IGVFDS6138PRFG

released
No limitations
{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS6138PRFG/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS6138PRFG",
    "aliases": [
        "ansuman-satpathy:multiseq_igvf11_10x4"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing publication",
                "detail": "Auxiliary set [IGVFDS6138PRFG](/auxiliary-sets/IGVFDS6138PRFG/) 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": "/auxiliary-sets/IGVFDS6138PRFG/"
            },
            {
                "category": "missing publication",
                "detail": "Multiplexed sample [IGVFSM8200CKYL](/multiplexed-samples/IGVFSM8200CKYL/) 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/IGVFSM8200CKYL/"
            }
        ]
    },
    "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": "2024-07-22T00:31:32.943698+00:00",
    "data_use_limitation_summaries": [
        "No limitations"
    ],
    "donors": [
        {
            "@id": "/human-donors/IGVFDO1756PPKO/",
            "accession": "IGVFDO1756PPKO",
            "aliases": [
                "igvf:donor_of_WTC11"
            ],
            "sex": "male",
            "status": "released",
            "taxa": "Homo sapiens"
        },
        {
            "@id": "/human-donors/IGVFDO7411YYYE/",
            "accession": "IGVFDO7411YYYE",
            "aliases": [
                "igvf:donor_of_h7"
            ],
            "sex": "female",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "file_set_type": "lipid-conjugated oligo sequencing",
    "files": [
        {
            "@id": "/sequence-files/IGVFFI5340XWGU/",
            "accession": "IGVFFI5340XWGU",
            "aliases": [
                "ansuman-satpathy:igvf_exp11_multi_10x4_NGS1_r1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-07-23T00:19:49.841165+00:00",
            "file_format": "fastq",
            "file_size": 5452510250,
            "href": "/sequence-files/IGVFFI5340XWGU/@@download/IGVFFI5340XWGU.fastq.gz",
            "md5sum": "57bef5155b03e89cfc7f9ebf1c9d6ebd",
            "s3_uri": "s3://igvf-files/2024/07/23/5f7e9fc2-fa05-47ea-bfac-2b92c7a7d3f1/IGVFFI5340XWGU.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0022840/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/projects/igvf/Projects/240424_IGVF11_McGinnis/MULTI/FASTQ/MULTI4_S29_L003_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI5726YOUZ/",
            "accession": "IGVFFI5726YOUZ",
            "aliases": [
                "ansuman-satpathy:igvf_exp11_multi_10x4_NGS1_r2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-07-23T00:20:22.608624+00:00",
            "file_format": "fastq",
            "file_size": 4727547966,
            "href": "/sequence-files/IGVFFI5726YOUZ/@@download/IGVFFI5726YOUZ.fastq.gz",
            "md5sum": "17e566163fa482f6f5a0264babbf29f8",
            "s3_uri": "s3://igvf-files/2024/07/23/4c56b1e2-bc05-4f97-8447-80069b3470b8/IGVFFI5726YOUZ.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0022840/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/projects/igvf/Projects/240424_IGVF11_McGinnis/MULTI/FASTQ/MULTI4_S29_L003_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI2837KHGX/",
            "accession": "IGVFFI2837KHGX",
            "aliases": [
                "ansuman-satpathy:igvf_exp11_multi_10x4_NGS1_i1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-07-23T00:19:19.937344+00:00",
            "file_format": "fastq",
            "file_size": 802065554,
            "href": "/sequence-files/IGVFFI2837KHGX/@@download/IGVFFI2837KHGX.fastq.gz",
            "md5sum": "95c9e686e5cff01b1d01ae0a790dc1df",
            "s3_uri": "s3://igvf-files/2024/07/23/8ac11347-fb12-48f7-a205-94c050b55c9d/IGVFFI2837KHGX.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0022840/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/projects/igvf/Projects/240424_IGVF11_McGinnis/MULTI/FASTQ/MULTI4_S29_L003_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI2963SHFI/",
            "accession": "IGVFFI2963SHFI",
            "aliases": [
                "ansuman-satpathy:igvf_exp11_multi_10x4_NGS1_i2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-07-23T00:19:31.306699+00:00",
            "file_format": "fastq",
            "file_size": 776495064,
            "href": "/sequence-files/IGVFFI2963SHFI/@@download/IGVFFI2963SHFI.fastq.gz",
            "md5sum": "bd40164eb949b9341a12f14ca459d5f7",
            "s3_uri": "s3://igvf-files/2024/07/23/bd6c2bca-dcff-4850-9497-862eee5a7908/IGVFFI2963SHFI.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0022840/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/projects/igvf/Projects/240424_IGVF11_McGinnis/MULTI/FASTQ/MULTI4_S29_L003_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI1281EAGG/",
            "accession": "IGVFFI1281EAGG",
            "aliases": [
                "ansuman-satpathy:igvf_exp11_multi_10x4_NGS2_i2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-07-23T00:21:02.093371+00:00",
            "file_format": "fastq",
            "file_size": 772613635,
            "href": "/sequence-files/IGVFFI1281EAGG/@@download/IGVFFI1281EAGG.fastq.gz",
            "md5sum": "bd87ba29fff55072916d22cf78e17fdc",
            "s3_uri": "s3://igvf-files/2024/07/23/7794b409-9d5d-41e7-84aa-f55eeeca8944/IGVFFI1281EAGG.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0022840/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/projects/igvf/Projects/240424_IGVF11_McGinnis/MULTI/FASTQ/MULTI4_S29_L004_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI1407IPAB/",
            "accession": "IGVFFI1407IPAB",
            "aliases": [
                "ansuman-satpathy:igvf_exp11_multi_10x4_NGS2_r2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-07-23T00:21:56.678949+00:00",
            "file_format": "fastq",
            "file_size": 4719485711,
            "href": "/sequence-files/IGVFFI1407IPAB/@@download/IGVFFI1407IPAB.fastq.gz",
            "md5sum": "ae0388c14673cca8a8858b1734356ef4",
            "s3_uri": "s3://igvf-files/2024/07/23/87cbd20d-95da-4046-bc94-b64c24bf54f8/IGVFFI1407IPAB.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0022840/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/projects/igvf/Projects/240424_IGVF11_McGinnis/MULTI/FASTQ/MULTI4_S29_L004_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3127HHFK/",
            "accession": "IGVFFI3127HHFK",
            "aliases": [
                "ansuman-satpathy:igvf_exp11_multi_10x4_NGS2_i1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-07-23T00:20:49.293755+00:00",
            "file_format": "fastq",
            "file_size": 799952047,
            "href": "/sequence-files/IGVFFI3127HHFK/@@download/IGVFFI3127HHFK.fastq.gz",
            "md5sum": "d3b273185627d0985d27686e84089f4c",
            "s3_uri": "s3://igvf-files/2024/07/23/db5b6054-4b39-4a21-b7bf-8cfd9af59b1d/IGVFFI3127HHFK.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0022840/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/projects/igvf/Projects/240424_IGVF11_McGinnis/MULTI/FASTQ/MULTI4_S29_L004_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8158WFRY/",
            "accession": "IGVFFI8158WFRY",
            "aliases": [
                "ansuman-satpathy:igvf_exp11_multi_10x4_NGS2_r1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-07-23T00:21:20.337028+00:00",
            "file_format": "fastq",
            "file_size": 5460795484,
            "href": "/sequence-files/IGVFFI8158WFRY/@@download/IGVFFI8158WFRY.fastq.gz",
            "md5sum": "3ca0bd4ffecd1ad36058b9c6bb043935",
            "s3_uri": "s3://igvf-files/2024/07/23/db120d38-b799-44de-a151-87fb02f45bed/IGVFFI8158WFRY.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0022840/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/projects/igvf/Projects/240424_IGVF11_McGinnis/MULTI/FASTQ/MULTI4_S29_L004_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI8128AZZC/",
            "accession": "IGVFFI8128AZZC",
            "aliases": [
                "ansuman-satpathy:seqspec_igvf_exp11_multi_10x4_NGS2"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-09-18T02:23:42.406586+00:00",
            "file_format": "yaml",
            "file_size": 1332,
            "href": "/configuration-files/IGVFFI8128AZZC/@@download/IGVFFI8128AZZC.yaml.gz",
            "md5sum": "238cc05464711cd56a2600f57b5a2102",
            "s3_uri": "s3://igvf-files/2024/09/18/b2157c94-0c5b-41f9-891c-8ee11d2e7f79/IGVFFI8128AZZC.yaml.gz",
            "status": "released",
            "submitted_file_name": "/home/users/cmcginni/igvf_utils_out/seqspec/igvf_exp11_multi_10x4_NGS2_multi_seqspec.yaml.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI6475XVAD/",
            "accession": "IGVFFI6475XVAD",
            "aliases": [
                "ansuman-satpathy:seqspec_igvf_exp11_multi_10x4_NGS1"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-09-18T02:23:38.913745+00:00",
            "file_format": "yaml",
            "file_size": 1332,
            "href": "/configuration-files/IGVFFI6475XVAD/@@download/IGVFFI6475XVAD.yaml.gz",
            "md5sum": "d32fd6549597f52c2455e658cdfee0a7",
            "s3_uri": "s3://igvf-files/2024/09/18/29359bd4-861b-490a-976e-6e98ba2a2909/IGVFFI6475XVAD.yaml.gz",
            "status": "released",
            "submitted_file_name": "/home/users/cmcginni/igvf_utils_out/seqspec/igvf_exp11_multi_10x4_NGS1_multi_seqspec.yaml.gz",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS6121CBDQ/"
    ],
    "lab": {
        "@id": "/labs/ansuman-satpathy/",
        "title": "Ansuman Satpathy, Stanford"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS6943MGVC/",
            "accession": "IGVFDS6943MGVC",
            "aliases": [
                "ansuman-satpathy:snRNA-seq_igvf11_10x4"
            ],
            "preferred_assay_title": "10x multiome with MULTI-seq",
            "status": "released"
        },
        {
            "@id": "/measurement-sets/IGVFDS1824DNGD/",
            "accession": "IGVFDS1824DNGD",
            "aliases": [
                "ansuman-satpathy:snATAC-seq_igvf11_10x4"
            ],
            "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": "2025-03-07T01:14:21.872604+00:00",
    "samples": [
        {
            "@id": "/multiplexed-samples/IGVFSM8200CKYL/",
            "@type": [
                "MultiplexedSample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM8200CKYL",
            "aliases": [
                "ansuman-satpathy:multiplexed_sample_igvf11_10x4"
            ],
            "classifications": [
                "differentiated cell specimen",
                "multiplexed sample"
            ],
            "disease_terms": [],
            "institutional_certificates": [
                {
                    "@id": "/institutional-certificates/e5598331-9e7c-4bd5-8e7b-64d5a4529006/",
                    "certificate_identifier": "IP115-21",
                    "controlled_access": false,
                    "status": "released"
                },
                {
                    "@id": "/institutional-certificates/f37dfa73-f4f1-4bfe-a312-9eade62d5988/",
                    "certificate_identifier": "IP115-15",
                    "controlled_access": false,
                    "status": "released"
                }
            ],
            "modifications": [],
            "sample_terms": [
                {
                    "@id": "/sample-terms/EFO_0005904/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
                        "Item"
                    ],
                    "aliases": [
                        "igvf:H7-hESC"
                    ],
                    "status": "released",
                    "summary": "H7-hESC",
                    "term_name": "H7-hESC"
                },
                {
                    "@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: Homo sapiens (female) H7-hESC differentiated cell specimen; Homo sapiens (male) GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 6 days; ... 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": "2024-07-23T00:19:19.937344+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": "12976c25-30da-4a2c-ab50-868e118998b3"
}