IGVFDS6638LYXU

{
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    "accession": "IGVFDS6638LYXU",
    "aliases": [
        "igvf:corces_measurementSet_RP028_G7_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 [IGVFDS6638LYXU](/measurement-sets/IGVFDS6638LYXU/) has sequence file(s): [IGVFFI3991GGBD](/sequence-files/IGVFFI3991GGBD/), [IGVFFI1063GQYS](/sequence-files/IGVFFI1063GQYS/), [IGVFFI6211NNHH](/sequence-files/IGVFFI6211NNHH/), [IGVFFI5143PVUV](/sequence-files/IGVFFI5143PVUV/), [IGVFFI2195CBHE](/sequence-files/IGVFFI2195CBHE/), [IGVFFI2348FNIL](/sequence-files/IGVFFI2348FNIL/), [IGVFFI6188PCMX](/sequence-files/IGVFFI6188PCMX/), [IGVFFI3189NKPT](/sequence-files/IGVFFI3189NKPT/), [IGVFFI6117EFJN](/sequence-files/IGVFFI6117EFJN/), [IGVFFI7572NPTS](/sequence-files/IGVFFI7572NPTS/), [IGVFFI8566BOHA](/sequence-files/IGVFFI8566BOHA/), [IGVFFI5815BLVD](/sequence-files/IGVFFI5815BLVD/), [IGVFFI5917JHQW](/sequence-files/IGVFFI5917JHQW/), [IGVFFI4797XFWM](/sequence-files/IGVFFI4797XFWM/), [IGVFFI2000NZAU](/sequence-files/IGVFFI2000NZAU/), [IGVFFI2843PGLR](/sequence-files/IGVFFI2843PGLR/) 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/IGVFDS6638LYXU/"
            },
            {
                "category": "missing strand specificity",
                "detail": "Measurement set [IGVFDS6638LYXU](/measurement-sets/IGVFDS6638LYXU/) 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/IGVFDS6638LYXU/"
            }
        ],
        "WARNING": [
            {
                "category": "missing analysis",
                "detail": "Measurement set [IGVFDS6638LYXU](/measurement-sets/IGVFDS6638LYXU/) 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/IGVFDS6638LYXU/"
            }
        ]
    },
    "award": {
        "@id": "/awards/HG012076/",
        "component": "mapping",
        "contact_pi": {
            "@id": "/users/eae4c275-1e07-45e4-ae67-3e437a8680bb/",
            "title": "Ansuman Satpathy"
        },
        "title": "Single-cell Mapping Center for Human Regulatory Elements and Gene Activity"
    },
    "control_for": [],
    "controlled_access": false,
    "creation_timestamp": "2025-03-19T19:57:56.602740+00:00",
    "data_use_limitation_summaries": [
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        },
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                "igvf:corces_donor_BANN1750"
            ],
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            "status": "preview",
            "taxa": "Homo sapiens"
        },
        {
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            ],
            "sex": "female",
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            "taxa": "Homo sapiens"
        },
        {
            "@id": "/human-donors/IGVFDO3501RYHX/",
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        },
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        },
        {
            "@id": "/human-donors/IGVFDO8800RKVB/",
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                "@id": "/platform-terms/EFO_0022840/",
                "status": "released",
                "term_name": "Illumina NovaSeq X"
            },
            "status": "preview",
            "submitted_file_name": "Multiome_ATAC_RP028_G7_L007_P077_S25_L006_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/IGVFDS6145VWNH/",
            "accession": "IGVFDS6145VWNH",
            "status": "preview"
        }
    ],
    "samples": [
        {
            "@id": "/multiplexed-samples/IGVFSM3393RSBM/",
            "@type": [
                "MultiplexedSample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM3393RSBM",
            "aliases": [
                "igvf:corces_multiplexedSample_RP028_G7"
            ],
            "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"
                },
                {
                    "@id": "/phenotype-terms/MONDO_0004975/",
                    "status": "released",
                    "term_name": "Alzheimer disease"
                }
            ],
            "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, 84 years) substantia nigra tissue associated with Parkinson's disease, mild cognitive impairment; Homo sapiens (male, 70 years) substantia nigra tissue associated with Alzheimer disease, Parkinson's disease; ... and 6 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": "2025-03-21T02:26:37.257463+00:00",
    "summary": "single-nucleus ATAC-seq (10x multiome)",
    "uuid": "0a7aa48f-22ce-4ab3-b205-bc1c9c0f89e4"
}