IGVFDS9248YEGX

{
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    "accession": "IGVFDS9248YEGX",
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        "igvf:corces_measurementSet_RP021_G2_RNA"
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        "assay_slims": [
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        "status": "released",
        "term_name": "single-nucleus RNA sequencing assay"
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                "detail": "Preview human donor [IGVFDO6316TGCK](/human-donors/IGVFDO6316TGCK/) has in progress subobject phenotypic feature [36f110b3-ce3c-4adb-acea-eaf2033ddc62](/phenotypic-features/36f110b3-ce3c-4adb-acea-eaf2033ddc62/).",
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            {
                "category": "mismatched status",
                "detail": "Preview human donor [IGVFDO6316TGCK](/human-donors/IGVFDO6316TGCK/) has in progress subobject phenotypic feature [ede77913-c99e-4e14-90ec-baf07e24b231](/phenotypic-features/ede77913-c99e-4e14-90ec-baf07e24b231/).",
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            {
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                "detail": "Preview human donor [IGVFDO6316TGCK](/human-donors/IGVFDO6316TGCK/) has in progress subobject phenotypic feature [d3b01418-90c3-49c1-a68a-c78b0c579754](/phenotypic-features/d3b01418-90c3-49c1-a68a-c78b0c579754/).",
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            {
                "category": "mismatched status",
                "detail": "Preview human donor [IGVFDO6316TGCK](/human-donors/IGVFDO6316TGCK/) has in progress subobject phenotypic feature [b56bf52d-97da-4084-bf29-fe5ddcbca885](/phenotypic-features/b56bf52d-97da-4084-bf29-fe5ddcbca885/).",
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            {
                "category": "mismatched status",
                "detail": "Preview human donor [IGVFDO8046LKFZ](/human-donors/IGVFDO8046LKFZ/) has in progress subobject phenotypic feature [eb1dccc8-a9b4-40ca-9e10-bf67678c6cc5](/phenotypic-features/eb1dccc8-a9b4-40ca-9e10-bf67678c6cc5/).",
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            {
                "category": "mismatched status",
                "detail": "Preview human donor [IGVFDO8046LKFZ](/human-donors/IGVFDO8046LKFZ/) has in progress subobject phenotypic feature [89a557dc-535c-4a80-b083-6a6fd0ab31e8](/phenotypic-features/89a557dc-535c-4a80-b083-6a6fd0ab31e8/).",
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            {
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            {
                "category": "mismatched status",
                "detail": "Preview human donor [IGVFDO8046LKFZ](/human-donors/IGVFDO8046LKFZ/) has in progress subobject phenotypic feature [30873f1f-93e3-45fa-b813-7a7c9c420ed2](/phenotypic-features/30873f1f-93e3-45fa-b813-7a7c9c420ed2/).",
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            {
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                "detail": "Preview human donor [IGVFDO8046LKFZ](/human-donors/IGVFDO8046LKFZ/) has in progress subobject phenotypic feature [39593b92-86ab-4512-ae6a-c5a8c8473cf4](/phenotypic-features/39593b92-86ab-4512-ae6a-c5a8c8473cf4/).",
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            {
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                "detail": "Preview human donor [IGVFDO8046LKFZ](/human-donors/IGVFDO8046LKFZ/) has in progress subobject phenotypic feature [933de8aa-498d-45bb-9b95-cf15aa70af80](/phenotypic-features/933de8aa-498d-45bb-9b95-cf15aa70af80/).",
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            {
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                "detail": "Preview human donor [IGVFDO2848YHMH](/human-donors/IGVFDO2848YHMH/) has in progress subobject phenotypic feature [f481e666-7b16-4e9b-ba1b-a05493449ec5](/phenotypic-features/f481e666-7b16-4e9b-ba1b-a05493449ec5/).",
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            {
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                "detail": "Preview human donor [IGVFDO2848YHMH](/human-donors/IGVFDO2848YHMH/) has in progress subobject phenotypic feature [3c37d880-9919-4b08-abae-044032116c62](/phenotypic-features/3c37d880-9919-4b08-abae-044032116c62/).",
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            {
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            {
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                "detail": "Preview human donor [IGVFDO2848YHMH](/human-donors/IGVFDO2848YHMH/) has in progress subobject phenotypic feature [994a7c3a-8577-4f5e-afa8-c2feb9095ae9](/phenotypic-features/994a7c3a-8577-4f5e-afa8-c2feb9095ae9/).",
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            {
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            {
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                "detail": "Preview human donor [IGVFDO6013FYCW](/human-donors/IGVFDO6013FYCW/) has in progress subobject phenotypic feature [b205a9bf-71f0-45f4-8fe9-d3ecd7e56b67](/phenotypic-features/b205a9bf-71f0-45f4-8fe9-d3ecd7e56b67/).",
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            {
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                "detail": "Preview human donor [IGVFDO6013FYCW](/human-donors/IGVFDO6013FYCW/) has in progress subobject phenotypic feature [b1bac7dd-412a-460a-9336-044c2b41f36b](/phenotypic-features/b1bac7dd-412a-460a-9336-044c2b41f36b/).",
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            {
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                "detail": "Preview human donor [IGVFDO6013FYCW](/human-donors/IGVFDO6013FYCW/) has in progress subobject phenotypic feature [25df185e-787e-41d8-b161-a524d1183f55](/phenotypic-features/25df185e-787e-41d8-b161-a524d1183f55/).",
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            {
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            {
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                "detail": "Preview human donor [IGVFDO6013FYCW](/human-donors/IGVFDO6013FYCW/) has in progress subobject phenotypic feature [61f3a82b-e754-457c-949c-01aeff12f1e1](/phenotypic-features/61f3a82b-e754-457c-949c-01aeff12f1e1/).",
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            {
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            {
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                "detail": "Preview human donor [IGVFDO6489DOPG](/human-donors/IGVFDO6489DOPG/) has in progress subobject phenotypic feature [5c44a3b3-503c-4045-becf-3e8a1f74fb42](/phenotypic-features/5c44a3b3-503c-4045-becf-3e8a1f74fb42/).",
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            {
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                "detail": "Preview human donor [IGVFDO6489DOPG](/human-donors/IGVFDO6489DOPG/) has in progress subobject phenotypic feature [d1b8d684-9089-4797-b468-e66e6208a6a4](/phenotypic-features/d1b8d684-9089-4797-b468-e66e6208a6a4/).",
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            {
                "category": "mismatched status",
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            {
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                "detail": "Preview human donor [IGVFDO6489DOPG](/human-donors/IGVFDO6489DOPG/) has in progress subobject phenotypic feature [5113685b-3e4a-4985-b418-d5b8a80c88fc](/phenotypic-features/5113685b-3e4a-4985-b418-d5b8a80c88fc/).",
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            {
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                "detail": "Preview human donor [IGVFDO6489DOPG](/human-donors/IGVFDO6489DOPG/) has in progress subobject phenotypic feature [d0cc65d7-25b6-4677-bb6b-fa3ad7d9776c](/phenotypic-features/d0cc65d7-25b6-4677-bb6b-fa3ad7d9776c/).",
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            {
                "category": "mismatched status",
                "detail": "Preview human donor [IGVFDO6489DOPG](/human-donors/IGVFDO6489DOPG/) has in progress subobject phenotypic feature [d0131e87-f69e-47de-a1f5-7dbda60dabef](/phenotypic-features/d0131e87-f69e-47de-a1f5-7dbda60dabef/).",
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            {
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                "detail": "Preview human donor [IGVFDO4783EEYU](/human-donors/IGVFDO4783EEYU/) has in progress subobject phenotypic feature [e84ce2e2-54f3-4a61-b8c5-16a291703b53](/phenotypic-features/e84ce2e2-54f3-4a61-b8c5-16a291703b53/).",
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            {
                "category": "mismatched status",
                "detail": "Preview human donor [IGVFDO4783EEYU](/human-donors/IGVFDO4783EEYU/) has in progress subobject phenotypic feature [0dc8abf0-5643-4b17-ac48-79009eced6e6](/phenotypic-features/0dc8abf0-5643-4b17-ac48-79009eced6e6/).",
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                "name": "audit_item_status",
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            },
            {
                "category": "mismatched status",
                "detail": "Preview human donor [IGVFDO4783EEYU](/human-donors/IGVFDO4783EEYU/) has in progress subobject phenotypic feature [f9a6203e-2901-4b9e-b33c-4acea01ed66b](/phenotypic-features/f9a6203e-2901-4b9e-b33c-4acea01ed66b/).",
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                "name": "audit_item_status",
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            {
                "category": "mismatched status",
                "detail": "Preview human donor [IGVFDO4783EEYU](/human-donors/IGVFDO4783EEYU/) has in progress subobject phenotypic feature [9d3918b7-b6f8-422a-a247-efbfaa6dfe34](/phenotypic-features/9d3918b7-b6f8-422a-a247-efbfaa6dfe34/).",
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                "name": "audit_item_status",
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            {
                "category": "mismatched status",
                "detail": "Preview human donor [IGVFDO4783EEYU](/human-donors/IGVFDO4783EEYU/) has in progress subobject phenotypic feature [29a379c5-5559-4a06-ae03-03203593b9de](/phenotypic-features/29a379c5-5559-4a06-ae03-03203593b9de/).",
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                "name": "audit_item_status",
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            {
                "category": "mismatched status",
                "detail": "Preview human donor [IGVFDO3317CNEB](/human-donors/IGVFDO3317CNEB/) has in progress subobject phenotypic feature [59e31a15-2cd7-4a9e-aa78-0c867a74f848](/phenotypic-features/59e31a15-2cd7-4a9e-aa78-0c867a74f848/).",
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                "name": "audit_item_status",
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            },
            {
                "category": "mismatched status",
                "detail": "Preview human donor [IGVFDO3317CNEB](/human-donors/IGVFDO3317CNEB/) has in progress subobject phenotypic feature [8cf8784c-3fbb-459c-b286-621ffef9f967](/phenotypic-features/8cf8784c-3fbb-459c-b286-621ffef9f967/).",
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                "name": "audit_item_status",
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            },
            {
                "category": "mismatched status",
                "detail": "Preview human donor [IGVFDO3317CNEB](/human-donors/IGVFDO3317CNEB/) has in progress subobject phenotypic feature [5e9a12df-1f24-45f8-91cf-10b0f75d7ed7](/phenotypic-features/5e9a12df-1f24-45f8-91cf-10b0f75d7ed7/).",
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                "name": "audit_item_status",
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            },
            {
                "category": "mismatched status",
                "detail": "Preview human donor [IGVFDO3317CNEB](/human-donors/IGVFDO3317CNEB/) has in progress subobject phenotypic feature [11da601f-3cb7-4a5c-9997-e902d23f26c5](/phenotypic-features/11da601f-3cb7-4a5c-9997-e902d23f26c5/).",
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                "name": "audit_item_status",
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            {
                "category": "mismatched status",
                "detail": "Preview human donor [IGVFDO3795BUZW](/human-donors/IGVFDO3795BUZW/) has in progress subobject phenotypic feature [9a07089a-e55f-4366-921e-fc24aeb5118a](/phenotypic-features/9a07089a-e55f-4366-921e-fc24aeb5118a/).",
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                "name": "audit_item_status",
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            },
            {
                "category": "mismatched status",
                "detail": "Preview human donor [IGVFDO3795BUZW](/human-donors/IGVFDO3795BUZW/) has in progress subobject phenotypic feature [3190b852-4196-43c9-9da6-03869014b3bb](/phenotypic-features/3190b852-4196-43c9-9da6-03869014b3bb/).",
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                "name": "audit_item_status",
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            },
            {
                "category": "mismatched status",
                "detail": "Preview human donor [IGVFDO3795BUZW](/human-donors/IGVFDO3795BUZW/) has in progress subobject phenotypic feature [05b2e6f0-0942-4a97-ba30-ab604675cecf](/phenotypic-features/05b2e6f0-0942-4a97-ba30-ab604675cecf/).",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_item_status",
                "path": "/human-donors/IGVFDO3795BUZW/"
            },
            {
                "category": "mismatched status",
                "detail": "Preview human donor [IGVFDO3795BUZW](/human-donors/IGVFDO3795BUZW/) has in progress subobject phenotypic feature [52075c15-8fbc-43f4-8ea7-daca38913ca8](/phenotypic-features/52075c15-8fbc-43f4-8ea7-daca38913ca8/).",
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        ],
        "NOT_COMPLIANT": [
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS9248YEGX](/measurement-sets/IGVFDS9248YEGX/) has sequence file(s): [IGVFFI4170YQIW](/sequence-files/IGVFFI4170YQIW/), [IGVFFI5900LQUA](/sequence-files/IGVFFI5900LQUA/), [IGVFFI4021WYNN](/sequence-files/IGVFFI4021WYNN/), [IGVFFI8192VCPZ](/sequence-files/IGVFFI8192VCPZ/), [IGVFFI6603ECLC](/sequence-files/IGVFFI6603ECLC/), [IGVFFI1147SEOB](/sequence-files/IGVFFI1147SEOB/), [IGVFFI6673RFQN](/sequence-files/IGVFFI6673RFQN/), [IGVFFI1254UCUF](/sequence-files/IGVFFI1254UCUF/), [IGVFFI3318ZRTY](/sequence-files/IGVFFI3318ZRTY/), [IGVFFI7176VHRJ](/sequence-files/IGVFFI7176VHRJ/), [IGVFFI2566QTBV](/sequence-files/IGVFFI2566QTBV/), [IGVFFI5336RXZZ](/sequence-files/IGVFFI5336RXZZ/), [IGVFFI1079FNVT](/sequence-files/IGVFFI1079FNVT/), [IGVFFI9123MPLV](/sequence-files/IGVFFI9123MPLV/), [IGVFFI1118OOAF](/sequence-files/IGVFFI1118OOAF/), [IGVFFI2634QXBE](/sequence-files/IGVFFI2634QXBE/) which do not have any `seqspecs`. Sequence files in a file set associated with single cell data are expected to link to a sequence specification file.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_missing_seqspec",
                "path": "/measurement-sets/IGVFDS9248YEGX/"
            },
            {
                "category": "missing strand specificity",
                "detail": "Measurement set [IGVFDS9248YEGX](/measurement-sets/IGVFDS9248YEGX/) is missing required `strand_specificity`. Single-cell assays are expected to specify strand specificity.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_missing_strand_specificity",
                "path": "/measurement-sets/IGVFDS9248YEGX/"
            }
        ],
        "WARNING": [
            {
                "category": "missing analysis",
                "detail": "Measurement set [IGVFDS9248YEGX](/measurement-sets/IGVFDS9248YEGX/) is a raw data set with files, but is not listed in any `input_file_sets` for any analysis sets. Raw data sets with files are expected to be associated with at least one analysis set.",
                "level": 40,
                "level_name": "WARNING",
                "name": "audit_input_for",
                "path": "/measurement-sets/IGVFDS9248YEGX/"
            }
        ]
    },
    "award": {
        "@id": "/awards/HG012076/",
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                "term_name": "Illumina NovaSeq X"
            },
            "status": "preview",
            "submitted_file_name": "Multiome_RNA_RP021_G2_L002_P066_S40_L005_R1_001.fastq.gz",
            "upload_status": "validated"
        }
    ],
    "input_for": [],
    "lab": {
        "@id": "/labs/ryan-corces/",
        "title": "Ryan Corces, Gladstone Institute UCSF"
    },
    "multiome_size": 2,
    "onlist_files": [
        "/tabular-files/IGVFFI8751YQRY/"
    ],
    "onlist_method": "no combination",
    "preferred_assay_title": "10x multiome",
    "protocols": [
        "https://www.protocols.io/view/chromium-next-gem-single-cell-multiome-atac-gene-e-d5k784zn"
    ],
    "related_multiome_datasets": [
        {
            "@id": "/measurement-sets/IGVFDS4482JTLK/",
            "accession": "IGVFDS4482JTLK",
            "status": "preview"
        }
    ],
    "samples": [
        {
            "@id": "/multiplexed-samples/IGVFSM2242CVZD/",
            "@type": [
                "MultiplexedSample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM2242CVZD",
            "aliases": [
                "igvf:corces_multiplexedSample_RP021_G2"
            ],
            "classifications": [
                "tissue",
                "multiplexed sample"
            ],
            "disease_terms": [
                {
                    "@id": "/phenotype-terms/DOID_0080832/",
                    "status": "in progress",
                    "term_name": "mild cognitive impairment"
                },
                {
                    "@id": "/phenotype-terms/DOID_14330/",
                    "status": "in progress",
                    "term_name": "Parkinson's disease"
                },
                {
                    "@id": "/phenotype-terms/DOID_9246/",
                    "status": "in progress",
                    "term_name": "cerebral amyloid angiopathy"
                }
            ],
            "institutional_certificates": [
                {
                    "@id": "/institutional-certificates/f7742e0d-bba4-4ca3-ab80-71c7364f24e7/",
                    "certificate_identifier": "IP115-05",
                    "controlled_access": false,
                    "status": "in progress"
                }
            ],
            "modifications": [],
            "sample_terms": [
                {
                    "@id": "/sample-terms/UBERON_0001874/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
                        "Item"
                    ],
                    "status": "preview",
                    "summary": "putamen",
                    "term_name": "putamen"
                },
                {
                    "@id": "/sample-terms/UBERON_0002038/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
                        "Item"
                    ],
                    "status": "preview",
                    "summary": "substantia nigra",
                    "term_name": "substantia nigra"
                },
                {
                    "@id": "/sample-terms/UBERON_0002740/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
                        "Item"
                    ],
                    "status": "preview",
                    "summary": "posterior cingulate gyrus",
                    "term_name": "posterior cingulate gyrus"
                },
                {
                    "@id": "/sample-terms/UBERON_0002771/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
                        "Item"
                    ],
                    "status": "preview",
                    "summary": "middle temporal gyrus",
                    "term_name": "middle temporal gyrus"
                }
            ],
            "status": "preview",
            "summary": "multiplexed sample: Homo sapiens (female, 88 years) putamen tissue associated with Parkinson's disease, mild cognitive impairment; Homo sapiens (male, 80 years) substantia nigra tissue associated with Parkinson's disease; ... and 14 more samples",
            "taxa": "Homo sapiens",
            "treatments": []
        }
    ],
    "schema_version": "26",
    "status": "preview",
    "submitted_by": {
        "@id": "/users/c13db3ca-f844-4a69-9056-5fbc4a100f36/",
        "title": "Ryan Corces"
    },
    "submitted_files_timestamp": "2025-03-20T22:29:47.557236+00:00",
    "summary": "single-nucleus RNA sequencing assay (10x multiome)",
    "uuid": "a919fa54-ddd9-48ee-aec5-d18c062a5d09"
}