IGVFDS1689MMMU

released
{
    "@context": "/terms/",
    "@id": "/analysis-sets/IGVFDS1689MMMU/",
    "@type": [
        "AnalysisSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS1689MMMU",
    "aliases": [
        "ali-mortazavi:igvf_007_Subpool_13_total+core"
    ],
    "assay_titles": [
        "Parse SPLiT-seq"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing demultiplexed sample",
                "detail": "Analysis set [IGVFDS1689MMMU](/analysis-sets/IGVFDS1689MMMU/) has `input_file_sets` with multiplexed samples: [IGVFSM5898DEVL](/multiplexed-samples/IGVFSM5898DEVL/) but no `demultiplexed_sample`. Analysis sets with multiplexed samples are expected to specify a demultiplexed sample.",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_analysis_set_multiplexed_samples",
                "path": "/analysis-sets/IGVFDS1689MMMU/"
            },
            {
                "category": "missing publication",
                "detail": "Analysis set [IGVFDS1689MMMU](/analysis-sets/IGVFDS1689MMMU/) has no `publications`. Released and archived file sets are expected to be associated with a publication.",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_file_set_missing_publication",
                "path": "/analysis-sets/IGVFDS1689MMMU/"
            },
            {
                "category": "mismatched status",
                "detail": "Released multiplexed sample [IGVFSM5898DEVL](/multiplexed-samples/IGVFSM5898DEVL/) has in progress subobject tabular file [IGVFFI4658LINI](/tabular-files/IGVFFI4658LINI/).",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_item_status",
                "path": "/multiplexed-samples/IGVFSM5898DEVL/"
            },
            {
                "category": "missing publication",
                "detail": "Multiplexed sample [IGVFSM5898DEVL](/multiplexed-samples/IGVFSM5898DEVL/) has no `publications`. Released and archived samples are expected to be associated with a publication.",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_sample_missing_publication",
                "path": "/multiplexed-samples/IGVFSM5898DEVL/"
            }
        ]
    },
    "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": "2025-04-05T02:04:39.203418+00:00",
    "data_use_limitation_summaries": [
        "no certificate"
    ],
    "description": "8 cube mouse founder strains plate igvf_007 Subpool_13 with Diencephalon/Pituitary as the primary tissue and Gonads as the genetically multiplexed tissue",
    "documents": [
        "/documents/126b728e-08ae-48e3-a25e-c71b5278ff00/"
    ],
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        },
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        },
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        },
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        },
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        },
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            "@id": "/rodent-donors/IGVFDO2301HIUQ/",
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            "strain_background": "NOD/ShiLtJ (NOD)",
            "taxa": "Mus musculus"
        },
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            "@id": "/rodent-donors/IGVFDO3207TERA/",
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            "aliases": [
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            "sex": "female",
            "status": "released",
            "strain_background": "CAST/EiJ (CAST)",
            "taxa": "Mus musculus"
        },
        {
            "@id": "/rodent-donors/IGVFDO3662UKFW/",
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            "aliases": [
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            "sex": "male",
            "status": "released",
            "strain_background": "CAST/EiJ (CAST)",
            "taxa": "Mus musculus"
        },
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            "@id": "/rodent-donors/IGVFDO0853BCOL/",
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            "aliases": [
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            "sex": "female",
            "status": "released",
            "strain_background": "WSB/EiJ (WSB)",
            "taxa": "Mus musculus"
        },
        {
            "@id": "/rodent-donors/IGVFDO2106EEWB/",
            "accession": "IGVFDO2106EEWB",
            "aliases": [
                "ali-mortazavi:078_PWKJ_10F"
            ],
            "sex": "female",
            "status": "released",
            "strain_background": "PWK/PhJ (PWK)",
            "taxa": "Mus musculus"
        },
        {
            "@id": "/rodent-donors/IGVFDO9340WGNV/",
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            "aliases": [
                "ali-mortazavi:037_129S1J_10M"
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            "sex": "male",
            "status": "released",
            "strain_background": "129S1/SvImJ (129)",
            "taxa": "Mus musculus"
        },
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            "@id": "/rodent-donors/IGVFDO9199TPBC/",
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            "aliases": [
                "ali-mortazavi:071_NODJ_10M"
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            "sex": "male",
            "status": "released",
            "strain_background": "NOD/ShiLtJ (NOD)",
            "taxa": "Mus musculus"
        },
        {
            "@id": "/rodent-donors/IGVFDO0696DMIA/",
            "accession": "IGVFDO0696DMIA",
            "aliases": [
                "ali-mortazavi:057_WSBJ_10M"
            ],
            "sex": "male",
            "status": "released",
            "strain_background": "WSB/EiJ (WSB)",
            "taxa": "Mus musculus"
        },
        {
            "@id": "/rodent-donors/IGVFDO7957DMLJ/",
            "accession": "IGVFDO7957DMLJ",
            "aliases": [
                "ali-mortazavi:033_AJ_10M"
            ],
            "sex": "male",
            "status": "released",
            "strain_background": "A/J (AJ)",
            "taxa": "Mus musculus"
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    ],
    "file_set_type": "intermediate analysis",
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            "@id": "/matrix-files/IGVFFI4717RVCZ/",
            "accession": "IGVFFI4717RVCZ",
            "content_type": "sparse gene count matrix",
            "creation_timestamp": "2025-04-06T22:45:40.254921+00:00",
            "derived_from": [
                "/sequence-files/IGVFFI4215VVIV/",
                "/sequence-files/IGVFFI4623JUUR/",
                "/sequence-files/IGVFFI0559WNME/",
                "/sequence-files/IGVFFI0396ZZQB/",
                "/sequence-files/IGVFFI9939YYBL/",
                "/sequence-files/IGVFFI0544BESN/",
                "/sequence-files/IGVFFI3525BNWJ/",
                "/sequence-files/IGVFFI2273DILP/",
                "/sequence-files/IGVFFI0869UKQY/",
                "/sequence-files/IGVFFI4003JXZS/",
                "/sequence-files/IGVFFI3172SFBQ/",
                "/sequence-files/IGVFFI2900KLVY/",
                "/sequence-files/IGVFFI8472YLTQ/",
                "/sequence-files/IGVFFI5618YTFY/",
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            "md5sum": "b7bef680b2b96825da51a1fca6ae9da7",
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            "status": "released",
            "submitted_file_name": "igvf_007/igvf_007_Subpool_13_total+core.tar.gz",
            "upload_status": "validated"
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    "functional_assay_mechanisms": [],
    "input_file_sets": [
        {
            "@id": "/measurement-sets/IGVFDS8310XEDQ/",
            "accession": "IGVFDS8310XEDQ",
            "aliases": [
                "ali-mortazavi:007_67L_illumina"
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            "file_set_type": "experimental data",
            "status": "released"
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    "input_for": [
        "/analysis-sets/IGVFDS0751LIZC/",
        "/analysis-sets/IGVFDS1666GZSV/",
        "/analysis-sets/IGVFDS5397SEOD/"
    ],
    "lab": {
        "@id": "/labs/ali-mortazavi/",
        "title": "Ali Mortazavi, UCI"
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    "protocols": [
        "https://www.protocols.io/view/evercode-single-index-pcr-5jyl82k9rl2w/v1",
        "https://www.protocols.io/view/protocol-to-isolate-and-fix-nuclei-from-flash-froz-36wgq3e3ylk5/v1",
        "https://www.protocols.io/view/protocol-to-isolate-and-fix-nuclei-from-flash-froz-5qpvo3837v4o/v1",
        "https://www.protocols.io/view/protocol-to-isolate-and-fix-nuclei-from-flash-froz-n92ldm8b8l5b/v2",
        "https://www.protocols.io/view/evercode-wt-mega-v2-2-1-8epv5xxrng1b/v1"
    ],
    "release_timestamp": "2025-04-19T03:24:54.322420+00:00",
    "sample_summary": "Mus musculus multiplexed sample of epididymis, hypothalamus, ovary, oviduct, pituitary gland, testis",
    "samples": [
        {
            "@id": "/multiplexed-samples/IGVFSM5898DEVL/",
            "@type": [
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                "Sample",
                "Item"
            ],
            "accession": "IGVFSM5898DEVL",
            "aliases": [
                "ali-mortazavi:subpool_007_67L"
            ],
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            "classifications": [
                "tissue",
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            "institutional_certificates": [],
            "modifications": [],
            "sample_terms": [
                {
                    "@id": "/sample-terms/UBERON_0000007/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
                        "Item"
                    ],
                    "status": "released",
                    "summary": "pituitary gland",
                    "term_name": "pituitary gland"
                },
                {
                    "@id": "/sample-terms/UBERON_0000473/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
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                    "status": "released",
                    "summary": "testis",
                    "term_name": "testis"
                },
                {
                    "@id": "/sample-terms/UBERON_0000992/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
                        "Item"
                    ],
                    "status": "released",
                    "summary": "ovary",
                    "term_name": "ovary"
                },
                {
                    "@id": "/sample-terms/UBERON_0000993/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
                        "Item"
                    ],
                    "status": "released",
                    "summary": "oviduct",
                    "term_name": "oviduct"
                },
                {
                    "@id": "/sample-terms/UBERON_0001301/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
                        "Item"
                    ],
                    "status": "released",
                    "summary": "epididymis",
                    "term_name": "epididymis"
                },
                {
                    "@id": "/sample-terms/UBERON_0001898/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
                        "Item"
                    ],
                    "status": "released",
                    "summary": "hypothalamus",
                    "term_name": "hypothalamus"
                }
            ],
            "status": "released",
            "summary": "multiplexed sample: Mus musculus NOD/ShiLtJ (female, 72 days) pituitary gland tissue; Mus musculus CAST/EiJ (female, 69 days) pituitary gland tissue; ... and 254 more samples",
            "taxa": "Mus musculus",
            "treatments": []
        }
    ],
    "schema_version": "9",
    "status": "released",
    "submitted_by": {
        "@id": "/users/ebd1025b-e3ab-4e51-bfcd-1415f278281a/",
        "title": "Diane Trout"
    },
    "submitted_files_timestamp": "2025-04-06T22:45:40.254921+00:00",
    "summary": "Parse SPLiT-seq: sparse gene count matrix",
    "uuid": "dc21e110-72c5-41f1-9a72-38d4fbdc4801",
    "workflows": [
        {
            "@id": "/workflows/IGVFWF6241JYDF/",
            "accession": "IGVFWF6241JYDF",
            "name": "UCI snRNA-seq workflow",
            "status": "released"
        }
    ]
}