IGVFDS5693MIIK

released
{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS5693MIIK/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS5693MIIK",
    "aliases": [
        "ansuman-satpathy:multiseq_igvf3_10x3"
    ],
    "audit": {},
    "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": "2024-07-21T23:09:27.643587+00:00",
    "donors": [
        {
            "@id": "/human-donors/IGVFDO1756PPKO/",
            "accession": "IGVFDO1756PPKO",
            "aliases": [
                "igvf:donor_of_WTC11"
            ],
            "sex": "male",
            "status": "released",
            "taxa": "Homo sapiens"
        },
        {
            "@id": "/human-donors/IGVFDO2837BRET/",
            "accession": "IGVFDO2837BRET",
            "aliases": [
                "igvf:donor_of_HepG2"
            ],
            "sex": "male",
            "status": "released",
            "taxa": "Homo sapiens"
        },
        {
            "@id": "/human-donors/IGVFDO2718IDDQ/",
            "accession": "IGVFDO2718IDDQ",
            "aliases": [
                "igvf:donor_of_H9"
            ],
            "sex": "female",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "file_set_type": "lipid-conjugated oligo sequencing",
    "files": [
        {
            "@id": "/sequence-files/IGVFFI5757PBNP/",
            "accession": "IGVFFI5757PBNP",
            "aliases": [
                "ansuman-satpathy:igvf_exp3_multi_10x3_NGS1_r1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-07-21T23:30:22.798203+00:00",
            "file_format": "fastq",
            "file_size": 446959168,
            "href": "/sequence-files/IGVFFI5757PBNP/@@download/IGVFFI5757PBNP.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/07/21/2dd0193b-115b-4487-997b-d8134ddbbdc7/IGVFFI5757PBNP.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0022840/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/projects/igvf/Projects/230522_IGVF3_McGinnis/MULTI/FASTQ/MULTI_3_S7_L001_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI6977YZQX/",
            "accession": "IGVFFI6977YZQX",
            "aliases": [
                "ansuman-satpathy:igvf_exp3_multi_10x3_NGS1_i1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-07-21T23:30:42.445207+00:00",
            "file_format": "fastq",
            "file_size": 157668904,
            "href": "/sequence-files/IGVFFI6977YZQX/@@download/IGVFFI6977YZQX.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/07/21/81e752b0-5e58-460b-8ffc-97fc2ea0ef0d/IGVFFI6977YZQX.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0022840/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/projects/igvf/Projects/230522_IGVF3_McGinnis/MULTI/FASTQ/MULTI_3_S7_L001_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8269CDPO/",
            "accession": "IGVFFI8269CDPO",
            "aliases": [
                "ansuman-satpathy:igvf_exp3_multi_10x3_NGS2_i2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-07-21T23:31:29.533964+00:00",
            "file_format": "fastq",
            "file_size": 131256371,
            "href": "/sequence-files/IGVFFI8269CDPO/@@download/IGVFFI8269CDPO.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/07/21/33c3e872-5062-4a30-ab10-0a277ba14bbc/IGVFFI8269CDPO.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0022840/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/projects/igvf/Projects/230522_IGVF3_McGinnis/MULTI/FASTQ/MULTI_3_S7_L002_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3444BGRW/",
            "accession": "IGVFFI3444BGRW",
            "aliases": [
                "ansuman-satpathy:igvf_exp3_multi_10x3_NGS1_i2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-07-21T23:30:49.719600+00:00",
            "file_format": "fastq",
            "file_size": 128294148,
            "href": "/sequence-files/IGVFFI3444BGRW/@@download/IGVFFI3444BGRW.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/07/21/3474f3d1-18f4-493d-bc78-6b04b466d1c0/IGVFFI3444BGRW.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0022840/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/projects/igvf/Projects/230522_IGVF3_McGinnis/MULTI/FASTQ/MULTI_3_S7_L001_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI2104IMMZ/",
            "accession": "IGVFFI2104IMMZ",
            "aliases": [
                "ansuman-satpathy:igvf_exp3_multi_10x3_NGS2_i1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-07-21T23:31:23.069069+00:00",
            "file_format": "fastq",
            "file_size": 162639542,
            "href": "/sequence-files/IGVFFI2104IMMZ/@@download/IGVFFI2104IMMZ.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/07/21/38b8f20f-8ca6-4ebf-8053-f8cdb7bc5860/IGVFFI2104IMMZ.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0022840/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/projects/igvf/Projects/230522_IGVF3_McGinnis/MULTI/FASTQ/MULTI_3_S7_L002_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI0364NODZ/",
            "accession": "IGVFFI0364NODZ",
            "aliases": [
                "ansuman-satpathy:igvf_exp3_multi_10x3_NGS1_r2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-07-21T23:30:31.466887+00:00",
            "file_format": "fastq",
            "file_size": 998762766,
            "href": "/sequence-files/IGVFFI0364NODZ/@@download/IGVFFI0364NODZ.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/07/21/596f2d34-ed0b-40f1-ab8f-cc30447d32d3/IGVFFI0364NODZ.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0022840/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/projects/igvf/Projects/230522_IGVF3_McGinnis/MULTI/FASTQ/MULTI_3_S7_L001_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI7556SAMI/",
            "accession": "IGVFFI7556SAMI",
            "aliases": [
                "ansuman-satpathy:igvf_exp3_multi_10x3_NGS2_r1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-07-21T23:30:58.339410+00:00",
            "file_format": "fastq",
            "file_size": 453312004,
            "href": "/sequence-files/IGVFFI7556SAMI/@@download/IGVFFI7556SAMI.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/07/21/c62ef0b8-0a36-4d88-a733-d87a43b39193/IGVFFI7556SAMI.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0022840/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/projects/igvf/Projects/230522_IGVF3_McGinnis/MULTI/FASTQ/MULTI_3_S7_L002_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9921FXJW/",
            "accession": "IGVFFI9921FXJW",
            "aliases": [
                "ansuman-satpathy:igvf_exp3_multi_10x3_NGS2_r2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-07-21T23:31:09.976323+00:00",
            "file_format": "fastq",
            "file_size": 1013915552,
            "href": "/sequence-files/IGVFFI9921FXJW/@@download/IGVFFI9921FXJW.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/07/21/64cb69b9-1a47-40d7-b691-6363aa3940e0/IGVFFI9921FXJW.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0022840/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/projects/igvf/Projects/230522_IGVF3_McGinnis/MULTI/FASTQ/MULTI_3_S7_L002_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI8531NIMX/",
            "accession": "IGVFFI8531NIMX",
            "aliases": [
                "ansuman-satpathy:seqspec_igvf_exp3_multi_10x3_NGS1"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-09-18T02:36:43.987441+00:00",
            "file_format": "yaml",
            "file_size": 1337,
            "href": "/configuration-files/IGVFFI8531NIMX/@@download/IGVFFI8531NIMX.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/09/18/39c6d243-881a-4cf6-b972-7e5a6d8f1a6f/IGVFFI8531NIMX.yaml.gz",
            "status": "released",
            "submitted_file_name": "/home/users/cmcginni/igvf_utils_out/seqspec/igvf_exp3_multi_10x3_NGS1_multi_seqspec.yaml.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI2745VPQH/",
            "accession": "IGVFFI2745VPQH",
            "aliases": [
                "ansuman-satpathy:seqspec_igvf_exp3_multi_10x3_NGS2"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-09-18T02:36:47.680516+00:00",
            "file_format": "yaml",
            "file_size": 1337,
            "href": "/configuration-files/IGVFFI2745VPQH/@@download/IGVFFI2745VPQH.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/09/18/a3e1c597-1ca3-4216-a146-d1bf6f5af8cd/IGVFFI2745VPQH.yaml.gz",
            "status": "released",
            "submitted_file_name": "/home/users/cmcginni/igvf_utils_out/seqspec/igvf_exp3_multi_10x3_NGS2_multi_seqspec.yaml.gz",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS9170BNTS/"
    ],
    "lab": {
        "@id": "/labs/ansuman-satpathy/",
        "title": "Ansuman Satpathy, Stanford"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS1983YORK/",
            "accession": "IGVFDS1983YORK",
            "aliases": [
                "ansuman-satpathy:snRNA-seq_igvf3_10x3"
            ],
            "preferred_assay_title": "10x multiome with MULTI-seq",
            "status": "released"
        },
        {
            "@id": "/measurement-sets/IGVFDS1843ABDU/",
            "accession": "IGVFDS1843ABDU",
            "aliases": [
                "ansuman-satpathy:snATAC-seq_igvf3_10x3"
            ],
            "preferred_assay_title": "10x multiome with MULTI-seq",
            "status": "released"
        }
    ],
    "notes": "File_set_type enum oligo-conjugated lipids has been renamed to be lipid-conjugated oligo sequencing.",
    "release_timestamp": "2025-03-07T01:10:59.846332+00:00",
    "samples": [
        {
            "@id": "/multiplexed-samples/IGVFSM7454SJSO/",
            "@type": [
                "MultiplexedSample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM7454SJSO",
            "aliases": [
                "ansuman-satpathy:multiplexed_sample_igvf3_10x3"
            ],
            "classifications": [
                "cell line",
                "differentiated cell specimen",
                "multiplexed sample"
            ],
            "disease_terms": [],
            "institutional_certificates": [],
            "modifications": [],
            "sample_terms": [
                {
                    "@id": "/sample-terms/EFO_0001187/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
                        "Item"
                    ],
                    "aliases": [
                        "igvf:HepG2"
                    ],
                    "status": "released",
                    "summary": "HepG2",
                    "term_name": "HepG2"
                },
                {
                    "@id": "/sample-terms/EFO_0003045/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
                        "Item"
                    ],
                    "aliases": [
                        "igvf:H9"
                    ],
                    "status": "released",
                    "summary": "H9",
                    "term_name": "H9"
                },
                {
                    "@id": "/sample-terms/EFO_0009747/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
                        "Item"
                    ],
                    "aliases": [
                        "igvf:WTC11"
                    ],
                    "status": "released",
                    "summary": "GM25256 (WTC-11)",
                    "term_name": "GM25256 (WTC-11)"
                }
            ],
            "status": "released",
            "summary": "multiplexed sample: H9 differentiated cell specimen induced to cardiac muscle cell for 15 days, female, Homo sapiens; HepG2 cell line, male, Homo sapiens grown in DMEM without serum; ... and 10 more samples",
            "taxa": "Homo sapiens",
            "treatments": []
        }
    ],
    "schema_version": "12",
    "status": "released",
    "submitted_by": {
        "@id": "/users/353655bc-31a1-4cd9-bac3-c7d34faf722f/",
        "title": "Christopher Mcginnis"
    },
    "submitted_files_timestamp": "2024-07-21T23:30:22.798203+00:00",
    "summary": "lipid-conjugated oligo sequencing for single-nucleus RNA sequencing assay (10x multiome with MULTI-seq), single-nucleus ATAC-seq (10x multiome with MULTI-seq)",
    "uuid": "ec11051e-6af1-48f6-82fc-49eb18e1a494"
}