substantia nigra — IGVFSM0536KFDX

{
    "@context": "/terms/",
    "@id": "/tissues/IGVFSM0536KFDX/",
    "@type": [
        "Tissue",
        "Biosample",
        "Sample",
        "Item"
    ],
    "accession": "IGVFSM0536KFDX",
    "age": "70",
    "age_units": "year",
    "aliases": [
        "igvf:corces_tissue_BANN9902_SN"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "mismatched status",
                "detail": "Preview tissue [IGVFSM0536KFDX](/tissues/IGVFSM0536KFDX/) has in progress subobject phenotype term [DOID_9246](/phenotype-terms/DOID_9246/).",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_item_status",
                "path": "/tissues/IGVFSM0536KFDX/"
            },
            {
                "category": "missing CCF ID",
                "detail": "Tissue [IGVFSM0536KFDX](/tissues/IGVFSM0536KFDX/) is missing a `ccf_id`. Human tissues are expected to specify a common coordinate framework identifier (CCF ID).",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_tissue_ccf_id",
                "path": "/tissues/IGVFSM0536KFDX/"
            }
        ]
    },
    "award": {
        "@id": "/awards/HG012076/",
        "component": "mapping"
    },
    "classifications": [
        "tissue"
    ],
    "creation_timestamp": "2025-03-19T04:12:38.979171+00:00",
    "date_obtained": "2023-02-01",
    "disease_terms": [
        {
            "@id": "/phenotype-terms/DOID_9246/",
            "status": "in progress",
            "term_name": "cerebral amyloid angiopathy"
        }
    ],
    "donors": [
        {
            "@id": "/human-donors/IGVFDO7649CIGW/",
            "accession": "IGVFDO7649CIGW",
            "ethnicities": [
                "European"
            ],
            "status": "preview"
        }
    ],
    "file_sets": [
        {
            "@id": "/measurement-sets/IGVFDS2132XMHB/",
            "accession": "IGVFDS2132XMHB",
            "aliases": [
                "igvf:corces_measurementSet_X032_G4_ATAC"
            ],
            "file_set_type": "experimental data",
            "lab": {
                "title": "Ryan Corces, Gladstone Institute UCSF"
            },
            "preferred_assay_title": "10x multiome",
            "status": "preview",
            "summary": "single-nucleus ATAC-seq (10x multiome)"
        },
        {
            "@id": "/measurement-sets/IGVFDS3071WPNU/",
            "accession": "IGVFDS3071WPNU",
            "aliases": [
                "igvf:corces_measurementSet_X032_G4_RNA"
            ],
            "file_set_type": "experimental data",
            "lab": {
                "title": "Ryan Corces, Gladstone Institute UCSF"
            },
            "preferred_assay_title": "10x multiome",
            "status": "preview",
            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
        },
        {
            "@id": "/measurement-sets/IGVFDS2336BWET/",
            "accession": "IGVFDS2336BWET",
            "aliases": [
                "igvf:corces_measurementSet_X032_G8_ATAC"
            ],
            "file_set_type": "experimental data",
            "lab": {
                "title": "Ryan Corces, Gladstone Institute UCSF"
            },
            "preferred_assay_title": "10x multiome",
            "status": "preview",
            "summary": "single-nucleus ATAC-seq (10x multiome)"
        },
        {
            "@id": "/measurement-sets/IGVFDS7019JXXD/",
            "accession": "IGVFDS7019JXXD",
            "aliases": [
                "igvf:corces_measurementSet_X032_G8_RNA"
            ],
            "file_set_type": "experimental data",
            "lab": {
                "title": "Ryan Corces, Gladstone Institute UCSF"
            },
            "preferred_assay_title": "10x multiome",
            "status": "preview",
            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
        },
        {
            "@id": "/measurement-sets/IGVFDS3080TIMY/",
            "accession": "IGVFDS3080TIMY",
            "aliases": [
                "igvf:corces_measurementSet_X032_G1_ATAC"
            ],
            "file_set_type": "experimental data",
            "lab": {
                "title": "Ryan Corces, Gladstone Institute UCSF"
            },
            "preferred_assay_title": "10x multiome",
            "status": "preview",
            "summary": "single-nucleus ATAC-seq (10x multiome)"
        },
        {
            "@id": "/measurement-sets/IGVFDS3535IMWQ/",
            "accession": "IGVFDS3535IMWQ",
            "aliases": [
                "igvf:corces_measurementSet_X032_G1_RNA"
            ],
            "file_set_type": "experimental data",
            "lab": {
                "title": "Ryan Corces, Gladstone Institute UCSF"
            },
            "preferred_assay_title": "10x multiome",
            "status": "preview",
            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
        },
        {
            "@id": "/measurement-sets/IGVFDS4088CJJR/",
            "accession": "IGVFDS4088CJJR",
            "aliases": [
                "igvf:corces_measurementSet_X032_G7_ATAC"
            ],
            "file_set_type": "experimental data",
            "lab": {
                "title": "Ryan Corces, Gladstone Institute UCSF"
            },
            "preferred_assay_title": "10x multiome",
            "status": "preview",
            "summary": "single-nucleus ATAC-seq (10x multiome)"
        },
        {
            "@id": "/measurement-sets/IGVFDS7706LHLI/",
            "accession": "IGVFDS7706LHLI",
            "aliases": [
                "igvf:corces_measurementSet_X032_G7_RNA"
            ],
            "file_set_type": "experimental data",
            "lab": {
                "title": "Ryan Corces, Gladstone Institute UCSF"
            },
            "preferred_assay_title": "10x multiome",
            "status": "preview",
            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
        },
        {
            "@id": "/measurement-sets/IGVFDS7833BTPG/",
            "accession": "IGVFDS7833BTPG",
            "aliases": [
                "igvf:corces_measurementSet_X032_G3_ATAC"
            ],
            "file_set_type": "experimental data",
            "lab": {
                "title": "Ryan Corces, Gladstone Institute UCSF"
            },
            "preferred_assay_title": "10x multiome",
            "status": "preview",
            "summary": "single-nucleus ATAC-seq (10x multiome)"
        },
        {
            "@id": "/measurement-sets/IGVFDS9057KJEI/",
            "accession": "IGVFDS9057KJEI",
            "aliases": [
                "igvf:corces_measurementSet_X032_G3_RNA"
            ],
            "file_set_type": "experimental data",
            "lab": {
                "title": "Ryan Corces, Gladstone Institute UCSF"
            },
            "preferred_assay_title": "10x multiome",
            "status": "preview",
            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
        },
        {
            "@id": "/measurement-sets/IGVFDS6899OQTS/",
            "accession": "IGVFDS6899OQTS",
            "aliases": [
                "igvf:corces_measurementSet_X032_G2_ATAC"
            ],
            "file_set_type": "experimental data",
            "lab": {
                "title": "Ryan Corces, Gladstone Institute UCSF"
            },
            "preferred_assay_title": "10x multiome",
            "status": "preview",
            "summary": "single-nucleus ATAC-seq (10x multiome)"
        },
        {
            "@id": "/measurement-sets/IGVFDS0346MQLV/",
            "accession": "IGVFDS0346MQLV",
            "aliases": [
                "igvf:corces_measurementSet_X032_G2_RNA"
            ],
            "file_set_type": "experimental data",
            "lab": {
                "title": "Ryan Corces, Gladstone Institute UCSF"
            },
            "preferred_assay_title": "10x multiome",
            "status": "preview",
            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
        },
        {
            "@id": "/measurement-sets/IGVFDS5776BDPL/",
            "accession": "IGVFDS5776BDPL",
            "aliases": [
                "igvf:corces_measurementSet_X032_G5_ATAC"
            ],
            "file_set_type": "experimental data",
            "lab": {
                "title": "Ryan Corces, Gladstone Institute UCSF"
            },
            "preferred_assay_title": "10x multiome",
            "status": "preview",
            "summary": "single-nucleus ATAC-seq (10x multiome)"
        },
        {
            "@id": "/measurement-sets/IGVFDS6220QSDQ/",
            "accession": "IGVFDS6220QSDQ",
            "aliases": [
                "igvf:corces_measurementSet_X032_G5_RNA"
            ],
            "file_set_type": "experimental data",
            "lab": {
                "title": "Ryan Corces, Gladstone Institute UCSF"
            },
            "preferred_assay_title": "10x multiome",
            "status": "preview",
            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
        },
        {
            "@id": "/measurement-sets/IGVFDS2723SVTT/",
            "accession": "IGVFDS2723SVTT",
            "aliases": [
                "igvf:corces_measurementSet_X032_G6_ATAC"
            ],
            "file_set_type": "experimental data",
            "lab": {
                "title": "Ryan Corces, Gladstone Institute UCSF"
            },
            "preferred_assay_title": "10x multiome",
            "status": "preview",
            "summary": "single-nucleus ATAC-seq (10x multiome)"
        },
        {
            "@id": "/measurement-sets/IGVFDS5452ZVED/",
            "accession": "IGVFDS5452ZVED",
            "aliases": [
                "igvf:corces_measurementSet_X032_G6_RNA"
            ],
            "file_set_type": "experimental data",
            "lab": {
                "title": "Ryan Corces, Gladstone Institute UCSF"
            },
            "preferred_assay_title": "10x multiome",
            "status": "preview",
            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
        }
    ],
    "institutional_certificates": [
        {
            "@id": "/institutional-certificates/f7742e0d-bba4-4ca3-ab80-71c7364f24e7/",
            "certificate_identifier": "IP115-05",
            "controlled_access": false,
            "status": "in progress"
        }
    ],
    "lab": {
        "@id": "/labs/ryan-corces/",
        "title": "Ryan Corces, Gladstone Institute UCSF"
    },
    "lower_bound_age": 70,
    "lower_bound_age_in_hours": 613200,
    "multiplexed_in": [
        {
            "@id": "/multiplexed-samples/IGVFSM5595EQCW/",
            "accession": "IGVFSM5595EQCW",
            "status": "preview"
        },
        {
            "@id": "/multiplexed-samples/IGVFSM8574LYFF/",
            "accession": "IGVFSM8574LYFF",
            "status": "preview"
        },
        {
            "@id": "/multiplexed-samples/IGVFSM6835GLQE/",
            "accession": "IGVFSM6835GLQE",
            "status": "preview"
        },
        {
            "@id": "/multiplexed-samples/IGVFSM2646IJIB/",
            "accession": "IGVFSM2646IJIB",
            "status": "preview"
        },
        {
            "@id": "/multiplexed-samples/IGVFSM7956ZXDL/",
            "accession": "IGVFSM7956ZXDL",
            "status": "preview"
        },
        {
            "@id": "/multiplexed-samples/IGVFSM8298WTCX/",
            "accession": "IGVFSM8298WTCX",
            "status": "preview"
        },
        {
            "@id": "/multiplexed-samples/IGVFSM8487OHPZ/",
            "accession": "IGVFSM8487OHPZ",
            "status": "preview"
        },
        {
            "@id": "/multiplexed-samples/IGVFSM8028VLKJ/",
            "accession": "IGVFSM8028VLKJ",
            "status": "preview"
        }
    ],
    "origin_of": [],
    "parts": [],
    "pmi": 120,
    "pmi_units": "minute",
    "pooled_in": [],
    "preservation_method": "flash-freezing",
    "protocols": [
        "https://www.protocols.io/view/isolation-of-nuclei-from-frozen-tissue-for-snmulti-6uchesw"
    ],
    "sample_terms": [
        {
            "@id": "/sample-terms/UBERON_0002038/",
            "status": "preview",
            "term_name": "substantia nigra"
        }
    ],
    "schema_version": "21",
    "sex": "female",
    "sorted_fractions": [],
    "sources": [
        {
            "@id": "/sources/banner-health/",
            "status": "released",
            "title": "Banner Health"
        }
    ],
    "status": "preview",
    "submitted_by": {
        "@id": "/users/c13db3ca-f844-4a69-9056-5fbc4a100f36/",
        "title": "Ryan Corces"
    },
    "summary": "Homo sapiens (female, 70 years) substantia nigra tissue associated with cerebral amyloid angiopathy",
    "taxa": "Homo sapiens",
    "upper_bound_age": 70,
    "upper_bound_age_in_hours": 613200,
    "uuid": "bdc5cdd4-38eb-485c-8efd-e813d7aada4c",
    "virtual": false
}