IGVFDS2372JFBI

released
{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS2372JFBI/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS2372JFBI",
    "aliases": [
        "jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR1_Rep1_S116",
        "jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR1_Rep2_S171",
        "jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR2_Rep1_S122",
        "jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR2_Rep2_S177",
        "jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR3_Rep1_S128",
        "jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR3_Rep2_S183",
        "jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR4_Rep1_S134",
        "jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR4_Rep2_S189"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS2372JFBI](/auxiliary-sets/IGVFDS2372JFBI/) has sequence file(s) [IGVFFI7923UEBL](/sequence-files/IGVFFI7923UEBL/), [IGVFFI7683TXPK](/sequence-files/IGVFFI7683TXPK/), [IGVFFI5849CCCH](/sequence-files/IGVFFI5849CCCH/), [IGVFFI3283FABB](/sequence-files/IGVFFI3283FABB/), [IGVFFI1366IKMD](/sequence-files/IGVFFI1366IKMD/), [IGVFFI1641ICFG](/sequence-files/IGVFFI1641ICFG/), [IGVFFI9101IEYD](/sequence-files/IGVFFI9101IEYD/), [IGVFFI3695WJWY](/sequence-files/IGVFFI3695WJWY/) 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/IGVFDS2372JFBI/"
            }
        ]
    },
    "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": "2024-05-21T17:39:12.043233+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-BinF-PCR1_Rep1_S116"
            ],
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            "controlled_access": false,
            "creation_timestamp": "2024-06-01T02:03:51.825076+00:00",
            "file_format": "fastq",
            "file_size": 23751591,
            "href": "/sequence-files/IGVFFI7923UEBL/@@download/IGVFFI7923UEBL.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-BinF-PCR1-Rep1_S116_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI1645SYMG/",
            "accession": "IGVFFI1645SYMG",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR1_Rep1_S116"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:49:33.443851+00:00",
            "file_format": "yaml",
            "file_size": 912,
            "href": "/configuration-files/IGVFFI1645SYMG/@@download/IGVFFI1645SYMG.yaml.gz",
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            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF1-BinF-PCR1_Rep1_S116.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI7683TXPK/",
            "accession": "IGVFFI7683TXPK",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR1_Rep2_S171"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T02:04:12.221861+00:00",
            "file_format": "fastq",
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            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "status": "released",
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            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI5849CCCH/",
            "accession": "IGVFFI5849CCCH",
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                "jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR2_Rep1_S122"
            ],
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            "creation_timestamp": "2024-06-01T02:04:32.286509+00:00",
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            "status": "released",
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            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3283FABB/",
            "accession": "IGVFFI3283FABB",
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                "jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR3_Rep1_S128"
            ],
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            "controlled_access": false,
            "creation_timestamp": "2024-06-01T02:05:12.698646+00:00",
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            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI1366IKMD/",
            "accession": "IGVFFI1366IKMD",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR4_Rep2_S189"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T02:06:09.249109+00:00",
            "file_format": "fastq",
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            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin6hrs-FF1-BinF-PCR4-Rep2_S189_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI1641ICFG/",
            "accession": "IGVFFI1641ICFG",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR2_Rep2_S177"
            ],
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            "controlled_access": false,
            "creation_timestamp": "2024-06-01T02:04:52.822554+00:00",
            "file_format": "fastq",
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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-BinF-PCR2-Rep2_S177_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9101IEYD/",
            "accession": "IGVFFI9101IEYD",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR3_Rep2_S183"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T02:05:31.718473+00:00",
            "file_format": "fastq",
            "file_size": 20354004,
            "href": "/sequence-files/IGVFFI9101IEYD/@@download/IGVFFI9101IEYD.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-BinF-PCR3-Rep2_S183_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI2297PBGW/",
            "accession": "IGVFFI2297PBGW",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR3_Rep1_S128"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:50:32.562895+00:00",
            "file_format": "yaml",
            "file_size": 911,
            "href": "/configuration-files/IGVFFI2297PBGW/@@download/IGVFFI2297PBGW.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/4fe7a0ee-12fd-4709-9be0-8d5de997dc26/IGVFFI2297PBGW.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF1-BinF-PCR3_Rep1_S128.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3695WJWY/",
            "accession": "IGVFFI3695WJWY",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR4_Rep1_S134"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T02:05:50.229709+00:00",
            "file_format": "fastq",
            "file_size": 23077598,
            "href": "/sequence-files/IGVFFI3695WJWY/@@download/IGVFFI3695WJWY.fastq.gz",
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            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin6hrs-FF1-BinF-PCR4-Rep1_S134_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI6743FDDQ/",
            "accession": "IGVFFI6743FDDQ",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR2_Rep1_S122"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:50:03.255769+00:00",
            "file_format": "yaml",
            "file_size": 910,
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            "status": "released",
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            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI9003PVUZ/",
            "accession": "IGVFFI9003PVUZ",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR2_Rep2_S177"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:50:17.635560+00:00",
            "file_format": "yaml",
            "file_size": 910,
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            "status": "released",
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            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI1042MROS/",
            "accession": "IGVFFI1042MROS",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR1_Rep2_S171"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:49:48.229341+00:00",
            "file_format": "yaml",
            "file_size": 912,
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            "status": "released",
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            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI3921IQBX/",
            "accession": "IGVFFI3921IQBX",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR4_Rep1_S134"
            ],
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            "creation_timestamp": "2024-06-11T20:51:03.075520+00:00",
            "file_format": "yaml",
            "file_size": 913,
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            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF1-BinF-PCR4_Rep1_S134.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI3469LYTM/",
            "accession": "IGVFFI3469LYTM",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR3_Rep2_S183"
            ],
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            "creation_timestamp": "2024-06-11T20:50:47.192394+00:00",
            "file_format": "yaml",
            "file_size": 913,
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            "status": "released",
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            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI7439LMLL/",
            "accession": "IGVFFI7439LMLL",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR4_Rep2_S189"
            ],
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            "creation_timestamp": "2024-06-11T20:51:18.658071+00:00",
            "file_format": "yaml",
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            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF1-BinF-PCR4_Rep2_S189.yaml",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS4544YEQM/"
    ],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS6475UHMP/",
            "accession": "IGVFDS6475UHMP",
            "aliases": [
                "jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR1_Rep1_S116",
                "jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR1_Rep2_S171",
                "jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR2_Rep1_S122",
                "jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR2_Rep2_S177",
                "jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR3_Rep1_S128",
                "jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR3_Rep2_S183",
                "jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR4_Rep1_S134",
                "jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR4_Rep2_S189"
            ],
            "preferred_assay_title": "CRISPR FlowFISH screen",
            "status": "released"
        }
    ],
    "release_timestamp": "2024-07-10T20:21:24.755578+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM3998EEZS/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM3998EEZS",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR1_Rep1_S116",
                "jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR1_Rep2_S171",
                "jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR2_Rep1_S122",
                "jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR2_Rep2_S177",
                "jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR3_Rep1_S128",
                "jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR3_Rep2_S183",
                "jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR4_Rep1_S134",
                "jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR4_Rep2_S189"
            ],
            "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 F for 80-100% 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": "2024-06-01T02:03:51.825076+00:00",
    "summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "2e75aa19-c7b1-4773-bb78-d101c2bc4802"
}