IGVFDS4803WKTQ

released
{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS4803WKTQ/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS4803WKTQ",
    "aliases": [
        "ali-mortazavi:B01_13G_nanopore"
    ],
    "assay_term": {
        "@id": "/assay-terms/OBI_0003109/",
        "status": "released",
        "term_name": "single-nucleus RNA sequencing assay"
    },
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "NTR term ID",
                "detail": "Sample term for [NTR_0000646](/sample-terms/NTR_0000646/) has been newly requested. Ontology terms 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_ntr_term_id",
                "path": "/sample-terms/NTR_0000646/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS4803WKTQ](/measurement-sets/IGVFDS4803WKTQ/) has sequence file(s): [IGVFFI3397RQUC](/sequence-files/IGVFFI3397RQUC/), [IGVFFI2224QAWI](/sequence-files/IGVFFI2224QAWI/) 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/IGVFDS4803WKTQ/"
            }
        ]
    },
    "award": {
        "@id": "/awards/HG012077/",
        "component": "mapping",
        "contact_pi": {
            "@id": "/users/2c33e192-e815-4384-a220-72a0992cbe24/",
            "title": "Ali Mortazavi"
        },
        "title": "Center for Mouse Genomic Variation at Single Cell Resolution"
    },
    "control_for": [],
    "creation_timestamp": "2024-04-29T18:59:22.864605+00:00",
    "donors": [
        {
            "@id": "/rodent-donors/IGVFDO6942KQBN/",
            "accession": "IGVFDO6942KQBN",
            "aliases": [
                "ali-mortazavi:117_B6J_10M"
            ],
            "sex": "male",
            "status": "released",
            "taxa": "Mus musculus"
        },
        {
            "@id": "/rodent-donors/IGVFDO4816HOFW/",
            "accession": "IGVFDO4816HOFW",
            "aliases": [
                "ali-mortazavi:107_CASTJ_10M"
            ],
            "sex": "male",
            "status": "released",
            "taxa": "Mus musculus"
        },
        {
            "@id": "/rodent-donors/IGVFDO8652OFEQ/",
            "accession": "IGVFDO8652OFEQ",
            "aliases": [
                "ali-mortazavi:106_CASTJ_10F"
            ],
            "sex": "female",
            "status": "released",
            "taxa": "Mus musculus"
        },
        {
            "@id": "/rodent-donors/IGVFDO9333ACQP/",
            "accession": "IGVFDO9333ACQP",
            "aliases": [
                "ali-mortazavi:120_B6J_10F"
            ],
            "sex": "female",
            "status": "released",
            "taxa": "Mus musculus"
        },
        {
            "@id": "/rodent-donors/IGVFDO1486RZJK/",
            "accession": "IGVFDO1486RZJK",
            "aliases": [
                "ali-mortazavi:105_CASTJ_10M"
            ],
            "sex": "male",
            "status": "released",
            "taxa": "Mus musculus"
        },
        {
            "@id": "/rodent-donors/IGVFDO7361LABA/",
            "accession": "IGVFDO7361LABA",
            "aliases": [
                "ali-mortazavi:118_B6J_10F"
            ],
            "sex": "female",
            "status": "released",
            "taxa": "Mus musculus"
        },
        {
            "@id": "/rodent-donors/IGVFDO0493VGMC/",
            "accession": "IGVFDO0493VGMC",
            "aliases": [
                "ali-mortazavi:108_CASTJ_10F"
            ],
            "sex": "female",
            "status": "released",
            "taxa": "Mus musculus"
        },
        {
            "@id": "/rodent-donors/IGVFDO3261YWHI/",
            "accession": "IGVFDO3261YWHI",
            "aliases": [
                "ali-mortazavi:119_B6J_10M"
            ],
            "sex": "male",
            "status": "released",
            "taxa": "Mus musculus"
        }
    ],
    "externally_hosted": false,
    "file_set_type": "experimental data",
    "files": [
        {
            "@id": "/sequence-files/IGVFFI3397RQUC/",
            "accession": "IGVFFI3397RQUC",
            "aliases": [
                "ali-mortazavi:igvfB01_13G-gc_lig-ss_11.pod5"
            ],
            "content_type": "Nanopore reads",
            "controlled_access": false,
            "creation_timestamp": "2024-04-30T16:55:40.126406+00:00",
            "file_format": "pod5",
            "file_size": 1141803266280,
            "href": "/sequence-files/IGVFFI3397RQUC/@@download/IGVFFI3397RQUC.pod5",
            "s3_uri": "s3://igvf-files/2024/04/30/c6bec196-fe41-4d46-977b-1f31a8a72edf/IGVFFI3397RQUC.pod5",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0700019/",
                "status": "released",
                "term_name": "ONT PromethION 2 Solo"
            },
            "status": "released",
            "submitted_file_name": "igvf_b01/nanopore_p2/igvfb01_13G-gc_lig-ss_11.pod5",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI2224QAWI/",
            "accession": "IGVFFI2224QAWI",
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-05-01T02:08:54.793631+00:00",
            "file_format": "fastq",
            "file_size": 83297971550,
            "href": "/sequence-files/IGVFFI2224QAWI/@@download/IGVFFI2224QAWI.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/05/01/bc97e654-08b3-4533-b167-077ed920532f/IGVFFI2224QAWI.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0700019/",
                "status": "released",
                "term_name": "ONT PromethION 2 Solo"
            },
            "status": "released",
            "submitted_file_name": "igvf_b01/nanopore_p2/igvfb01_13G-gc_lig-ss_11.fastq.gz",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS4705QPIK/",
        "/analysis-sets/IGVFDS7467TPQO/",
        "/analysis-sets/IGVFDS4019MYIG/",
        "/analysis-sets/IGVFDS6540HMFT/",
        "/analysis-sets/IGVFDS3821ZEWS/"
    ],
    "lab": {
        "@id": "/labs/ali-mortazavi/",
        "title": "Ali Mortazavi, UCI"
    },
    "preferred_assay_title": "Parse SPLiT-seq",
    "protocols": [
        "https://www.protocols.io/view/evercode-wt-v2-2-1-eq2lyj9relx9/v1",
        "https://www.protocols.io/view/protocol-to-isolate-and-fix-nuclei-from-cryopreser-4r3l22y2pl1y/v1",
        "https://www.protocols.io/view/cdna-exome-capture-v1-0-1-36wgq3b83lk5/v1",
        "https://www.protocols.io/view/ont-library-prep-for-split-seq-cdna-eq2lyj1xmlx9/v1"
    ],
    "release_timestamp": "2024-05-08T23:38:43.026570+00:00",
    "samples": [
        {
            "@id": "/multiplexed-samples/IGVFSM8722YQAW/",
            "@type": [
                "MultiplexedSample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM8722YQAW",
            "aliases": [
                "ali-mortazavi:subpool_b01_13g"
            ],
            "classifications": [
                "multiplexed sample"
            ],
            "construct_library_sets": [],
            "disease_terms": [],
            "modifications": [],
            "sample_terms": [
                {
                    "@id": "/sample-terms/NTR_0000646/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
                        "Item"
                    ],
                    "status": "released",
                    "summary": "left cerebral cortex",
                    "term_name": "left cerebral cortex"
                }
            ],
            "status": "released",
            "summary": "multiplexed sample: left cerebral cortex tissue, female, Mus musculus CASTJ (72 days); left cerebral cortex tissue, male, Mus musculus B6J (72 days); ... and 6 more samples",
            "taxa": "Mus musculus",
            "treatments": []
        }
    ],
    "schema_version": "23",
    "sequencing_library_types": [
        "exome capture"
    ],
    "status": "released",
    "submitted_by": {
        "@id": "/users/ebd1025b-e3ab-4e51-bfcd-1415f278281a/",
        "title": "Diane Trout"
    },
    "submitted_files_timestamp": "2024-04-30T16:55:40.126406+00:00",
    "summary": "Parse SPLiT-seq",
    "uuid": "4a15cf9b-b172-4b42-bf9b-eb52600b7605"
}