IGVFDS4808GJDM

released
{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS4808GJDM/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS4808GJDM",
    "aliases": [
        "charles-gersbach:cd8-tcells-rna-seq-chronic-activation-gfp-rep3"
    ],
    "assay_term": {
        "@id": "/assay-terms/OBI_0003090/",
        "status": "released",
        "term_name": "bulk RNA-seq assay"
    },
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequencing kit",
                "detail": "Measurement set [IGVFDS4808GJDM](/measurement-sets/IGVFDS4808GJDM/) has sequence file(s) [IGVFFI9773SEVN](/sequence-files/IGVFFI9773SEVN/), [IGVFFI2464JMWS](/sequence-files/IGVFFI2464JMWS/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_inconsistent_sequencing_kit",
                "path": "/measurement-sets/IGVFDS4808GJDM/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS4808GJDM](/measurement-sets/IGVFDS4808GJDM/) has sequence file(s): [IGVFFI9773SEVN](/sequence-files/IGVFFI9773SEVN/), [IGVFFI2464JMWS](/sequence-files/IGVFFI2464JMWS/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_missing_seqspec",
                "path": "/measurement-sets/IGVFDS4808GJDM/"
            }
        ],
        "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/"
            }
        ]
    },
    "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": [
        {
            "@id": "/measurement-sets/IGVFDS1336JNHX/",
            "accession": "IGVFDS1336JNHX",
            "aliases": [
                "charles-gersbach:cd8-tcells-rna-seq-chronic-activation-batf3-rep3"
            ],
            "status": "released"
        }
    ],
    "creation_timestamp": "2023-11-08T21:12:48.988724+00:00",
    "donors": [
        {
            "@id": "/human-donors/IGVFDO8289ZMDD/",
            "accession": "IGVFDO8289ZMDD",
            "aliases": [
                "charles-gersbach:cd8-tcells-donor-11"
            ],
            "sex": "unspecified",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "externally_hosted": false,
    "file_set_type": "experimental data",
    "files": [
        {
            "@id": "/sequence-files/IGVFFI9773SEVN/",
            "accession": "IGVFFI9773SEVN",
            "aliases": [
                "charles-gersbach:cd8-tcells-rna-seq-chronic-activation-gfp-rep3-fastq-R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2023-11-08T21:13:24.096564+00:00",
            "file_format": "fastq",
            "file_size": 1754299075,
            "href": "/sequence-files/IGVFFI9773SEVN/@@download/IGVFFI9773SEVN.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/11/08/cd7d9329-4a8d-4eef-8887-9c013508123a/IGVFFI9773SEVN.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0008637/",
                "status": "released",
                "term_name": "Illumina NovaSeq 6000"
            },
            "status": "released",
            "submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/raw_data/AIM_2_T_cell_project_1/pSM7-IL-2-D3_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI2464JMWS/",
            "accession": "IGVFFI2464JMWS",
            "aliases": [
                "charles-gersbach:cd8-tcells-rna-seq-chronic-activation-gfp-rep3-fastq-R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2023-11-08T21:14:24.087930+00:00",
            "file_format": "fastq",
            "file_size": 1822464805,
            "href": "/sequence-files/IGVFFI2464JMWS/@@download/IGVFFI2464JMWS.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/11/08/06058854-6818-4db3-a10a-3ebc3b1b445d/IGVFFI2464JMWS.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0008637/",
                "status": "released",
                "term_name": "Illumina NovaSeq 6000"
            },
            "status": "released",
            "submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/raw_data/AIM_2_T_cell_project_1/pSM7-IL-2-D3_R2_001.fastq.gz",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS3105CGSW/"
    ],
    "lab": {
        "@id": "/labs/charles-gersbach/",
        "title": "Charles Gersbach, Duke"
    },
    "notes": "This file_set previously had f9e9ffe1-b463-4b15-964c-e926bfcf58a8 submitted as library_construction_platform, but the property library_construction_platform has been now removed.",
    "preferred_assay_title": "RNA-seq",
    "protocols": [
        "https://www.protocols.io/view/rnaseq-of-primary-human-t-cells-overexpressing-bat-c5pdy5i6"
    ],
    "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": "2024-10-29T17:38:49.708350+00:00",
    "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": [
                {
                    "@id": "/construct-library-sets/IGVFDS5584SPIV/",
                    "accession": "IGVFDS5584SPIV",
                    "file_set_type": "expression vector library",
                    "status": "released",
                    "summary": "control transduction expression vector library"
                }
            ],
            "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": "23",
    "status": "released",
    "submitted_by": {
        "@id": "/users/29f5f78d-ac90-421e-90c6-a90e1dc407a7/",
        "title": "Alejandro Barrera"
    },
    "submitted_files_timestamp": "2023-11-08T21:13:24.096564+00:00",
    "summary": "RNA-seq integrating a control transduction expression vector library",
    "uuid": "81b443ec-7ce8-4110-8e79-47b45c71e197"
}