IGVFDS9907QGGC

released
{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS9907QGGC/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS9907QGGC",
    "aliases": [
        "jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF2-BinD-PCR1_S64",
        "jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF2-BinD-PCR2_S70",
        "jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF2-BinD-PCR3_S160",
        "jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF2-BinD-PCR4_S166"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS9907QGGC](/auxiliary-sets/IGVFDS9907QGGC/) has sequence file(s) [IGVFFI1843RRPT](/sequence-files/IGVFFI1843RRPT/), [IGVFFI3411QDKP](/sequence-files/IGVFFI3411QDKP/), [IGVFFI3360ZAFX](/sequence-files/IGVFFI3360ZAFX/), [IGVFFI8684DGZI](/sequence-files/IGVFFI8684DGZI/) 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/IGVFDS9907QGGC/"
            }
        ]
    },
    "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": "2024-05-16T17:59:37.396866+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/IGVFFI1843RRPT/",
            "accession": "IGVFFI1843RRPT",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF2-BinD-PCR1_S64"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-03T15:22:34.824110+00:00",
            "file_format": "fastq",
            "file_size": 9223559,
            "href": "/sequence-files/IGVFFI1843RRPT/@@download/IGVFFI1843RRPT.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/03/36993756-0de4-4903-9bd4-8dece0eb9c65/IGVFFI1843RRPT.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-BinD-PCR1_S64_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI1267PVEU/",
            "accession": "IGVFFI1267PVEU",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF2-BinD-PCR1_S64"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T22:10:25.862221+00:00",
            "file_format": "yaml",
            "file_size": 900,
            "href": "/configuration-files/IGVFFI1267PVEU/@@download/IGVFFI1267PVEU.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/57de2c76-12f9-4893-a4ae-e032bfde5afa/IGVFFI1267PVEU.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF2-BinD-PCR1_S64.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3411QDKP/",
            "accession": "IGVFFI3411QDKP",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF2-BinD-PCR4_S166"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-03T15:26:35.983621+00:00",
            "file_format": "fastq",
            "file_size": 14034354,
            "href": "/sequence-files/IGVFFI3411QDKP/@@download/IGVFFI3411QDKP.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/03/d36f07fd-7f3b-4135-9f6e-c23c20d7a0cd/IGVFFI3411QDKP.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-BinD-PCR4_S166_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3360ZAFX/",
            "accession": "IGVFFI3360ZAFX",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF2-BinD-PCR3_S160"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-03T15:26:15.151160+00:00",
            "file_format": "fastq",
            "file_size": 14238686,
            "href": "/sequence-files/IGVFFI3360ZAFX/@@download/IGVFFI3360ZAFX.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/03/07ba3510-a4c2-4e42-ab4f-be73833c0821/IGVFFI3360ZAFX.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-BinD-PCR3_S160_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8684DGZI/",
            "accession": "IGVFFI8684DGZI",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF2-BinD-PCR2_S70"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-03T15:22:51.353949+00:00",
            "file_format": "fastq",
            "file_size": 8909639,
            "href": "/sequence-files/IGVFFI8684DGZI/@@download/IGVFFI8684DGZI.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/03/3191743a-2d2f-4748-a275-d7f46da8f845/IGVFFI8684DGZI.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-BinD-PCR2_S70_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI1486JESD/",
            "accession": "IGVFFI1486JESD",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF2-BinD-PCR2_S70"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T22:10:40.730991+00:00",
            "file_format": "yaml",
            "file_size": 902,
            "href": "/configuration-files/IGVFFI1486JESD/@@download/IGVFFI1486JESD.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/6a1229a8-e5c1-4561-99d2-5c5af70180b4/IGVFFI1486JESD.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF2-BinD-PCR2_S70.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI5749UYDF/",
            "accession": "IGVFFI5749UYDF",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF2-BinD-PCR4_S166"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T22:11:12.160222+00:00",
            "file_format": "yaml",
            "file_size": 903,
            "href": "/configuration-files/IGVFFI5749UYDF/@@download/IGVFFI5749UYDF.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/1a3e2b55-4432-4d27-ae53-1028b6dba1b1/IGVFFI5749UYDF.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF2-BinD-PCR4_S166.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI4776XMGE/",
            "accession": "IGVFFI4776XMGE",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF2-BinD-PCR3_S160"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T22:10:57.760639+00:00",
            "file_format": "yaml",
            "file_size": 904,
            "href": "/configuration-files/IGVFFI4776XMGE/@@download/IGVFFI4776XMGE.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/a4cd95f4-0db2-4bf0-a4e9-4aa6550d0f96/IGVFFI4776XMGE.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF2-BinD-PCR3_S160.yaml",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS6482AXWW/"
    ],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS3328PNPV/",
            "accession": "IGVFDS3328PNPV",
            "aliases": [
                "jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF2-BinD-PCR1_S64",
                "jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF2-BinD-PCR2_S70",
                "jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF2-BinD-PCR3_S160",
                "jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF2-BinD-PCR4_S166"
            ],
            "preferred_assay_title": "CRISPR FlowFISH screen",
            "status": "released"
        }
    ],
    "release_timestamp": "2024-07-10T20:17:26.040014+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM8586BMQG/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM8586BMQG",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF2-BinD-PCR1_S64",
                "jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF2-BinD-PCR2_S70",
                "jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF2-BinD-PCR3_S160",
                "jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF2-BinD-PCR4_S166"
            ],
            "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 D for 55-65% 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": "2024-06-03T15:22:34.824110+00:00",
    "summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "219f61fe-6a92-4622-9a1e-02156616c40b"
}