IGVFDS6943MGVC

released
{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS6943MGVC/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS6943MGVC",
    "aliases": [
        "ansuman-satpathy:snRNA-seq_igvf11_10x4"
    ],
    "assay_term": {
        "@id": "/assay-terms/OBI_0003109/",
        "assay_slims": [
            "gene expression"
        ],
        "status": "released",
        "term_name": "single-nucleus RNA sequencing assay"
    },
    "audit": {},
    "auxiliary_sets": [
        {
            "@id": "/auxiliary-sets/IGVFDS6138PRFG/",
            "accession": "IGVFDS6138PRFG",
            "aliases": [
                "ansuman-satpathy:multiseq_igvf11_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": "2024-07-22T00:32:07.938285+00:00",
    "donors": [
        {
            "@id": "/human-donors/IGVFDO7411YYYE/",
            "accession": "IGVFDO7411YYYE",
            "aliases": [
                "igvf:donor_of_h7"
            ],
            "sex": "female",
            "status": "released",
            "taxa": "Homo sapiens"
        },
        {
            "@id": "/human-donors/IGVFDO1756PPKO/",
            "accession": "IGVFDO1756PPKO",
            "aliases": [
                "igvf:donor_of_WTC11"
            ],
            "sex": "male",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "externally_hosted": false,
    "file_set_type": "experimental data",
    "files": [
        {
            "@id": "/sequence-files/IGVFFI5653UGYL/",
            "accession": "IGVFFI5653UGYL",
            "aliases": [
                "ansuman-satpathy:igvf_exp11_rna_10x4_NGS1_i1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-07-22T21:21:16.253060+00:00",
            "file_format": "fastq",
            "file_size": 3056482242,
            "href": "/sequence-files/IGVFFI5653UGYL/@@download/IGVFFI5653UGYL.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/07/22/06d62ad0-ac61-42fa-9ef4-acf39ee9dab8/IGVFFI5653UGYL.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0022840/",
                "status": "released",
                "term_name": "Illumina NovaSeq X"
            },
            "status": "released",
            "submitted_file_name": "/oak/stanford/projects/igvf/Projects/240424_IGVF11_McGinnis/GEX/FASTQ/GEX4_S25_L003_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI2989EVRF/",
            "accession": "IGVFFI2989EVRF",
            "aliases": [
                "ansuman-satpathy:igvf_exp11_rna_10x4_NGS1_i2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-07-22T21:21:41.461432+00:00",
            "file_format": "fastq",
            "file_size": 3490244157,
            "href": "/sequence-files/IGVFFI2989EVRF/@@download/IGVFFI2989EVRF.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/07/22/a133fe42-2bbb-4b99-b0a9-917ab8fff452/IGVFFI2989EVRF.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0022840/",
                "status": "released",
                "term_name": "Illumina NovaSeq X"
            },
            "status": "released",
            "submitted_file_name": "/oak/stanford/projects/igvf/Projects/240424_IGVF11_McGinnis/GEX/FASTQ/GEX4_S25_L003_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI2470GRMJ/",
            "accession": "IGVFFI2470GRMJ",
            "aliases": [
                "ansuman-satpathy:igvf_exp11_rna_10x4_NGS2_r2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-07-23T00:06:10.143624+00:00",
            "file_format": "fastq",
            "file_size": 31890341553,
            "href": "/sequence-files/IGVFFI2470GRMJ/@@download/IGVFFI2470GRMJ.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/07/23/8942e34b-60fe-4f8e-8f93-8906c5f3c49b/IGVFFI2470GRMJ.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0022840/",
                "status": "released",
                "term_name": "Illumina NovaSeq X"
            },
            "status": "released",
            "submitted_file_name": "/oak/stanford/projects/igvf/Projects/240424_IGVF11_McGinnis/GEX/FASTQ/GEX4_S25_L004_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI0985MPWL/",
            "accession": "IGVFFI0985MPWL",
            "aliases": [
                "ansuman-satpathy:igvf_exp11_rna_10x4_NGS2_r1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-07-23T00:02:54.616549+00:00",
            "file_format": "fastq",
            "file_size": 37148097240,
            "href": "/sequence-files/IGVFFI0985MPWL/@@download/IGVFFI0985MPWL.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/07/23/5a22daa5-7a55-4f57-9dac-2169ac6cf0d5/IGVFFI0985MPWL.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0022840/",
                "status": "released",
                "term_name": "Illumina NovaSeq X"
            },
            "status": "released",
            "submitted_file_name": "/oak/stanford/projects/igvf/Projects/240424_IGVF11_McGinnis/GEX/FASTQ/GEX4_S25_L004_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3153SRRQ/",
            "accession": "IGVFFI3153SRRQ",
            "aliases": [
                "ansuman-satpathy:igvf_exp11_rna_10x4_NGS2_i2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-07-23T00:01:31.992708+00:00",
            "file_format": "fastq",
            "file_size": 3442653721,
            "href": "/sequence-files/IGVFFI3153SRRQ/@@download/IGVFFI3153SRRQ.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/07/23/517fc43f-4101-4e1a-a443-4aa311e6ffc3/IGVFFI3153SRRQ.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0022840/",
                "status": "released",
                "term_name": "Illumina NovaSeq X"
            },
            "status": "released",
            "submitted_file_name": "/oak/stanford/projects/igvf/Projects/240424_IGVF11_McGinnis/GEX/FASTQ/GEX4_S25_L004_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI0807IMSL/",
            "accession": "IGVFFI0807IMSL",
            "aliases": [
                "ansuman-satpathy:igvf_exp11_rna_10x4_NGS1_r1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-07-22T23:55:56.524006+00:00",
            "file_format": "fastq",
            "file_size": 36885509491,
            "href": "/sequence-files/IGVFFI0807IMSL/@@download/IGVFFI0807IMSL.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/07/22/2abe8bf1-960e-4ac1-8f85-a52c4eb4d476/IGVFFI0807IMSL.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0022840/",
                "status": "released",
                "term_name": "Illumina NovaSeq X"
            },
            "status": "released",
            "submitted_file_name": "/oak/stanford/projects/igvf/Projects/240424_IGVF11_McGinnis/GEX/FASTQ/GEX4_S25_L003_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI2029TAMT/",
            "accession": "IGVFFI2029TAMT",
            "aliases": [
                "ansuman-satpathy:igvf_exp11_rna_10x4_NGS1_r2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-07-22T23:59:02.133131+00:00",
            "file_format": "fastq",
            "file_size": 31783319466,
            "href": "/sequence-files/IGVFFI2029TAMT/@@download/IGVFFI2029TAMT.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/07/22/9572b903-9e56-4bc2-acdd-bf1f85a66f76/IGVFFI2029TAMT.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0022840/",
                "status": "released",
                "term_name": "Illumina NovaSeq X"
            },
            "status": "released",
            "submitted_file_name": "/oak/stanford/projects/igvf/Projects/240424_IGVF11_McGinnis/GEX/FASTQ/GEX4_S25_L003_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI6001CIBT/",
            "accession": "IGVFFI6001CIBT",
            "aliases": [
                "ansuman-satpathy:igvf_exp11_rna_10x4_NGS2_i1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-07-23T00:01:08.839741+00:00",
            "file_format": "fastq",
            "file_size": 3055921825,
            "href": "/sequence-files/IGVFFI6001CIBT/@@download/IGVFFI6001CIBT.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/07/23/5918b35b-f5b6-4bdc-af15-7582b8970838/IGVFFI6001CIBT.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0022840/",
                "status": "released",
                "term_name": "Illumina NovaSeq X"
            },
            "status": "released",
            "submitted_file_name": "/oak/stanford/projects/igvf/Projects/240424_IGVF11_McGinnis/GEX/FASTQ/GEX4_S25_L004_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI7422YTYA/",
            "accession": "IGVFFI7422YTYA",
            "aliases": [
                "ansuman-satpathy:seqspec_igvf_exp11_rna_10x4_NGS2"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-09-18T02:24:10.871544+00:00",
            "file_format": "yaml",
            "file_size": 1391,
            "href": "/configuration-files/IGVFFI7422YTYA/@@download/IGVFFI7422YTYA.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/09/18/63053962-b8f0-4b71-a845-b9b1513cdb44/IGVFFI7422YTYA.yaml.gz",
            "status": "released",
            "submitted_file_name": "/home/users/cmcginni/igvf_utils_out/seqspec/igvf_exp11_rna_10x4_NGS2_rna_seqspec.yaml.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI9810ZIQO/",
            "accession": "IGVFFI9810ZIQO",
            "aliases": [
                "ansuman-satpathy:seqspec_igvf_exp11_rna_10x4_NGS1"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-09-18T02:24:06.942882+00:00",
            "file_format": "yaml",
            "file_size": 1387,
            "href": "/configuration-files/IGVFFI9810ZIQO/@@download/IGVFFI9810ZIQO.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/09/18/ffb3e263-a107-451c-b322-60f18d1bc7e1/IGVFFI9810ZIQO.yaml.gz",
            "status": "released",
            "submitted_file_name": "/home/users/cmcginni/igvf_utils_out/seqspec/igvf_exp11_rna_10x4_NGS1_rna_seqspec.yaml.gz",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS8136ENRY/"
    ],
    "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/IGVFDS1824DNGD/",
            "accession": "IGVFDS1824DNGD",
            "status": "released"
        }
    ],
    "release_timestamp": "2025-03-07T01:14:44.284406+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": [],
            "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: H7-hESC differentiated cell specimen, female, Homo sapiens; GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 6 days, male, Homo sapiens; ... and 10 more samples",
            "taxa": "Homo sapiens",
            "treatments": []
        }
    ],
    "schema_version": "25",
    "status": "released",
    "submitted_by": {
        "@id": "/users/353655bc-31a1-4cd9-bac3-c7d34faf722f/",
        "title": "Christopher Mcginnis"
    },
    "submitted_files_timestamp": "2024-07-22T21:21:16.253060+00:00",
    "summary": "single-nucleus RNA sequencing assay (10x multiome with MULTI-seq)",
    "uuid": "73a1cc9a-a69d-4be0-871d-017405642bf1"
}