IGVFDS2834VAYS

released
{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS2834VAYS/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS2834VAYS",
    "aliases": [
        "jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR1_Rep1_S26",
        "jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR1_Rep2_S81",
        "jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR2_Rep1_S32",
        "jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR2_Rep2_S87",
        "jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR3_Rep1_S38",
        "jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR3_Rep2_S93",
        "jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR4_Rep1_S44",
        "jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR4_Rep2_S99"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS2834VAYS](/auxiliary-sets/IGVFDS2834VAYS/) has sequence file(s) [IGVFFI7807KLUU](/sequence-files/IGVFFI7807KLUU/), [IGVFFI3275WQZQ](/sequence-files/IGVFFI3275WQZQ/), [IGVFFI4298DZIN](/sequence-files/IGVFFI4298DZIN/), [IGVFFI2362LKOQ](/sequence-files/IGVFFI2362LKOQ/), [IGVFFI5870UCTK](/sequence-files/IGVFFI5870UCTK/), [IGVFFI1545RRLD](/sequence-files/IGVFFI1545RRLD/), [IGVFFI9245IPZR](/sequence-files/IGVFFI9245IPZR/), [IGVFFI9172PREQ](/sequence-files/IGVFFI9172PREQ/) 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/IGVFDS2834VAYS/"
            }
        ]
    },
    "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": "2024-05-21T17:13:07.300301+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-Auxin0hrs-FF2-BinB-PCR1_Rep1_S26"
            ],
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            "controlled_access": false,
            "creation_timestamp": "2024-06-01T02:00:48.191718+00:00",
            "file_format": "fastq",
            "file_size": 52386666,
            "href": "/sequence-files/IGVFFI7807KLUU/@@download/IGVFFI7807KLUU.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/46576688-e224-4930-ad48-e405c210bbcb/IGVFFI7807KLUU.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF2-BinB-PCR1-Rep1_S26_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI8168MZFJ/",
            "accession": "IGVFFI8168MZFJ",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR1_Rep1_S26"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:47:27.584218+00:00",
            "file_format": "yaml",
            "file_size": 911,
            "href": "/configuration-files/IGVFFI8168MZFJ/@@download/IGVFFI8168MZFJ.yaml.gz",
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            "status": "released",
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            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3275WQZQ/",
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            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR1_Rep2_S81"
            ],
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            "controlled_access": false,
            "creation_timestamp": "2024-06-01T02:01:08.892229+00:00",
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            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "status": "released",
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            "upload_status": "validated"
        },
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            "@id": "/sequence-files/IGVFFI4298DZIN/",
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                "jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR3_Rep1_S38"
            ],
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            "controlled_access": false,
            "creation_timestamp": "2024-06-01T02:02:15.190391+00:00",
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            "href": "/sequence-files/IGVFFI4298DZIN/@@download/IGVFFI4298DZIN.fastq.gz",
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            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI1435OZLL/",
            "accession": "IGVFFI1435OZLL",
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                "jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR4_Rep1_S44"
            ],
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            "creation_timestamp": "2024-06-11T20:48:53.703128+00:00",
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            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF2-BinB-PCR4_Rep1_S44.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI2362LKOQ/",
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                "jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR4_Rep1_S44"
            ],
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            "controlled_access": false,
            "creation_timestamp": "2024-06-01T02:02:56.247963+00:00",
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            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI7331TUOS/",
            "accession": "IGVFFI7331TUOS",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR4_Rep2_S99"
            ],
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            "creation_timestamp": "2024-06-11T20:49:08.624866+00:00",
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            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF2-BinB-PCR4_Rep2_S99.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI5870UCTK/",
            "accession": "IGVFFI5870UCTK",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR2_Rep1_S32"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T02:01:33.300910+00:00",
            "file_format": "fastq",
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            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF2-BinB-PCR2-Rep1_S32_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI1545RRLD/",
            "accession": "IGVFFI1545RRLD",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR2_Rep2_S87"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T02:01:53.919516+00:00",
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            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9245IPZR/",
            "accession": "IGVFFI9245IPZR",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR3_Rep2_S93"
            ],
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            "creation_timestamp": "2024-06-01T02:02:35.609914+00:00",
            "file_format": "fastq",
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            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9172PREQ/",
            "accession": "IGVFFI9172PREQ",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR4_Rep2_S99"
            ],
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            "controlled_access": false,
            "creation_timestamp": "2024-06-01T02:03:17.734658+00:00",
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            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI6802YWSU/",
            "accession": "IGVFFI6802YWSU",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR1_Rep2_S81"
            ],
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            "creation_timestamp": "2024-06-11T20:47:42.097358+00:00",
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            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI2068XJOM/",
            "accession": "IGVFFI2068XJOM",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR2_Rep1_S32"
            ],
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            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI2467IQLT/",
            "accession": "IGVFFI2467IQLT",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR3_Rep2_S93"
            ],
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            "creation_timestamp": "2024-06-11T20:48:39.216286+00:00",
            "file_format": "yaml",
            "file_size": 911,
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            "status": "released",
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            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI8314LAZS/",
            "accession": "IGVFFI8314LAZS",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR2_Rep2_S87"
            ],
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            "creation_timestamp": "2024-06-11T20:48:10.824663+00:00",
            "file_format": "yaml",
            "file_size": 911,
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            "status": "released",
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            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI2350VRGN/",
            "accession": "IGVFFI2350VRGN",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR3_Rep1_S38"
            ],
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            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF2-BinB-PCR3_Rep1_S38.yaml",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS4544YEQM/"
    ],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS0398KCYH/",
            "accession": "IGVFDS0398KCYH",
            "aliases": [
                "jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR1_Rep1_S26",
                "jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR1_Rep2_S81",
                "jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR2_Rep1_S32",
                "jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR2_Rep2_S87",
                "jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR3_Rep1_S38",
                "jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR3_Rep2_S93",
                "jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR4_Rep1_S44",
                "jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR4_Rep2_S99"
            ],
            "preferred_assay_title": "CRISPR FlowFISH screen",
            "status": "released"
        }
    ],
    "release_timestamp": "2024-07-10T20:20:06.844779+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM2313EONT/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM2313EONT",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR1_Rep1_S26",
                "jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR1_Rep2_S81",
                "jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR2_Rep1_S32",
                "jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR2_Rep2_S87",
                "jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR3_Rep1_S38",
                "jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR3_Rep2_S93",
                "jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR4_Rep1_S44",
                "jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR4_Rep2_S99"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS7857SYCK/"
            ],
            "modifications": [
                {
                    "@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
                    "modality": "interference",
                    "status": "released"
                },
                {
                    "@id": "/degron-modifications/2e8d10cc-fc98-44d5-a7d9-e2892e16c98a/",
                    "modality": "degradation",
                    "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) modified with CRISPRi Sp-dCas9-KOX1-KRAB, inactive AID system targeting RAD21, transfected with a guide library",
            "taxa": "Homo sapiens"
        }
    ],
    "schema_version": "12",
    "status": "released",
    "submitted_by": {
        "@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
        "title": "Chongyon Park"
    },
    "submitted_files_timestamp": "2024-06-01T02:00:48.191718+00:00",
    "summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "97595564-a0c8-4dc3-8969-0d92c2bfcee5"
}