IGVFDS2590SMEJ

released
{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS2590SMEJ/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS2590SMEJ",
    "aliases": [
        "charles-gersbach:measurement-set-bulk-rna-chir4um-ipsc-cm-rep3"
    ],
    "assay_term": {
        "@id": "/assay-terms/OBI_0003090/",
        "status": "released",
        "term_name": "bulk RNA-seq assay"
    },
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS2590SMEJ](/measurement-sets/IGVFDS2590SMEJ/) has sequence file(s): [IGVFFI3789TSVB](/sequence-files/IGVFFI3789TSVB/), [IGVFFI4288WBKI](/sequence-files/IGVFFI4288WBKI/) 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/IGVFDS2590SMEJ/"
            }
        ]
    },
    "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_file_sets": [
        {
            "@id": "/measurement-sets/IGVFDS3697TBRV/",
            "accession": "IGVFDS3697TBRV",
            "aliases": [
                "charles-gersbach:measurement-set-bulk-rna-control-ipsc-cm-rep3"
            ],
            "status": "released"
        }
    ],
    "control_for": [],
    "creation_timestamp": "2024-10-23T19:18:43.904786+00:00",
    "donors": [
        {
            "@id": "/human-donors/IGVFDO3212TBUN/",
            "accession": "IGVFDO3212TBUN",
            "aliases": [
                "charles-gersbach:human-donor-WTC11"
            ],
            "sex": "male",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "externally_hosted": false,
    "file_set_type": "experimental data",
    "files": [
        {
            "@id": "/sequence-files/IGVFFI3789TSVB/",
            "accession": "IGVFFI3789TSVB",
            "aliases": [
                "charles-gersbach:measurement-set-bulk-rna-chir4um-ipsc-cm-rep3-R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-10-23T19:28:44.788271+00:00",
            "file_format": "fastq",
            "file_size": 2818703778,
            "href": "/sequence-files/IGVFFI3789TSVB/@@download/IGVFFI3789TSVB.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/10/23/2f08783f-d1cd-4ffd-b9f9-2edad6062eec/IGVFFI3789TSVB.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0008637/",
                "status": "released",
                "term_name": "Illumina NovaSeq 6000"
            },
            "status": "released",
            "submitted_file_name": "/datacommons/gersbachlab/tda17/Anglen_7276_210923B6_RNAseq/data/rna_seq/processed_raw_reads/Anglen_7276_210923B6_RNAseq/chir4um.3.rna.R1.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI4288WBKI/",
            "accession": "IGVFFI4288WBKI",
            "aliases": [
                "charles-gersbach:measurement-set-bulk-rna-chir4um-ipsc-cm-rep3-R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-10-23T19:28:46.029111+00:00",
            "file_format": "fastq",
            "file_size": 2956751180,
            "href": "/sequence-files/IGVFFI4288WBKI/@@download/IGVFFI4288WBKI.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/10/23/08479b7f-df48-40fb-a988-4763fc527f58/IGVFFI4288WBKI.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0008637/",
                "status": "released",
                "term_name": "Illumina NovaSeq 6000"
            },
            "status": "released",
            "submitted_file_name": "/datacommons/gersbachlab/tda17/Anglen_7276_210923B6_RNAseq/data/rna_seq/processed_raw_reads/Anglen_7276_210923B6_RNAseq/chir4um.3.rna.R2.fastq.gz",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS7046PDMA/"
    ],
    "lab": {
        "@id": "/labs/charles-gersbach/",
        "title": "Charles Gersbach, Duke"
    },
    "preferred_assay_title": "RNA-seq",
    "protocols": [
        "https://www.protocols.io/view/rna-seq-for-human-ipsc-cm-following-gsk3-inhibitio-kqdg32rb1v25"
    ],
    "release_timestamp": "2024-12-10T00:24:34.820242+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM2298AOEQ/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM2298AOEQ",
            "aliases": [
                "charles-gersbach:in-vitro-system-bulk-rna-chir4um-ipsc-cm-rep3"
            ],
            "classifications": [
                "differentiated cell specimen"
            ],
            "sample_terms": [
                {
                    "@id": "/sample-terms/EFO_0009747/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
                        "Item"
                    ],
                    "aliases": [
                        "igvf:WTC11"
                    ],
                    "status": "released",
                    "summary": "GM25256 (WTC-11)",
                    "term_name": "GM25256 (WTC-11)"
                }
            ],
            "status": "released",
            "summary": "GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 28 days, male, Homo sapiens treated with 4 μM GSK3 inhibition for 7 days",
            "targeted_sample_term": {
                "@id": "/sample-terms/CL_0000746/",
                "status": "released",
                "term_name": "cardiac muscle cell"
            },
            "taxa": "Homo sapiens",
            "treatments": [
                {
                    "@id": "/treatments/98ba0c5c-8005-41bc-bcbb-6c6eff41af4e/",
                    "status": "released",
                    "treatment_term_name": "GSK3 inhibition"
                }
            ]
        }
    ],
    "schema_version": "23",
    "status": "released",
    "submitted_by": {
        "@id": "/users/3782ce69-0e9f-4b46-91f9-4578139785c7/",
        "title": "Ruhi Rai"
    },
    "submitted_files_timestamp": "2024-10-23T19:28:44.788271+00:00",
    "summary": "RNA-seq",
    "uuid": "8791fa14-f0d9-43ed-9adc-1d8ec1e67d83"
}