IGVFDS0835JNKZ

released
{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS0835JNKZ/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS0835JNKZ",
    "aliases": [
        "jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin6hrs-FF2-BinA-PCR1-Rep1_S145",
        "jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin6hrs-FF2-BinA-PCR2-Rep1_S151",
        "jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin6hrs-FF2-BinA-PCR3-Rep1_S199",
        "jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin6hrs-FF2-BinA-PCR4-Rep1_S205"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS0835JNKZ](/auxiliary-sets/IGVFDS0835JNKZ/) has sequence file(s) [IGVFFI4353EABL](/sequence-files/IGVFFI4353EABL/), [IGVFFI7697RLSM](/sequence-files/IGVFFI7697RLSM/), [IGVFFI4301VZBV](/sequence-files/IGVFFI4301VZBV/), [IGVFFI8756OKRA](/sequence-files/IGVFFI8756OKRA/) 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/IGVFDS0835JNKZ/"
            }
        ]
    },
    "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": "2024-05-14T16:51:32.801012+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/IGVFFI4353EABL/",
            "accession": "IGVFFI4353EABL",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF2-BinA-PCR1-Rep1_S145"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:54:33.198114+00:00",
            "file_format": "fastq",
            "file_size": 24041524,
            "href": "/sequence-files/IGVFFI4353EABL/@@download/IGVFFI4353EABL.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/f836496b-2491-40b8-b071-3e2fab9438d5/IGVFFI4353EABL.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/FAM3C-Auxin6hrs-FF2-BinA-PCR1-Rep1_S145_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI6521QYYB/",
            "accession": "IGVFFI6521QYYB",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF2-BinA-PCR1-Rep1_S145"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:44:36.652871+00:00",
            "file_format": "yaml",
            "file_size": 914,
            "href": "/configuration-files/IGVFFI6521QYYB/@@download/IGVFFI6521QYYB.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/d024105e-bd8a-441f-8d91-d77693434872/IGVFFI6521QYYB.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF2-BinA-PCR1-Rep1_S145.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI7697RLSM/",
            "accession": "IGVFFI7697RLSM",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF2-BinA-PCR4-Rep1_S205"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:55:28.089976+00:00",
            "file_format": "fastq",
            "file_size": 23140878,
            "href": "/sequence-files/IGVFFI7697RLSM/@@download/IGVFFI7697RLSM.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/39f2c7cc-991e-4779-a494-3f93e0211360/IGVFFI7697RLSM.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/FAM3C-Auxin6hrs-FF2-BinA-PCR4-Rep1_S205_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI3518JXAP/",
            "accession": "IGVFFI3518JXAP",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF2-BinA-PCR2-Rep1_S151"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:44:51.436459+00:00",
            "file_format": "yaml",
            "file_size": 915,
            "href": "/configuration-files/IGVFFI3518JXAP/@@download/IGVFFI3518JXAP.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/494bb01f-df96-49eb-8a21-d29ccca7ca8e/IGVFFI3518JXAP.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF2-BinA-PCR2-Rep1_S151.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI4301VZBV/",
            "accession": "IGVFFI4301VZBV",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF2-BinA-PCR2-Rep1_S151"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:54:51.165695+00:00",
            "file_format": "fastq",
            "file_size": 11283403,
            "href": "/sequence-files/IGVFFI4301VZBV/@@download/IGVFFI4301VZBV.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/e01f9ac4-04c5-40a6-85d8-2e9e30732563/IGVFFI4301VZBV.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/FAM3C-Auxin6hrs-FF2-BinA-PCR2-Rep1_S151_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8756OKRA/",
            "accession": "IGVFFI8756OKRA",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF2-BinA-PCR3-Rep1_S199"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:55:09.399166+00:00",
            "file_format": "fastq",
            "file_size": 29602750,
            "href": "/sequence-files/IGVFFI8756OKRA/@@download/IGVFFI8756OKRA.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/cde377ca-4e18-4d29-a672-5fddbfc63b7e/IGVFFI8756OKRA.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/FAM3C-Auxin6hrs-FF2-BinA-PCR3-Rep1_S199_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI8640KFXU/",
            "accession": "IGVFFI8640KFXU",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF2-BinA-PCR4-Rep1_S205"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:45:18.652785+00:00",
            "file_format": "yaml",
            "file_size": 913,
            "href": "/configuration-files/IGVFFI8640KFXU/@@download/IGVFFI8640KFXU.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/597fdfd5-ac46-40a7-8a7e-c43eac03bf90/IGVFFI8640KFXU.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF2-BinA-PCR4-Rep1_S205.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI9965KSVR/",
            "accession": "IGVFFI9965KSVR",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF2-BinA-PCR3-Rep1_S199"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:45:05.196202+00:00",
            "file_format": "yaml",
            "file_size": 913,
            "href": "/configuration-files/IGVFFI9965KSVR/@@download/IGVFFI9965KSVR.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/2b4e5029-eff8-44b9-8a8c-161e1d6e7bd2/IGVFFI9965KSVR.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF2-BinA-PCR3-Rep1_S199.yaml",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS5239VQTN/"
    ],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS5833OTRY/",
            "accession": "IGVFDS5833OTRY",
            "aliases": [
                "jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF2-BinA-PCR1-Rep1_S145",
                "jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF2-BinA-PCR2-Rep1_S151",
                "jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF2-BinA-PCR3-Rep1_S199",
                "jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF2-BinA-PCR4-Rep1_S205"
            ],
            "preferred_assay_title": "CRISPR FlowFISH screen",
            "status": "released"
        }
    ],
    "release_timestamp": "2024-07-10T20:12:48.845093+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM3488NLFX/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM3488NLFX",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF2-BinA-PCR1-Rep1_S145",
                "jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF2-BinA-PCR2-Rep1_S151",
                "jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF2-BinA-PCR3-Rep1_S199",
                "jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF2-BinA-PCR4-Rep1_S205"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS1891GTLU/"
            ],
            "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 FAM3C) 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": "2024-06-01T01:54:33.198114+00:00",
    "summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "7e1c3b65-3fb5-406a-810f-fa6553aaf6f8"
}