IGVFDS5027XUOE

released
{
    "@context": "/terms/",
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    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS5027XUOE",
    "aliases": [
        "ansuman-satpathy:multiseq_igvf18_10x2"
    ],
    "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/"
            }
        ]
    },
    "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"
    },
    "barcode_map": "/tabular-files/IGVFFI8343LJPE/",
    "control_for": [],
    "creation_timestamp": "2025-01-27T22:55:22.037487+00:00",
    "donors": [
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            "accession": "IGVFDO4200NZSV",
            "aliases": [
                "igvf:donor_of_IMR90"
            ],
            "sex": "female",
            "status": "released",
            "taxa": "Homo sapiens"
        },
        {
            "@id": "/human-donors/IGVFDO0384OZRW/",
            "accession": "IGVFDO0384OZRW",
            "aliases": [
                "igvf:donor_of_HCT116"
            ],
            "sex": "male",
            "status": "released",
            "taxa": "Homo sapiens"
        },
        {
            "@id": "/human-donors/IGVFDO3459DFTW/",
            "accession": "IGVFDO3459DFTW",
            "aliases": [
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            ],
            "sex": "female",
            "status": "released",
            "taxa": "Homo sapiens"
        },
        {
            "@id": "/human-donors/IGVFDO7503RZHO/",
            "accession": "IGVFDO7503RZHO",
            "aliases": [
                "igvf:donor_of_MCF7"
            ],
            "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/IGVFDO9018OPIO/",
            "accession": "IGVFDO9018OPIO",
            "aliases": [
                "igvf:donor_of_SKNSH"
            ],
            "sex": "female",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "file_set_type": "lipid-conjugated oligo sequencing",
    "files": [
        {
            "@id": "/sequence-files/IGVFFI9582EFDE/",
            "accession": "IGVFFI9582EFDE",
            "aliases": [
                "ansuman-satpathy:igvf_exp18_multi_10x2_NGS1_r2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2025-01-28T04:16:41.502749+00:00",
            "file_format": "fastq",
            "file_size": 495689082,
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            "sequencing_platform": "/platform-terms/EFO_0022840/",
            "status": "released",
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            "upload_status": "validated"
        },
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            "@id": "/sequence-files/IGVFFI7825JGXB/",
            "accession": "IGVFFI7825JGXB",
            "aliases": [
                "ansuman-satpathy:igvf_exp18_multi_10x2_NGS1_i1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2025-01-28T04:16:26.134258+00:00",
            "file_format": "fastq",
            "file_size": 80814172,
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            "sequencing_platform": "/platform-terms/EFO_0022840/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/igvf18/MULTI/IGVF18_MULTI2-CMAS24_S57_L004_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9418YXBX/",
            "accession": "IGVFFI9418YXBX",
            "aliases": [
                "ansuman-satpathy:igvf_exp18_multi_10x2_NGS1_r1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2025-01-28T04:16:33.245306+00:00",
            "file_format": "fastq",
            "file_size": 210142006,
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            "s3_uri": "s3://igvf-files/2025/01/28/c9690962-8644-48f4-82bc-b5767e6ee43e/IGVFFI9418YXBX.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0022840/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/igvf18/MULTI/IGVF18_MULTI2-CMAS24_S57_L004_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI7324IAQV/",
            "accession": "IGVFFI7324IAQV",
            "aliases": [
                "ansuman-satpathy:seqspec_igvf_exp18_multi_10x2_NGS1"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2025-02-26T01:45:23.271650+00:00",
            "file_format": "yaml",
            "file_size": 1336,
            "href": "/configuration-files/IGVFFI7324IAQV/@@download/IGVFFI7324IAQV.yaml.gz",
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            "status": "released",
            "submitted_file_name": "/home/users/cmcginni/igvf_utils_out/seqspec_new/igvf_exp18_multi_10x2_NGS1_multi_seqspec.yaml.gz",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS4963SRAJ/"
    ],
    "lab": {
        "@id": "/labs/ansuman-satpathy/",
        "title": "Ansuman Satpathy, Stanford"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS7744TQIF/",
            "accession": "IGVFDS7744TQIF",
            "aliases": [
                "ansuman-satpathy:snATAC-seq_igvf18_10x2"
            ],
            "preferred_assay_title": "10x multiome with MULTI-seq",
            "status": "released"
        },
        {
            "@id": "/measurement-sets/IGVFDS9859SAHD/",
            "accession": "IGVFDS9859SAHD",
            "aliases": [
                "ansuman-satpathy:snRNA-seq_igvf18_10x2"
            ],
            "preferred_assay_title": "10x multiome with MULTI-seq",
            "status": "released"
        }
    ],
    "release_timestamp": "2025-03-07T01:18:01.047517+00:00",
    "samples": [
        {
            "@id": "/multiplexed-samples/IGVFSM9642EHZY/",
            "@type": [
                "MultiplexedSample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM9642EHZY",
            "aliases": [
                "ansuman-satpathy:multiplexed_sample_igvf18_10x2"
            ],
            "cellular_sub_pool": "2",
            "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": "12",
    "status": "released",
    "submitted_by": {
        "@id": "/users/353655bc-31a1-4cd9-bac3-c7d34faf722f/",
        "title": "Christopher Mcginnis"
    },
    "submitted_files_timestamp": "2025-01-28T04:16:26.134258+00:00",
    "summary": "lipid-conjugated oligo sequencing for single-nucleus ATAC-seq (10x multiome with MULTI-seq), single-nucleus RNA sequencing assay (10x multiome with MULTI-seq)",
    "uuid": "64c614be-5540-4f95-90d5-c8e5c9a687c5"
}