IGVFDS8719WWWS

released
{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS8719WWWS/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS8719WWWS",
    "aliases": [
        "jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF3-BinD-PCR1_S28",
        "jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF3-BinD-PCR2_S34",
        "jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF3-BinD-PCR3_S124",
        "jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF3-BinD-PCR4_S130"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS8719WWWS](/auxiliary-sets/IGVFDS8719WWWS/) has sequence file(s) [IGVFFI1457EKWS](/sequence-files/IGVFFI1457EKWS/), [IGVFFI6514JTIC](/sequence-files/IGVFFI6514JTIC/), [IGVFFI4376KAKY](/sequence-files/IGVFFI4376KAKY/), [IGVFFI4369YDEU](/sequence-files/IGVFFI4369YDEU/) 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/IGVFDS8719WWWS/"
            }
        ]
    },
    "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": "2024-05-16T17:41:59.769246+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/IGVFFI1457EKWS/",
            "accession": "IGVFFI1457EKWS",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF3-BinD-PCR1_S28"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T02:17:33.774408+00:00",
            "file_format": "fastq",
            "file_size": 9690717,
            "href": "/sequence-files/IGVFFI1457EKWS/@@download/IGVFFI1457EKWS.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/0e9b4aa7-de8e-495d-b4ac-7457d0263f91/IGVFFI1457EKWS.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF3-BinD-PCR1_S28_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI1149KOYD/",
            "accession": "IGVFFI1149KOYD",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF3-BinD-PCR1_S28"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T22:07:35.760798+00:00",
            "file_format": "yaml",
            "file_size": 902,
            "href": "/configuration-files/IGVFFI1149KOYD/@@download/IGVFFI1149KOYD.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/5efd1b99-5540-4a78-9c05-4fd02b7ae686/IGVFFI1149KOYD.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF3-BinD-PCR1_S28.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI6514JTIC/",
            "accession": "IGVFFI6514JTIC",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF3-BinD-PCR3_S124"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T02:18:09.739332+00:00",
            "file_format": "fastq",
            "file_size": 14976861,
            "href": "/sequence-files/IGVFFI6514JTIC/@@download/IGVFFI6514JTIC.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/1e3ad7b9-fb63-41a1-a4cd-cdd3cac19a9a/IGVFFI6514JTIC.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF3-BinD-PCR3_S124_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI5189ZWRI/",
            "accession": "IGVFFI5189ZWRI",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF3-BinD-PCR4_S130"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T22:08:15.623998+00:00",
            "file_format": "yaml",
            "file_size": 905,
            "href": "/configuration-files/IGVFFI5189ZWRI/@@download/IGVFFI5189ZWRI.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/b8c5f31f-2cde-4c8e-8afe-0b59ca558b9b/IGVFFI5189ZWRI.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF3-BinD-PCR4_S130.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI7135SUWD/",
            "accession": "IGVFFI7135SUWD",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF3-BinD-PCR2_S34"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T22:07:49.107063+00:00",
            "file_format": "yaml",
            "file_size": 902,
            "href": "/configuration-files/IGVFFI7135SUWD/@@download/IGVFFI7135SUWD.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/7b91610b-f973-4802-8c66-6dcf41ff21ac/IGVFFI7135SUWD.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF3-BinD-PCR2_S34.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI4376KAKY/",
            "accession": "IGVFFI4376KAKY",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF3-BinD-PCR2_S34"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T02:17:51.855556+00:00",
            "file_format": "fastq",
            "file_size": 10933667,
            "href": "/sequence-files/IGVFFI4376KAKY/@@download/IGVFFI4376KAKY.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/09edb302-5744-4d76-99bc-fc8459a75105/IGVFFI4376KAKY.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF3-BinD-PCR2_S34_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI4369YDEU/",
            "accession": "IGVFFI4369YDEU",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF3-BinD-PCR4_S130"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T02:18:27.785290+00:00",
            "file_format": "fastq",
            "file_size": 20531648,
            "href": "/sequence-files/IGVFFI4369YDEU/@@download/IGVFFI4369YDEU.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/1a7b76b3-afd6-40ed-aa66-fce0d3509606/IGVFFI4369YDEU.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF3-BinD-PCR4_S130_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI1137LHCT/",
            "accession": "IGVFFI1137LHCT",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF3-BinD-PCR3_S124"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T22:08:02.351965+00:00",
            "file_format": "yaml",
            "file_size": 901,
            "href": "/configuration-files/IGVFFI1137LHCT/@@download/IGVFFI1137LHCT.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/0aae9ad4-6a8b-4540-a350-d8d1ab9f87bd/IGVFFI1137LHCT.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF3-BinD-PCR3_S124.yaml",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS6482AXWW/"
    ],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS6007VHUG/",
            "accession": "IGVFDS6007VHUG",
            "aliases": [
                "jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF3-BinD-PCR1_S28",
                "jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF3-BinD-PCR2_S34",
                "jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF3-BinD-PCR3_S124",
                "jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF3-BinD-PCR4_S130"
            ],
            "preferred_assay_title": "CRISPR FlowFISH screen",
            "status": "released"
        }
    ],
    "release_timestamp": "2024-07-10T20:15:16.857439+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM3068ZYXS/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM3068ZYXS",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF3-BinD-PCR1_S28",
                "jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF3-BinD-PCR2_S34",
                "jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF3-BinD-PCR3_S124",
                "jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF3-BinD-PCR4_S130"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS7846UISG/"
            ],
            "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 D for 55-65% expression of KITLG) 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": "2024-06-01T02:17:33.774408+00:00",
    "summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "2e297e60-bd99-4078-af3f-5475a668965b"
}