{
"@context": "/terms/",
"@id": "/analysis-sets/IGVFDS2302NLIO/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2302NLIO",
"aliases": [
"charles-gersbach:cd8-tcells-analysis-set-atac-seq-acute-activation-batf3"
],
"assay_titles": [
"ATAC-seq"
],
"audit": {
"WARNING": [
{
"category": "missing age",
"detail": "Primary cell [IGVFSM3998OQDA](/primary-cells/IGVFSM3998OQDA/) 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/IGVFSM3998OQDA/"
},
{
"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,
"level_name": "WARNING",
"name": "audit_biosample_age",
"path": "/primary-cells/IGVFSM0066TACG/"
},
{
"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,
"level_name": "WARNING",
"name": "audit_biosample_age",
"path": "/primary-cells/IGVFSM0293OVAT/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM8800PZZL](/primary-cells/IGVFSM8800PZZL/) 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/IGVFSM8800PZZL/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM6851CRLW](/primary-cells/IGVFSM6851CRLW/) 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/IGVFSM6851CRLW/"
},
{
"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,
"level_name": "WARNING",
"name": "audit_biosample_age",
"path": "/primary-cells/IGVFSM4716FORO/"
}
]
},
"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": "2024-08-30T18:03:11.676153+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/IGVFDO8289ZMDD/",
"accession": "IGVFDO8289ZMDD",
"aliases": [
"charles-gersbach:cd8-tcells-donor-11"
],
"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": "principal analysis",
"files": [
{
"@id": "/tabular-files/IGVFFI2320OTYL/",
"accession": "IGVFFI2320OTYL",
"aliases": [
"charles-gersbach:cd8-tcells-deseq2-results-atac-seq-acute-activation"
],
"assembly": "GRCh38",
"content_type": "fold change over control",
"creation_timestamp": "2024-09-05T20:42:48.546501+00:00",
"file_format": "tsv",
"file_size": 4295918,
"href": "/tabular-files/IGVFFI2320OTYL/@@download/IGVFFI2320OTYL.tsv.gz",
"s3_uri": "s3://igvf-files/2024/09/05/22e59bab-c954-4ef0-8238-4b04518b7f39/IGVFFI2320OTYL.tsv.gz",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/DESeq2.BATF3.vs.control.chronic.simple.txt.gz",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI4701TPMH/",
"accession": "IGVFFI4701TPMH",
"aliases": [
"charles-gersbach:cd8-tcells-counts-atac-seq-acute-activation"
],
"assembly": "GRCh38",
"content_type": "peak quantifications",
"creation_timestamp": "2024-09-20T18:53:48.515093+00:00",
"file_format": "tsv",
"file_size": 2451571,
"href": "/tabular-files/IGVFFI4701TPMH/@@download/IGVFFI4701TPMH.tsv.gz",
"s3_uri": "s3://igvf-files/2024/09/20/45ac2773-caf4-4e0b-8182-e289e6a6d82e/IGVFFI4701TPMH.tsv.gz",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/cd8_tcells.acute_activation_batf3.atacseq.counts.txt.gz",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/analysis-sets/IGVFDS1013MILB/",
"accession": "IGVFDS1013MILB",
"aliases": [
"charles-gersbach:cd8-tcells-intermediate-set-atac-seq-acute-activation-batf3"
],
"file_set_type": "intermediate analysis"
},
{
"@id": "/analysis-sets/IGVFDS7714RCSY/",
"accession": "IGVFDS7714RCSY",
"aliases": [
"charles-gersbach:cd8-tcells-intermediate-set-atac-seq-acute-activation-gfp"
],
"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": "2024-10-29T17:33:34.389360+00:00",
"sample_summary": "CD8-positive, alpha-beta memory T cell primary cell, transfected with a expression vector library",
"samples": [
{
"@id": "/primary-cells/IGVFSM6851CRLW/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6851CRLW",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-acute-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/IGVFSM8800PZZL/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8800PZZL",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-acute-activation-gfp-rep3"
],
"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/IGVFSM3998OQDA/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3998OQDA",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-acute-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"
},
{
"@id": "/primary-cells/IGVFSM0066TACG/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0066TACG",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-acute-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/IGVFSM0293OVAT/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0293OVAT",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-acute-activation-batf3-rep3"
],
"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/IGVFSM4716FORO/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4716FORO",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-acute-activation-batf3-rep2"
],
"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"
}
],
"schema_version": "9",
"status": "released",
"submitted_by": {
"@id": "/users/29f5f78d-ac90-421e-90c6-a90e1dc407a7/",
"title": "Alejandro Barrera"
},
"submitted_files_timestamp": "2024-09-05T20:42:48.546501+00:00",
"summary": "ATAC-seq: fold change over control, peak quantifications",
"uuid": "dddf113e-e357-4ec4-bb4f-ab705219db19",
"workflows": [
{
"@id": "/workflows/IGVFWF6411VZLF/",
"accession": "IGVFWF6411VZLF",
"name": "Gersbach GGR ATAC-seq Pipeline"
}
]
}