IGVFDS1260SOEX

{
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    "accession": "IGVFDS1260SOEX",
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        "igvf:corces_measurementSet_RP029_G6_ATAC"
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        "assay_slims": [
            "chromatin accessibility"
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        "status": "released",
        "term_name": "single-nucleus ATAC-seq"
    },
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            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS1260SOEX](/measurement-sets/IGVFDS1260SOEX/) has sequence file(s): [IGVFFI6987SURR](/sequence-files/IGVFFI6987SURR/), [IGVFFI6199WMUC](/sequence-files/IGVFFI6199WMUC/), [IGVFFI2756YPWT](/sequence-files/IGVFFI2756YPWT/), [IGVFFI0333RIZL](/sequence-files/IGVFFI0333RIZL/), [IGVFFI7969CTKK](/sequence-files/IGVFFI7969CTKK/), [IGVFFI9537SNFF](/sequence-files/IGVFFI9537SNFF/), [IGVFFI9471APSJ](/sequence-files/IGVFFI9471APSJ/), [IGVFFI3598RCOS](/sequence-files/IGVFFI3598RCOS/), [IGVFFI7203QRWN](/sequence-files/IGVFFI7203QRWN/), [IGVFFI6092TISV](/sequence-files/IGVFFI6092TISV/), [IGVFFI6446RQXS](/sequence-files/IGVFFI6446RQXS/), [IGVFFI2080MMYD](/sequence-files/IGVFFI2080MMYD/), [IGVFFI8732MCEJ](/sequence-files/IGVFFI8732MCEJ/), [IGVFFI2341ZQOM](/sequence-files/IGVFFI2341ZQOM/), [IGVFFI8966PJWQ](/sequence-files/IGVFFI8966PJWQ/), [IGVFFI4998HRUF](/sequence-files/IGVFFI4998HRUF/) 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/IGVFDS1260SOEX/"
            },
            {
                "category": "missing strand specificity",
                "detail": "Measurement set [IGVFDS1260SOEX](/measurement-sets/IGVFDS1260SOEX/) 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/IGVFDS1260SOEX/"
            }
        ],
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            {
                "category": "missing analysis",
                "detail": "Measurement set [IGVFDS1260SOEX](/measurement-sets/IGVFDS1260SOEX/) 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.",
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            "sequencing_platform": {
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                "status": "released",
                "term_name": "Illumina NovaSeq X"
            },
            "status": "preview",
            "submitted_file_name": "Multiome_ATAC_RP029_G6_L006_P077_S32_L005_R2_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/IGVFFI7587TJLC/"
    ],
    "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/IGVFDS3236ZDII/",
            "accession": "IGVFDS3236ZDII",
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        }
    ],
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        {
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            "@type": [
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            ],
            "accession": "IGVFSM1252DLAM",
            "aliases": [
                "igvf:corces_multiplexedSample_RP029_G6"
            ],
            "classifications": [
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            "disease_terms": [
                {
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                    "status": "in progress",
                    "term_name": "mild cognitive impairment"
                },
                {
                    "@id": "/phenotype-terms/DOID_14330/",
                    "status": "in progress",
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                {
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                    "status": "in progress",
                    "term_name": "cerebral amyloid angiopathy"
                },
                {
                    "@id": "/phenotype-terms/MONDO_0004975/",
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                    "term_name": "Alzheimer disease"
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            ],
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                    "@id": "/institutional-certificates/f7742e0d-bba4-4ca3-ab80-71c7364f24e7/",
                    "certificate_identifier": "IP115-05",
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            ],
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            "sample_terms": [
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                    "status": "preview",
                    "summary": "putamen",
                    "term_name": "putamen"
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                        "OntologyTerm",
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                    "summary": "substantia nigra",
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                    "status": "preview",
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            ],
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            "summary": "multiplexed sample: Homo sapiens (male, 74 years) putamen tissue associated with Parkinson's disease; Homo sapiens (male, 89 years) posterior cingulate gyrus tissue; ... and 6 more samples",
            "taxa": "Homo sapiens",
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    "submitted_by": {
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        "title": "Ryan Corces"
    },
    "submitted_files_timestamp": "2025-03-21T03:07:11.250376+00:00",
    "summary": "single-nucleus ATAC-seq (10x multiome)",
    "uuid": "e3424a09-2a78-44ce-bb1b-dfbe3305f90a"
}