{
"@context": "/terms/",
"@id": "/analysis-sets/IGVFDS4582MPNU/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4582MPNU",
"aliases": [
"charles-gersbach:cd8-tcells-analysis-set-rna-seq-batf3-overexpression"
],
"assay_titles": [
"RNA-seq"
],
"audit": {
"WARNING": [
{
"category": "missing age",
"detail": "Primary cell [IGVFSM4633QTQY](/primary-cells/IGVFSM4633QTQY/) 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/IGVFSM4633QTQY/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM0218YCAH](/primary-cells/IGVFSM0218YCAH/) 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/IGVFSM0218YCAH/"
},
{
"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/"
},
{
"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": "2024-08-30T18:03:14.197613+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO8289ZMDD/",
"accession": "IGVFDO8289ZMDD",
"aliases": [
"charles-gersbach:cd8-tcells-donor-11"
],
"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"
},
{
"@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/IGVFFI8256POEO/",
"accession": "IGVFFI8256POEO",
"aliases": [
"charles-gersbach:cd8-tcells-deseq2-results-rna-seq-batf3-overexpression"
],
"assembly": "GRCh38",
"content_type": "fold change over control",
"creation_timestamp": "2024-09-05T20:42:10.337751+00:00",
"file_format": "tsv",
"file_size": 1162206,
"href": "/tabular-files/IGVFFI8256POEO/@@download/IGVFFI8256POEO.tsv.gz",
"s3_uri": "s3://igvf-files/2024/09/05/8f1c6208-1fb9-4c88-8551-81bbcfb3c04d/IGVFFI8256POEO.tsv.gz",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/T4A_Complete_BATF3_ORF_RNA-seq.simple.txt.gz",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI8674KIMY/",
"accession": "IGVFFI8674KIMY",
"aliases": [
"charles-gersbach:cd8-tcells-counts-rna-seq-batf3-overexpression"
],
"assembly": "GRCh38",
"content_type": "transcript quantifications",
"creation_timestamp": "2024-09-20T18:40:40.293875+00:00",
"file_format": "tsv",
"file_size": 504716,
"href": "/tabular-files/IGVFFI8674KIMY/@@download/IGVFFI8674KIMY.tsv.gz",
"s3_uri": "s3://igvf-files/2024/09/20/c8de7fc8-52d2-4f01-a97b-05caa4f2fba6/IGVFFI8674KIMY.tsv.gz",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/cd8.rnaseq.batf3_overexpression.star2.featurecounts.counts.txt.gz",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/analysis-sets/IGVFDS5066GYDY/",
"accession": "IGVFDS5066GYDY",
"aliases": [
"charles-gersbach:cd8-tcells-intermediate-analysis-rna-seq-batf3-overexpression-batf3"
],
"file_set_type": "intermediate analysis"
},
{
"@id": "/analysis-sets/IGVFDS3105CGSW/",
"accession": "IGVFDS3105CGSW",
"aliases": [
"charles-gersbach:cd8-tcells-intermediate-analysis-rna-seq-batf3-overexpression-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": "2024-10-29T17:38:51.143775+00:00",
"sample_summary": "CD8-positive, alpha-beta memory T cell primary cell, transfected with a expression vector library",
"samples": [
{
"@id": "/primary-cells/IGVFSM4633QTQY/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4633QTQY",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-chronic-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/IGVFSM7232YAVV/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7232YAVV",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-chronic-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"
},
{
"@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/IGVFSM0218YCAH/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0218YCAH",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-chronic-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/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"
},
{
"@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"
}
],
"schema_version": "9",
"status": "released",
"submitted_by": {
"@id": "/users/29f5f78d-ac90-421e-90c6-a90e1dc407a7/",
"title": "Alejandro Barrera"
},
"submitted_files_timestamp": "2024-09-05T20:42:10.337751+00:00",
"summary": "RNA-seq: fold change over control, transcript quantifications",
"uuid": "25476ba5-abdf-49e7-8a37-14a48fa7c22f",
"workflows": [
{
"@id": "/workflows/IGVFWF6270QWBB/",
"accession": "IGVFWF6270QWBB",
"name": "Gersbach GGR RNA-seq Pipeline"
}
]
}