IGVFDS2486FLEH

released
{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS2486FLEH/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS2486FLEH",
    "aliases": [
        "jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF3-BinA-PCR1_S73",
        "jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF3-BinA-PCR2_S79",
        "jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF3-BinA-PCR3_S169",
        "jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF3-BinA-PCR4_S175"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS2486FLEH](/auxiliary-sets/IGVFDS2486FLEH/) has sequence file(s) [IGVFFI4055KBRJ](/sequence-files/IGVFFI4055KBRJ/), [IGVFFI9532FPLV](/sequence-files/IGVFFI9532FPLV/), [IGVFFI8139XLPP](/sequence-files/IGVFFI8139XLPP/), [IGVFFI6385TRDU](/sequence-files/IGVFFI6385TRDU/) 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/IGVFDS2486FLEH/"
            }
        ]
    },
    "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": "2024-05-16T17:59:54.926912+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/IGVFFI4055KBRJ/",
            "accession": "IGVFFI4055KBRJ",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF3-BinA-PCR1_S73"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-03T15:26:44.938512+00:00",
            "file_format": "fastq",
            "file_size": 6909652,
            "href": "/sequence-files/IGVFFI4055KBRJ/@@download/IGVFFI4055KBRJ.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/03/7598ed17-e1fd-45d4-ae2a-b8bfff8251f4/IGVFFI4055KBRJ.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-FF3-BinA-PCR1_S73_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI0193GCPM/",
            "accession": "IGVFFI0193GCPM",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF3-BinA-PCR1_S73"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T22:11:19.327232+00:00",
            "file_format": "yaml",
            "file_size": 902,
            "href": "/configuration-files/IGVFFI0193GCPM/@@download/IGVFFI0193GCPM.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/01cf0f23-1913-4007-9b98-d3df6c16a4e7/IGVFFI0193GCPM.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF3-BinA-PCR1_S73.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9532FPLV/",
            "accession": "IGVFFI9532FPLV",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF3-BinA-PCR4_S175"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-03T15:27:34.034339+00:00",
            "file_format": "fastq",
            "file_size": 9835599,
            "href": "/sequence-files/IGVFFI9532FPLV/@@download/IGVFFI9532FPLV.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/03/8cb11afd-498d-4502-89b6-331be6a4d012/IGVFFI9532FPLV.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-FF3-BinA-PCR4_S175_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI2538KHLW/",
            "accession": "IGVFFI2538KHLW",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF3-BinA-PCR3_S169"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T22:11:48.333703+00:00",
            "file_format": "yaml",
            "file_size": 902,
            "href": "/configuration-files/IGVFFI2538KHLW/@@download/IGVFFI2538KHLW.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/6b3559de-9c7f-4ef0-95d7-8fb9b923b995/IGVFFI2538KHLW.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF3-BinA-PCR3_S169.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI0188JCNR/",
            "accession": "IGVFFI0188JCNR",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF3-BinA-PCR2_S79"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T22:11:33.676095+00:00",
            "file_format": "yaml",
            "file_size": 902,
            "href": "/configuration-files/IGVFFI0188JCNR/@@download/IGVFFI0188JCNR.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/55409adb-d877-4624-b13f-e41e2a4701c7/IGVFFI0188JCNR.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF3-BinA-PCR2_S79.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8139XLPP/",
            "accession": "IGVFFI8139XLPP",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF3-BinA-PCR2_S79"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-03T15:27:01.221570+00:00",
            "file_format": "fastq",
            "file_size": 4477129,
            "href": "/sequence-files/IGVFFI8139XLPP/@@download/IGVFFI8139XLPP.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/03/804fbc70-fb59-4beb-8b16-5962422143f9/IGVFFI8139XLPP.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-FF3-BinA-PCR2_S79_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI6385TRDU/",
            "accession": "IGVFFI6385TRDU",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF3-BinA-PCR3_S169"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-03T15:27:16.909657+00:00",
            "file_format": "fastq",
            "file_size": 11750327,
            "href": "/sequence-files/IGVFFI6385TRDU/@@download/IGVFFI6385TRDU.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/03/ee124551-bf64-4942-97d2-7014aed8604f/IGVFFI6385TRDU.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-FF3-BinA-PCR3_S169_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI4861EWNQ/",
            "accession": "IGVFFI4861EWNQ",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF3-BinA-PCR4_S175"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T22:12:03.013322+00:00",
            "file_format": "yaml",
            "file_size": 902,
            "href": "/configuration-files/IGVFFI4861EWNQ/@@download/IGVFFI4861EWNQ.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/258ac20a-2947-41ee-99af-bee49a1f0057/IGVFFI4861EWNQ.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF3-BinA-PCR4_S175.yaml",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS6482AXWW/"
    ],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS2213NJWP/",
            "accession": "IGVFDS2213NJWP",
            "aliases": [
                "jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF3-BinA-PCR1_S73",
                "jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF3-BinA-PCR2_S79",
                "jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF3-BinA-PCR3_S169",
                "jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF3-BinA-PCR4_S175"
            ],
            "preferred_assay_title": "CRISPR FlowFISH screen",
            "status": "released"
        }
    ],
    "release_timestamp": "2024-07-10T20:17:47.319684+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM5527SWPI/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM5527SWPI",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF3-BinA-PCR1_S73",
                "jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF3-BinA-PCR2_S79",
                "jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF3-BinA-PCR3_S169",
                "jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF3-BinA-PCR4_S175"
            ],
            "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 A for 0-10% 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": "2024-06-03T15:26:44.938512+00:00",
    "summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "d8fbc675-2805-4ee3-b1c6-852be2964d88"
}