a7/",
"title": "Alejandro Barrera"
},
"submitted_files_timestamp": "2024-10-14T21:06:40.648784+00:00",
"summary": "ATAC-seq: alignments",
"uuid": "6fa0baa8-8e86-4903-8cd6-a10a46123b0e",
"workflows": [
{
"@id": "/workflows/IGVFWF6411VZLF/",
"accession": "IGVFWF6411VZLF",
"name": "Gersbach GGR ATAC-seq Pipeline"
}
]
}