{
"@context": "/terms/",
"@id": "/analysis-sets/IGVFDS9202ZPBI/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9202ZPBI",
"aliases": [
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],
"assay_titles": [
"ATAC-seq"
],
"audit": {
"WARNING": [
{
"category": "missing age",
"detail": "Primary cell [IGVFSM8821YQXI](/primary-cells/IGVFSM8821YQXI/) 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/IGVFSM8821YQXI/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM7232YAVV](/primary-cells/IGVFSM7232YAVV/) 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/IGVFSM7232YAVV/"
}
]
},
"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": "2024-09-20T18:53:33.900990+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO1522NSLA/",
"accession": "IGVFDO1522NSLA",
"aliases": [
"charles-gersbach:cd8-tcells-donor-10"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO9588OERW/",
"accession": "IGVFDO9588OERW",
"aliases": [
"charles-gersbach:cd8-tcells-donor-9"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "intermediate analysis",
"files": [
{
"@id": "/alignment-files/IGVFFI2041YQHB/",
"accession": "IGVFFI2041YQHB",
"aliases": [
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],
"assembly": "GRCh38",
"content_type": "alignments",
"creation_timestamp": "2024-10-14T21:08:31.217342+00:00",
"file_format": "bam",
"file_size": 1873245689,
"href": "/alignment-files/IGVFFI2041YQHB/@@download/IGVFFI2041YQHB.bam",
"s3_uri": "s3://igvf-files/2024/10/14/b63932d4-d1a8-4880-84f8-911b0b77f110/IGVFFI2041YQHB.bam",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/SCM-C70-rep1.masked.dups_marked.bam",
"upload_status": "validated"
},
{
"@id": "/alignment-files/IGVFFI9649KWTN/",
"accession": "IGVFFI9649KWTN",
"aliases": [
"charles-gersbach:cd8-tcells-atac-seq-chronic-activation-batf3-bam-rep2"
],
"assembly": "GRCh38",
"content_type": "alignments",
"creation_timestamp": "2024-10-14T21:09:30.432955+00:00",
"file_format": "bam",
"file_size": 1923865155,
"href": "/alignment-files/IGVFFI9649KWTN/@@download/IGVFFI9649KWTN.bam",
"s3_uri": "s3://igvf-files/2024/10/14/be800da9-b7a6-4899-95f6-90111c7bb2e4/IGVFFI9649KWTN.bam",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/SCM-C70-rep2.masked.dups_marked.bam",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/measurement-sets/IGVFDS0986HRDF/",
"accession": "IGVFDS0986HRDF",
"aliases": [
"charles-gersbach:cd8-tcells-atac-seq-chronic-activation-batf3-rep1"
],
"file_set_type": "experimental data"
},
{
"@id": "/measurement-sets/IGVFDS5328ZNKL/",
"accession": "IGVFDS5328ZNKL",
"aliases": [
"charles-gersbach:cd8-tcells-atac-seq-chronic-activation-batf3-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": "2024-10-29T17:33:31.224552+00:00",
"sample_summary": "CD8-positive, alpha-beta memory T cell primary cell, transfected with a expression vector library",
"samples": [
{
"@id": "/primary-cells/IGVFSM8821YQXI/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8821YQXI",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-chronic-activation-batf3-rep1"
],
"classifications": [
"primary cell"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS1868WXHB/"
],
"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/IGVFSM7232YAVV/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7232YAVV",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-chronic-activation-batf3-rep2"
],
"classifications": [
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],
"construct_library_sets": [
"/construct-library-sets/IGVFDS1868WXHB/"
],
"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": "2024-10-14T21:08:31.217342+00:00",
"summary": "ATAC-seq: alignments",
"uuid": "fdbe1d71-d4b0-4025-a01e-46b963a45785",
"workflows": [
{
"@id": "/workflows/IGVFWF6411VZLF/",
"accession": "IGVFWF6411VZLF",
"name": "Gersbach GGR ATAC-seq Pipeline"
}
]
}