IGVFDS0078EAAP

released
{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS0078EAAP/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS0078EAAP",
    "aliases": [
        "jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF2-BinF-PCR1_S66",
        "jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF2-BinF-PCR2_S72",
        "jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF2-BinF-PCR3_S162",
        "jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF2-BinF-PCR4_S168"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "mismatched status",
                "detail": "Released human donor [IGVFDO0384OZRW](/human-donors/IGVFDO0384OZRW/) has in progress subobject publication [155f24ce-5c2c-4400-8651-da9447eaca25](/publications/155f24ce-5c2c-4400-8651-da9447eaca25/).",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_item_status",
                "path": "/human-donors/IGVFDO0384OZRW/"
            },
            {
                "category": "mismatched status",
                "detail": "Released in vitro system [IGVFSM4713PHAB](/in-vitro-systems/IGVFSM4713PHAB/) has in progress subobject treatment [d35868d1-c45b-49ae-8ff3-a9c0c22551c2](/treatments/d35868d1-c45b-49ae-8ff3-a9c0c22551c2/).",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_item_status",
                "path": "/in-vitro-systems/IGVFSM4713PHAB/"
            }
        ],
        "NOT_COMPLIANT": [
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS0078EAAP](/auxiliary-sets/IGVFDS0078EAAP/) has sequence file(s) [IGVFFI0574QGWX](/sequence-files/IGVFFI0574QGWX/), [IGVFFI7101MEEN](/sequence-files/IGVFFI7101MEEN/), [IGVFFI2836GXUE](/sequence-files/IGVFFI2836GXUE/), [IGVFFI8827QTFJ](/sequence-files/IGVFFI8827QTFJ/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_inconsistent_sequencing_kit",
                "path": "/auxiliary-sets/IGVFDS0078EAAP/"
            }
        ]
    },
    "award": {
        "@id": "/awards/HG011972/",
        "component": "functional characterization",
        "contact_pi": {
            "@id": "/users/6c75dbfa-635e-4a7a-8ec8-9e51e9c380a4/",
            "title": "Jesse Engreitz"
        },
        "title": "Stanford Center for Connecting DNA Variants to Function and Phenotype"
    },
    "control_for": [],
    "creation_timestamp": "2024-05-16T17:59:38.856195+00:00",
    "donors": [
        {
            "@id": "/human-donors/IGVFDO0384OZRW/",
            "accession": "IGVFDO0384OZRW",
            "aliases": [
                "igvf:donor_of_HCT116"
            ],
            "sex": "male",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "file_set_type": "gRNA sequencing",
    "files": [
        {
            "@id": "/sequence-files/IGVFFI0574QGWX/",
            "accession": "IGVFFI0574QGWX",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF2-BinF-PCR1_S66"
            ],
            "content_type": "reads",
            "creation_timestamp": "2024-06-03T15:22:40.455461+00:00",
            "file_format": "fastq",
            "file_size": 7190465,
            "href": "/sequence-files/IGVFFI0574QGWX/@@download/IGVFFI0574QGWX.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/03/9d77375f-9544-4bc0-b557-2771696b7ed4/IGVFFI0574QGWX.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF2-BinF-PCR1_S66_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI1999NLYB/",
            "accession": "IGVFFI1999NLYB",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF2-BinF-PCR1_S66"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T22:10:30.809820+00:00",
            "file_format": "yaml",
            "file_size": 902,
            "href": "/configuration-files/IGVFFI1999NLYB/@@download/IGVFFI1999NLYB.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/00bc944e-64f3-421e-962d-b7eab6d981df/IGVFFI1999NLYB.yaml.gz",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF2-BinF-PCR1_S66.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI7101MEEN/",
            "accession": "IGVFFI7101MEEN",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF2-BinF-PCR2_S72"
            ],
            "content_type": "reads",
            "creation_timestamp": "2024-06-03T15:22:57.025875+00:00",
            "file_format": "fastq",
            "file_size": 13013915,
            "href": "/sequence-files/IGVFFI7101MEEN/@@download/IGVFFI7101MEEN.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/03/c7b74f92-4016-4c75-a4a3-5f927205528f/IGVFFI7101MEEN.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF2-BinF-PCR2_S72_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI2836GXUE/",
            "accession": "IGVFFI2836GXUE",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF2-BinF-PCR3_S162"
            ],
            "content_type": "reads",
            "creation_timestamp": "2024-06-03T15:26:24.459928+00:00",
            "file_format": "fastq",
            "file_size": 16180873,
            "href": "/sequence-files/IGVFFI2836GXUE/@@download/IGVFFI2836GXUE.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/03/1937eec8-b3fd-44af-b9fd-d802981edb56/IGVFFI2836GXUE.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF2-BinF-PCR3_S162_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8827QTFJ/",
            "accession": "IGVFFI8827QTFJ",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF2-BinF-PCR4_S168"
            ],
            "content_type": "reads",
            "creation_timestamp": "2024-06-03T15:26:42.124213+00:00",
            "file_format": "fastq",
            "file_size": 28437769,
            "href": "/sequence-files/IGVFFI8827QTFJ/@@download/IGVFFI8827QTFJ.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/03/82fe7be8-bfdd-4844-b23f-88393b6695f8/IGVFFI8827QTFJ.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF2-BinF-PCR4_S168_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI2875SNJW/",
            "accession": "IGVFFI2875SNJW",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF2-BinF-PCR2_S72"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T22:10:45.597684+00:00",
            "file_format": "yaml",
            "file_size": 902,
            "href": "/configuration-files/IGVFFI2875SNJW/@@download/IGVFFI2875SNJW.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/116ad698-cabe-42ff-9ebb-8c97c1a77407/IGVFFI2875SNJW.yaml.gz",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF2-BinF-PCR2_S72.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI8909CZJU/",
            "accession": "IGVFFI8909CZJU",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF2-BinF-PCR3_S162"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T22:11:02.635611+00:00",
            "file_format": "yaml",
            "file_size": 903,
            "href": "/configuration-files/IGVFFI8909CZJU/@@download/IGVFFI8909CZJU.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/d64dd6cc-f5ca-43f2-bcf7-978e83c0865d/IGVFFI8909CZJU.yaml.gz",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF2-BinF-PCR3_S162.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI5051VBYP/",
            "accession": "IGVFFI5051VBYP",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF2-BinF-PCR4_S168"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T22:11:16.922592+00:00",
            "file_format": "yaml",
            "file_size": 902,
            "href": "/configuration-files/IGVFFI5051VBYP/@@download/IGVFFI5051VBYP.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/8892ef60-e13a-4e8e-b71f-2220e05f8c6a/IGVFFI5051VBYP.yaml.gz",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF2-BinF-PCR4_S168.yaml",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS6482AXWW/"
    ],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS8445NSWZ/",
            "accession": "IGVFDS8445NSWZ",
            "aliases": [
                "jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF2-BinF-PCR1_S66",
                "jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF2-BinF-PCR2_S72",
                "jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF2-BinF-PCR3_S162",
                "jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF2-BinF-PCR4_S168"
            ],
            "preferred_assay_title": "CRISPR FlowFISH screen"
        }
    ],
    "release_timestamp": "2024-07-10T20:17:40.455079+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM4713PHAB/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM4713PHAB",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF2-BinF-PCR1_S66",
                "jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF2-BinF-PCR2_S72",
                "jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF2-BinF-PCR3_S162",
                "jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF2-BinF-PCR4_S168"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS7846UISG/"
            ],
            "modifications": [
                "/degron-modifications/95081d1b-08b4-49ed-b324-e53fc43d8456/",
                "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/"
            ],
            "sample_terms": [
                {
                    "@id": "/sample-terms/EFO_0002824/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
                        "Item"
                    ],
                    "aliases": [
                        "igvf:HCT116"
                    ],
                    "status": "released",
                    "summary": "HCT116",
                    "term_name": "HCT116"
                }
            ],
            "status": "released",
            "summary": "HCT116 cell line, male, Homo sapiens (sorting details: FACS bin F for 80-100% expression of KITLG) treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours, modified with AID system targeting RAD21, CRISPRi Sp-dCas9-KOX1-KRAB, transfected with a guide library",
            "taxa": "Homo sapiens",
            "treatments": [
                "/treatments/d35868d1-c45b-49ae-8ff3-a9c0c22551c2/"
            ]
        }
    ],
    "schema_version": "11",
    "status": "released",
    "submitted_by": {
        "@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
        "title": "Chongyon Park"
    },
    "submitted_files_timestamp": "2024-06-03T15:22:40.455461+00:00",
    "summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "f35880a7-bca0-4049-8a1d-30f137477c08"
}