IGVFDS3914IPWH

released
{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS3914IPWH/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS3914IPWH",
    "aliases": [
        "jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinB-PCR1_Rep1_S112",
        "jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinB-PCR1_Rep2_S167",
        "jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinB-PCR2_Rep1_S118",
        "jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinB-PCR2_Rep2_S173",
        "jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinB-PCR3_Rep1_S124",
        "jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinB-PCR3_Rep2_S179",
        "jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinB-PCR4_Rep1_S130",
        "jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinB-PCR4_Rep2_S185"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS3914IPWH](/auxiliary-sets/IGVFDS3914IPWH/) has sequence file(s) [IGVFFI4264KJXK](/sequence-files/IGVFFI4264KJXK/), [IGVFFI3058GAYK](/sequence-files/IGVFFI3058GAYK/), [IGVFFI8232UPNC](/sequence-files/IGVFFI8232UPNC/), [IGVFFI7993WRUA](/sequence-files/IGVFFI7993WRUA/), [IGVFFI8689TPHH](/sequence-files/IGVFFI8689TPHH/), [IGVFFI1193HDXG](/sequence-files/IGVFFI1193HDXG/), [IGVFFI1593YXMS](/sequence-files/IGVFFI1593YXMS/), [IGVFFI6277LDPG](/sequence-files/IGVFFI6277LDPG/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_inconsistent_sequencing_kit",
                "path": "/auxiliary-sets/IGVFDS3914IPWH/"
            }
        ]
    },
    "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": "2024-05-21T17:39:07.102437+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",
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                "jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF1-BinB-PCR1_Rep1_S112"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T02:03:38.334076+00:00",
            "file_format": "fastq",
            "file_size": 18100081,
            "href": "/sequence-files/IGVFFI4264KJXK/@@download/IGVFFI4264KJXK.fastq.gz",
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            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin6hrs-FF1-BinB-PCR1-Rep1_S112_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI4823SDRE/",
            "accession": "IGVFFI4823SDRE",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF1-BinB-PCR1_Rep1_S112"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:49:23.590667+00:00",
            "file_format": "yaml",
            "file_size": 913,
            "href": "/configuration-files/IGVFFI4823SDRE/@@download/IGVFFI4823SDRE.yaml.gz",
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            "status": "released",
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            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3058GAYK/",
            "accession": "IGVFFI3058GAYK",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF1-BinB-PCR3_Rep2_S179"
            ],
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            "controlled_access": false,
            "creation_timestamp": "2024-06-01T02:05:19.001380+00:00",
            "file_format": "fastq",
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            "status": "released",
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            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI9689CPCW/",
            "accession": "IGVFFI9689CPCW",
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                "jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF1-BinB-PCR4_Rep2_S185"
            ],
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            "creation_timestamp": "2024-06-11T20:51:08.781958+00:00",
            "file_format": "yaml",
            "file_size": 912,
            "href": "/configuration-files/IGVFFI9689CPCW/@@download/IGVFFI9689CPCW.yaml.gz",
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            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8232UPNC/",
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                "jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF1-BinB-PCR4_Rep1_S130"
            ],
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            "controlled_access": false,
            "creation_timestamp": "2024-06-01T02:05:37.654908+00:00",
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            "sequencing_platform": "/platform-terms/EFO_0008565/",
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            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin6hrs-FF1-BinB-PCR4-Rep1_S130_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI1475ALYJ/",
            "accession": "IGVFFI1475ALYJ",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF1-BinB-PCR3_Rep1_S124"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:50:22.664598+00:00",
            "file_format": "yaml",
            "file_size": 911,
            "href": "/configuration-files/IGVFFI1475ALYJ/@@download/IGVFFI1475ALYJ.yaml.gz",
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            "status": "released",
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            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI7993WRUA/",
            "accession": "IGVFFI7993WRUA",
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                "jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF1-BinB-PCR1_Rep2_S167"
            ],
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            "controlled_access": false,
            "creation_timestamp": "2024-06-01T02:03:58.458025+00:00",
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            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8689TPHH/",
            "accession": "IGVFFI8689TPHH",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF1-BinB-PCR2_Rep2_S173"
            ],
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            "controlled_access": false,
            "creation_timestamp": "2024-06-01T02:04:38.923088+00:00",
            "file_format": "fastq",
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            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI1193HDXG/",
            "accession": "IGVFFI1193HDXG",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF1-BinB-PCR4_Rep2_S185"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T02:05:56.450179+00:00",
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            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI1593YXMS/",
            "accession": "IGVFFI1593YXMS",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF1-BinB-PCR2_Rep1_S118"
            ],
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            "creation_timestamp": "2024-06-01T02:04:18.764544+00:00",
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            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI6277LDPG/",
            "accession": "IGVFFI6277LDPG",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF1-BinB-PCR3_Rep1_S124"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T02:04:59.376438+00:00",
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            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI1900MCOG/",
            "accession": "IGVFFI1900MCOG",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF1-BinB-PCR3_Rep2_S179"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:50:37.651034+00:00",
            "file_format": "yaml",
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            "status": "released",
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            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI5990DFIF/",
            "accession": "IGVFFI5990DFIF",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF1-BinB-PCR1_Rep2_S167"
            ],
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            "creation_timestamp": "2024-06-11T20:49:38.515876+00:00",
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            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI8825EPCR/",
            "accession": "IGVFFI8825EPCR",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF1-BinB-PCR2_Rep1_S118"
            ],
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            "creation_timestamp": "2024-06-11T20:49:53.020446+00:00",
            "file_format": "yaml",
            "file_size": 913,
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            "status": "released",
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            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI5156TDWH/",
            "accession": "IGVFFI5156TDWH",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF1-BinB-PCR2_Rep2_S173"
            ],
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            "creation_timestamp": "2024-06-11T20:50:08.092968+00:00",
            "file_format": "yaml",
            "file_size": 911,
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            "status": "released",
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            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI7482TIZK/",
            "accession": "IGVFFI7482TIZK",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF1-BinB-PCR4_Rep1_S130"
            ],
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            "creation_timestamp": "2024-06-11T20:50:52.183375+00:00",
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            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS4544YEQM/"
    ],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS6517MOFU/",
            "accession": "IGVFDS6517MOFU",
            "aliases": [
                "jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinB-PCR1_Rep1_S112",
                "jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinB-PCR1_Rep2_S167",
                "jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinB-PCR2_Rep1_S118",
                "jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinB-PCR2_Rep2_S173",
                "jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinB-PCR3_Rep1_S124",
                "jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinB-PCR3_Rep2_S179",
                "jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinB-PCR4_Rep1_S130",
                "jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinB-PCR4_Rep2_S185"
            ],
            "preferred_assay_title": "CRISPR FlowFISH screen",
            "status": "released"
        }
    ],
    "release_timestamp": "2024-07-10T20:20:54.278106+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM0361IFQU/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM0361IFQU",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinB-PCR1_Rep1_S112",
                "jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinB-PCR1_Rep2_S167",
                "jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinB-PCR2_Rep1_S118",
                "jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinB-PCR2_Rep2_S173",
                "jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinB-PCR3_Rep1_S124",
                "jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinB-PCR3_Rep2_S179",
                "jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinB-PCR4_Rep1_S130",
                "jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinB-PCR4_Rep2_S185"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS7857SYCK/"
            ],
            "modifications": [
                {
                    "@id": "/degron-modifications/95081d1b-08b4-49ed-b324-e53fc43d8456/",
                    "modality": "degradation",
                    "status": "released"
                },
                {
                    "@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
                    "modality": "interference",
                    "status": "released"
                }
            ],
            "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 B for 10-20% expression of MYC) 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": [
                {
                    "@id": "/treatments/d35868d1-c45b-49ae-8ff3-a9c0c22551c2/",
                    "status": "released",
                    "treatment_term_name": "5-Phenyl-1H-indole-3-acetic acid"
                }
            ]
        }
    ],
    "schema_version": "12",
    "status": "released",
    "submitted_by": {
        "@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
        "title": "Chongyon Park"
    },
    "submitted_files_timestamp": "2024-06-01T02:03:38.334076+00:00",
    "summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "134a2818-52d3-4762-aa07-8b604a23ea3a"
}