{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7967GRIT/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7967GRIT",
"aliases": [
"charles-gersbach:cd8-tcells-atac-seq-acute-activation-gfp-rep1"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003089/",
"assay_slims": [
"chromatin accessibility"
],
"status": "released",
"term_name": "bulk assay for transposase-accessible chromatin using sequencing"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS7967GRIT](/measurement-sets/IGVFDS7967GRIT/) has sequence file(s): [IGVFFI8771CBJP](/sequence-files/IGVFFI8771CBJP/), [IGVFFI7894RJHG](/sequence-files/IGVFFI7894RJHG/) which do not have any `seqspecs`. Sequence files in a file set associated with bulk data are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS7967GRIT/"
},
{
"category": "NTR term ID",
"detail": "Treatment term for [725c21b1-d202-4a6c-89a4-e4fc05a001e8](/treatments/725c21b1-d202-4a6c-89a4-e4fc05a001e8/) has been newly requested. Treatments with a newly requested term ID are expected to have it updated following its addition to the appropriate ontology database.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_treatment_term_id_check",
"path": "/treatments/725c21b1-d202-4a6c-89a4-e4fc05a001e8/"
},
{
"category": "mismatched status",
"detail": "Released primary cell [IGVFSM3998OQDA](/primary-cells/IGVFSM3998OQDA/) has in progress subobject treatment [725c21b1-d202-4a6c-89a4-e4fc05a001e8](/treatments/725c21b1-d202-4a6c-89a4-e4fc05a001e8/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/primary-cells/IGVFSM3998OQDA/"
}
],
"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/"
}
]
},
"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"
},
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS5584SPIV/",
"accession": "IGVFDS5584SPIV",
"file_set_type": "expression vector library",
"status": "released",
"summary": "control transduction expression vector library"
}
],
"control_for": [
{
"@id": "/measurement-sets/IGVFDS1619VKNB/",
"accession": "IGVFDS1619VKNB",
"aliases": [
"charles-gersbach:cd8-tcells-atac-seq-acute-activation-batf3-rep1"
],
"status": "released"
}
],
"control_type": "control transduction",
"controlled_access": false,
"creation_timestamp": "2023-11-08T19:33:11.372249+00:00",
"data_use_limitation_summaries": [
"No limitations"
],
"donors": [
{
"@id": "/human-donors/IGVFDO9588OERW/",
"accession": "IGVFDO9588OERW",
"aliases": [
"charles-gersbach:cd8-tcells-donor-9"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI8771CBJP/",
"accession": "IGVFFI8771CBJP",
"aliases": [
"charles-gersbach:cd8-tcells-atac-seq-acute-activation-gfp-rep1-fastq-R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-11-08T20:52:32.031236+00:00",
"file_format": "fastq",
"file_size": 1310290860,
"href": "/sequence-files/IGVFFI8771CBJP/@@download/IGVFFI8771CBJP.fastq.gz",
"s3_uri": "s3://igvf-files/2023/11/08/fce1e0a0-a26c-4767-a622-54f3cce9050c/IGVFFI8771CBJP.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0010963/",
"status": "released",
"term_name": "Illumina NextSeq 2000"
},
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/raw_data/AIM_2_T_cell_project_1/69-1_S6_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7894RJHG/",
"accession": "IGVFFI7894RJHG",
"aliases": [
"charles-gersbach:cd8-tcells-atac-seq-acute-activation-gfp-rep1-fastq-R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-11-08T20:53:19.699801+00:00",
"file_format": "fastq",
"file_size": 1317322082,
"href": "/sequence-files/IGVFFI7894RJHG/@@download/IGVFFI7894RJHG.fastq.gz",
"s3_uri": "s3://igvf-files/2023/11/08/7bdad9c6-4418-4d1d-95ec-1219c6b5597b/IGVFFI7894RJHG.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0010963/",
"status": "released",
"term_name": "Illumina NextSeq 2000"
},
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/raw_data/AIM_2_T_cell_project_1/69-1_S6_L001_R2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS2302NLIO/"
],
"lab": {
"@id": "/labs/charles-gersbach/",
"title": "Charles Gersbach, Duke"
},
"notes": "This file_set previously had 22cd001f-ba76-475a-a132-5c619f57d61d submitted as library_construction_platform, but the property library_construction_platform has been now removed.",
"preferred_assay_title": "ATAC-seq",
"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"
],
"status": "released"
}
],
"release_timestamp": "2024-10-29T17:33:35.167856+00:00",
"samples": [
{
"@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"
],
"institutional_certificates": [
{
"@id": "/institutional-certificates/e1533003-0a58-47b1-aa1a-615dbb6aafb2/",
"certificate_identifier": "IP117-01",
"controlled_access": false,
"status": "released"
}
],
"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": "Homo sapiens CD8-positive, alpha-beta memory T cell treated with 300 percent Antibody Coated Bead, transduced (lentivirus) with a expression vector library",
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/725c21b1-d202-4a6c-89a4-e4fc05a001e8/",
"purpose": "stimulation",
"status": "in progress",
"summary": "Treatment of 300 percent Antibody Coated Bead",
"treatment_type": "protein"
}
]
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/29f5f78d-ac90-421e-90c6-a90e1dc407a7/",
"title": "Alejandro Barrera"
},
"submitted_files_timestamp": "2023-11-08T20:52:32.031236+00:00",
"summary": "control transduction ATAC-seq integrating a control transduction expression vector library",
"uuid": "48d87a85-315a-4857-b070-2b15e9e6b11c"
}