IGVFDS1005OGXR

released
{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS1005OGXR/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS1005OGXR",
    "aliases": [
        "jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF2-BinE-PCR1_S65",
        "jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF2-BinE-PCR2_S71",
        "jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF2-BinE-PCR3_S161",
        "jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF2-BinE-PCR4_S167"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS1005OGXR](/auxiliary-sets/IGVFDS1005OGXR/) has sequence file(s) [IGVFFI2496VSIB](/sequence-files/IGVFFI2496VSIB/), [IGVFFI8901VLCQ](/sequence-files/IGVFFI8901VLCQ/), [IGVFFI9347INON](/sequence-files/IGVFFI9347INON/), [IGVFFI3706KVDE](/sequence-files/IGVFFI3706KVDE/) 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/IGVFDS1005OGXR/"
            }
        ]
    },
    "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": "2024-05-16T17:59:38.086372+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/IGVFFI2496VSIB/",
            "accession": "IGVFFI2496VSIB",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF2-BinE-PCR1_S65"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-03T15:22:37.706324+00:00",
            "file_format": "fastq",
            "file_size": 11268605,
            "href": "/sequence-files/IGVFFI2496VSIB/@@download/IGVFFI2496VSIB.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/03/317fe048-ccf9-445c-a7c6-37f8d0dea87d/IGVFFI2496VSIB.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF2-BinE-PCR1_S65_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI0348GTHV/",
            "accession": "IGVFFI0348GTHV",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF2-BinE-PCR1_S65"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T22:10:28.364332+00:00",
            "file_format": "yaml",
            "file_size": 901,
            "href": "/configuration-files/IGVFFI0348GTHV/@@download/IGVFFI0348GTHV.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/11febd52-8c0b-49f9-8dce-bbb028e9a1f1/IGVFFI0348GTHV.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF2-BinE-PCR1_S65.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8901VLCQ/",
            "accession": "IGVFFI8901VLCQ",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF2-BinE-PCR3_S161"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-03T15:26:18.022484+00:00",
            "file_format": "fastq",
            "file_size": 27447252,
            "href": "/sequence-files/IGVFFI8901VLCQ/@@download/IGVFFI8901VLCQ.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/03/4b1c95f0-bb2d-4ca6-94e9-e5844aae3852/IGVFFI8901VLCQ.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF2-BinE-PCR3_S161_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9347INON/",
            "accession": "IGVFFI9347INON",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF2-BinE-PCR4_S167"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-03T15:26:39.094421+00:00",
            "file_format": "fastq",
            "file_size": 18989850,
            "href": "/sequence-files/IGVFFI9347INON/@@download/IGVFFI9347INON.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/03/e89cfb2b-3c49-4fc3-9401-a8eae098ce14/IGVFFI9347INON.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF2-BinE-PCR4_S167_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3706KVDE/",
            "accession": "IGVFFI3706KVDE",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF2-BinE-PCR2_S71"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-03T15:22:54.065163+00:00",
            "file_format": "fastq",
            "file_size": 10247671,
            "href": "/sequence-files/IGVFFI3706KVDE/@@download/IGVFFI3706KVDE.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/03/e3e0b014-7c32-4012-8d33-3c7575cf2f29/IGVFFI3706KVDE.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF2-BinE-PCR2_S71_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI5203MRMY/",
            "accession": "IGVFFI5203MRMY",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF2-BinE-PCR2_S71"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T22:10:43.115072+00:00",
            "file_format": "yaml",
            "file_size": 902,
            "href": "/configuration-files/IGVFFI5203MRMY/@@download/IGVFFI5203MRMY.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/e0d2194e-d035-4c81-a89a-c119fa45c7e2/IGVFFI5203MRMY.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF2-BinE-PCR2_S71.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI8401BOPY/",
            "accession": "IGVFFI8401BOPY",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF2-BinE-PCR4_S167"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T22:11:14.548748+00:00",
            "file_format": "yaml",
            "file_size": 902,
            "href": "/configuration-files/IGVFFI8401BOPY/@@download/IGVFFI8401BOPY.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/540bec21-b98c-4c19-aee1-93642f126c10/IGVFFI8401BOPY.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF2-BinE-PCR4_S167.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI5245IYGK/",
            "accession": "IGVFFI5245IYGK",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF2-BinE-PCR3_S161"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T22:11:00.223354+00:00",
            "file_format": "yaml",
            "file_size": 902,
            "href": "/configuration-files/IGVFFI5245IYGK/@@download/IGVFFI5245IYGK.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/36cb5b09-3cce-4e89-ac68-d0cd461f709e/IGVFFI5245IYGK.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF2-BinE-PCR3_S161.yaml",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS6482AXWW/"
    ],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS0548YILY/",
            "accession": "IGVFDS0548YILY",
            "aliases": [
                "jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF2-BinE-PCR1_S65",
                "jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF2-BinE-PCR2_S71",
                "jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF2-BinE-PCR3_S161",
                "jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF2-BinE-PCR4_S167"
            ],
            "preferred_assay_title": "CRISPR FlowFISH screen",
            "status": "released"
        }
    ],
    "release_timestamp": "2024-07-10T20:17:33.154250+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM4441KRKU/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM4441KRKU",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF2-BinE-PCR1_S65",
                "jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF2-BinE-PCR2_S71",
                "jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF2-BinE-PCR3_S161",
                "jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF2-BinE-PCR4_S167"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS7846UISG/"
            ],
            "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 E for 80-90% 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": [
                {
                    "@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": "2024-06-03T15:22:37.706324+00:00",
    "summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "51e5775c-650f-447d-90af-1deeb7ebb8cd"
}