IGVFDS7744TQIF

released
{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS7744TQIF/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS7744TQIF",
    "aliases": [
        "ansuman-satpathy:snATAC-seq_igvf18_10x2"
    ],
    "assay_term": {
        "@id": "/assay-terms/OBI_0002762/",
        "assay_slims": [
            "chromatin accessibility"
        ],
        "status": "released",
        "term_name": "single-nucleus ATAC-seq"
    },
    "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/IGVFDS5027XUOE/",
            "accession": "IGVFDS5027XUOE",
            "aliases": [
                "ansuman-satpathy:multiseq_igvf18_10x2"
            ],
            "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": "2025-01-27T22:55:49.255106+00:00",
    "donors": [
        {
            "@id": "/human-donors/IGVFDO4200NZSV/",
            "accession": "IGVFDO4200NZSV",
            "aliases": [
                "igvf:donor_of_IMR90"
            ],
            "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/IGVFDO3459DFTW/",
            "accession": "IGVFDO3459DFTW",
            "aliases": [
                "igvf:donor_of_teloHAEC"
            ],
            "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/IGVFDO0384OZRW/",
            "accession": "IGVFDO0384OZRW",
            "aliases": [
                "igvf:donor_of_HCT116"
            ],
            "sex": "male",
            "status": "released",
            "taxa": "Homo sapiens"
        },
        {
            "@id": "/human-donors/IGVFDO9018OPIO/",
            "accession": "IGVFDO9018OPIO",
            "aliases": [
                "igvf:donor_of_SKNSH"
            ],
            "sex": "female",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "externally_hosted": false,
    "file_set_type": "experimental data",
    "files": [
        {
            "@id": "/sequence-files/IGVFFI8408YXMK/",
            "accession": "IGVFFI8408YXMK",
            "aliases": [
                "ansuman-satpathy:igvf_exp18_atac_10x2_NGS1_r1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2025-01-28T03:50:17.072741+00:00",
            "file_format": "fastq",
            "file_size": 25368222299,
            "href": "/sequence-files/IGVFFI8408YXMK/@@download/IGVFFI8408YXMK.fastq.gz",
            "s3_uri": "s3://igvf-files/2025/01/28/97ba7196-cd80-4121-a5f4-c090a3fcb0ba/IGVFFI8408YXMK.fastq.gz",
            "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/ATAC/ATAC2-CMAS23A_S34_L006_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI1280ZQJU/",
            "accession": "IGVFFI1280ZQJU",
            "aliases": [
                "ansuman-satpathy:igvf_exp18_atac_10x2_NGS1_r3"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2025-01-28T04:00:41.785160+00:00",
            "file_format": "fastq",
            "file_size": 25349069593,
            "href": "/sequence-files/IGVFFI1280ZQJU/@@download/IGVFFI1280ZQJU.fastq.gz",
            "s3_uri": "s3://igvf-files/2025/01/28/008e1282-5554-4bf5-bdca-d915833f6c5f/IGVFFI1280ZQJU.fastq.gz",
            "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/ATAC/ATAC2-CMAS23A_S34_L006_R3_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI6337LBXU/",
            "accession": "IGVFFI6337LBXU",
            "aliases": [
                "ansuman-satpathy:igvf_exp18_atac_10x2_NGS1_i1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2025-01-28T03:49:07.123154+00:00",
            "file_format": "fastq",
            "file_size": 6421696010,
            "href": "/sequence-files/IGVFFI6337LBXU/@@download/IGVFFI6337LBXU.fastq.gz",
            "s3_uri": "s3://igvf-files/2025/01/28/51a0ff77-45b4-46cf-aeef-4e30d98daeba/IGVFFI6337LBXU.fastq.gz",
            "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/ATAC/ATAC2-CMAS23A_S34_L006_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI0241PHEX/",
            "accession": "IGVFFI0241PHEX",
            "aliases": [
                "ansuman-satpathy:igvf_exp18_atac_10x2_NGS1_r2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2025-01-28T03:52:11.134322+00:00",
            "file_format": "fastq",
            "file_size": 14521059693,
            "href": "/sequence-files/IGVFFI0241PHEX/@@download/IGVFFI0241PHEX.fastq.gz",
            "s3_uri": "s3://igvf-files/2025/01/28/446fcb20-0244-4b40-a6aa-2a7682c9c15d/IGVFFI0241PHEX.fastq.gz",
            "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/ATAC/ATAC2-CMAS23A_S34_L006_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI2154CUWA/",
            "accession": "IGVFFI2154CUWA",
            "aliases": [
                "ansuman-satpathy:seqspec_igvf_exp18_atac_10x2_NGS1"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2025-02-26T01:45:06.644619+00:00",
            "file_format": "yaml",
            "file_size": 1377,
            "href": "/configuration-files/IGVFFI2154CUWA/@@download/IGVFFI2154CUWA.yaml.gz",
            "s3_uri": "s3://igvf-files/2025/02/26/19b7039b-42c7-4a4c-b31c-3c4e3ecbea3f/IGVFFI2154CUWA.yaml.gz",
            "status": "released",
            "submitted_file_name": "/home/users/cmcginni/igvf_utils_out/seqspec_new/igvf_exp18_atac_10x2_NGS1_atac_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/IGVFFI7587TJLC/"
    ],
    "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/IGVFDS9859SAHD/",
            "accession": "IGVFDS9859SAHD",
            "status": "released"
        }
    ],
    "release_timestamp": "2025-03-07T01:18:00.830214+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": "25",
    "status": "released",
    "submitted_by": {
        "@id": "/users/353655bc-31a1-4cd9-bac3-c7d34faf722f/",
        "title": "Christopher Mcginnis"
    },
    "submitted_files_timestamp": "2025-01-28T03:49:07.123154+00:00",
    "summary": "single-nucleus ATAC-seq (10x multiome with MULTI-seq)",
    "uuid": "06de6e7a-420b-4028-ad2e-7bd03fb20e39"
}