IGVFDS4170WANT

released
{
    "@context": "/terms/",
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    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS4170WANT",
    "aliases": [
        "ansuman-satpathy:snRNA-seq_igvf18_10x4"
    ],
    "assay_term": {
        "@id": "/assay-terms/OBI_0003109/",
        "assay_slims": [
            "gene expression"
        ],
        "status": "released",
        "term_name": "single-nucleus RNA sequencing assay"
    },
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "NTR term ID",
                "detail": "Sample term for [NTR_0000753](/sample-terms/NTR_0000753/) has been newly requested. Ontology terms with a newly requested term ID are expected to have it updated following its addition to the appropriate ontology database.",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_ntr_term_id",
                "path": "/sample-terms/NTR_0000753/"
            }
        ]
    },
    "auxiliary_sets": [
        {
            "@id": "/auxiliary-sets/IGVFDS6039YTCL/",
            "accession": "IGVFDS6039YTCL",
            "aliases": [
                "ansuman-satpathy:multiseq_igvf18_10x4"
            ],
            "file_set_type": "lipid-conjugated oligo sequencing",
            "status": "released"
        }
    ],
    "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": [],
    "creation_timestamp": "2025-01-27T22:55:50.847170+00:00",
    "donors": [
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            ],
            "sex": "female",
            "status": "released",
            "taxa": "Homo sapiens"
        },
        {
            "@id": "/human-donors/IGVFDO4200NZSV/",
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                "igvf:donor_of_IMR90"
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            "sex": "female",
            "status": "released",
            "taxa": "Homo sapiens"
        },
        {
            "@id": "/human-donors/IGVFDO9018OPIO/",
            "accession": "IGVFDO9018OPIO",
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                "igvf:donor_of_SKNSH"
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            "sex": "female",
            "status": "released",
            "taxa": "Homo sapiens"
        },
        {
            "@id": "/human-donors/IGVFDO0965QSBA/",
            "accession": "IGVFDO0965QSBA",
            "aliases": [
                "igvf:donor_of_HUDEP-2"
            ],
            "sex": "unspecified",
            "status": "released",
            "taxa": "Homo sapiens"
        },
        {
            "@id": "/human-donors/IGVFDO0384OZRW/",
            "accession": "IGVFDO0384OZRW",
            "aliases": [
                "igvf:donor_of_HCT116"
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            "sex": "male",
            "status": "released",
            "taxa": "Homo sapiens"
        },
        {
            "@id": "/human-donors/IGVFDO7503RZHO/",
            "accession": "IGVFDO7503RZHO",
            "aliases": [
                "igvf:donor_of_MCF7"
            ],
            "sex": "female",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "externally_hosted": false,
    "file_set_type": "experimental data",
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            "@id": "/sequence-files/IGVFFI0726OIUU/",
            "accession": "IGVFFI0726OIUU",
            "aliases": [
                "ansuman-satpathy:igvf_exp18_rna_10x4_NGS1_i1"
            ],
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            "controlled_access": false,
            "creation_timestamp": "2025-01-28T03:20:59.378633+00:00",
            "file_format": "fastq",
            "file_size": 7991937474,
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                "status": "released",
                "term_name": "Illumina NovaSeq X"
            },
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            "submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/igvf18/GEX/GEX4-CMAS23R_S28_L005_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI0348NYEX/",
            "accession": "IGVFFI0348NYEX",
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                "ansuman-satpathy:igvf_exp18_rna_10x4_NGS1_i2"
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            "creation_timestamp": "2025-01-28T03:21:57.262594+00:00",
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                "term_name": "Illumina NovaSeq X"
            },
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            "upload_status": "validated"
        },
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            "@id": "/sequence-files/IGVFFI9095DTVE/",
            "accession": "IGVFFI9095DTVE",
            "aliases": [
                "ansuman-satpathy:igvf_exp18_rna_10x4_NGS1_r2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2025-01-28T03:36:58.044393+00:00",
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                "status": "released",
                "term_name": "Illumina NovaSeq X"
            },
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            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI4339WSEZ/",
            "accession": "IGVFFI4339WSEZ",
            "aliases": [
                "ansuman-satpathy:igvf_exp18_rna_10x4_NGS1_r1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2025-01-28T03:26:13.808936+00:00",
            "file_format": "fastq",
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            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0022840/",
                "status": "released",
                "term_name": "Illumina NovaSeq X"
            },
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/igvf18/GEX/GEX4-CMAS23R_S28_L005_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI6118CRVV/",
            "accession": "IGVFFI6118CRVV",
            "aliases": [
                "ansuman-satpathy:seqspec_igvf_exp18_rna_10x4_NGS1"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2025-02-26T01:45:49.253062+00:00",
            "file_format": "yaml",
            "file_size": 1397,
            "href": "/configuration-files/IGVFFI6118CRVV/@@download/IGVFFI6118CRVV.yaml.gz",
            "s3_uri": "s3://igvf-files/2025/02/26/91cd625c-4a44-41d8-920b-6f133920d88b/IGVFFI6118CRVV.yaml.gz",
            "status": "released",
            "submitted_file_name": "/home/users/cmcginni/igvf_utils_out/seqspec_new/igvf_exp18_rna_10x4_NGS1_rna_seqspec.yaml.gz",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS4963SRAJ/"
    ],
    "lab": {
        "@id": "/labs/ansuman-satpathy/",
        "title": "Ansuman Satpathy, Stanford"
    },
    "multiome_size": 2,
    "onlist_files": [
        "/tabular-files/IGVFFI8751YQRY/"
    ],
    "onlist_method": "no combination",
    "preferred_assay_title": "10x multiome with MULTI-seq",
    "protocols": [
        "https://www.protocols.io/view/multi-seq-for-multiome-igvf-round-2-experiment-1-dfqp3mvn"
    ],
    "related_multiome_datasets": [
        {
            "@id": "/measurement-sets/IGVFDS9305YTYU/",
            "accession": "IGVFDS9305YTYU",
            "status": "released"
        }
    ],
    "release_timestamp": "2025-03-07T01:18:26.697674+00:00",
    "samples": [
        {
            "@id": "/multiplexed-samples/IGVFSM3125MLLP/",
            "@type": [
                "MultiplexedSample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM3125MLLP",
            "aliases": [
                "ansuman-satpathy:multiplexed_sample_igvf18_10x4"
            ],
            "cellular_sub_pool": "4",
            "classifications": [
                "cell line",
                "differentiated cell specimen",
                "multiplexed sample"
            ],
            "disease_terms": [],
            "institutional_certificates": [],
            "modifications": [],
            "sample_terms": [
                {
                    "@id": "/sample-terms/EFO_0001196/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
                        "Item"
                    ],
                    "status": "released",
                    "summary": "IMR-90",
                    "term_name": "IMR-90"
                },
                {
                    "@id": "/sample-terms/EFO_0001203/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
                        "Item"
                    ],
                    "status": "released",
                    "summary": "MCF-7",
                    "term_name": "MCF-7"
                },
                {
                    "@id": "/sample-terms/EFO_0002824/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
                        "Item"
                    ],
                    "aliases": [
                        "igvf:HCT116"
                    ],
                    "status": "released",
                    "summary": "HCT116",
                    "term_name": "HCT116"
                },
                {
                    "@id": "/sample-terms/EFO_0003072/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
                        "Item"
                    ],
                    "aliases": [
                        "igvf:SK-N-SH"
                    ],
                    "status": "released",
                    "summary": "SK-N-SH",
                    "term_name": "SK-N-SH"
                },
                {
                    "@id": "/sample-terms/EFO_0022838/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
                        "Item"
                    ],
                    "aliases": [
                        "igvf:HUDEP-2"
                    ],
                    "status": "released",
                    "summary": "HUDEP-2",
                    "term_name": "HUDEP-2"
                },
                {
                    "@id": "/sample-terms/NTR_0000753/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
                        "Item"
                    ],
                    "aliases": [
                        "igvf:TeloHAEC"
                    ],
                    "status": "released",
                    "summary": "TeloHAEC",
                    "term_name": "TeloHAEC"
                }
            ],
            "status": "released",
            "summary": "multiplexed sample: IMR-90 cell line, female, Homo sapiens; MCF-7 cell line, female, Homo sapiens; ... and 17 more samples",
            "taxa": "Homo sapiens",
            "treatments": [
                {
                    "@id": "/treatments/ff03c6ff-c1f5-4b47-bd9d-62f22d5794c5/",
                    "purpose": "perturbation",
                    "status": "in progress",
                    "summary": "Treatment of 3 μM Yoda1 for 4 hours",
                    "treatment_type": "chemical"
                }
            ]
        }
    ],
    "schema_version": "25",
    "status": "released",
    "submitted_by": {
        "@id": "/users/353655bc-31a1-4cd9-bac3-c7d34faf722f/",
        "title": "Christopher Mcginnis"
    },
    "submitted_files_timestamp": "2025-01-28T03:20:59.378633+00:00",
    "summary": "single-nucleus RNA sequencing assay (10x multiome with MULTI-seq)",
    "uuid": "54bcd272-0765-4ae6-a7ca-88749136586b"
}