IGVFDS9525OEUV

released
{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS9525OEUV/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS9525OEUV",
    "aliases": [
        "jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR1-Rep1_S136",
        "jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR2-Rep1_S142",
        "jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR3-Rep1_S190",
        "jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR4-Rep1_S196"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS9525OEUV](/auxiliary-sets/IGVFDS9525OEUV/) has sequence file(s) [IGVFFI8644ELSX](/sequence-files/IGVFFI8644ELSX/), [IGVFFI5753MODI](/sequence-files/IGVFFI5753MODI/), [IGVFFI8303KMQH](/sequence-files/IGVFFI8303KMQH/), [IGVFFI0003GKTA](/sequence-files/IGVFFI0003GKTA/) 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/IGVFDS9525OEUV/"
            }
        ]
    },
    "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": "2024-05-14T16:51:10.193383+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/IGVFFI8644ELSX/",
            "accession": "IGVFFI8644ELSX",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR1-Rep1_S136"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:53:28.759279+00:00",
            "file_format": "fastq",
            "file_size": 23487754,
            "href": "/sequence-files/IGVFFI8644ELSX/@@download/IGVFFI8644ELSX.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/13ee86c5-a85b-4fc0-be0b-9775e621b630/IGVFFI8644ELSX.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-FF1-BinD-PCR1-Rep1_S136_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI2872OELQ/",
            "accession": "IGVFFI2872OELQ",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR1-Rep1_S136"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:43:48.524116+00:00",
            "file_format": "yaml",
            "file_size": 915,
            "href": "/configuration-files/IGVFFI2872OELQ/@@download/IGVFFI2872OELQ.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/2a932c52-0b85-415b-a7e1-0023b54fcf03/IGVFFI2872OELQ.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF1-BinD-PCR1-Rep1_S136.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI5753MODI/",
            "accession": "IGVFFI5753MODI",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR2-Rep1_S142"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:53:47.027427+00:00",
            "file_format": "fastq",
            "file_size": 16779582,
            "href": "/sequence-files/IGVFFI5753MODI/@@download/IGVFFI5753MODI.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/a4b41623-608e-4802-b8ef-44b046dd49cb/IGVFFI5753MODI.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-FF1-BinD-PCR2-Rep1_S142_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8303KMQH/",
            "accession": "IGVFFI8303KMQH",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR3-Rep1_S190"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:54:05.364093+00:00",
            "file_format": "fastq",
            "file_size": 31644031,
            "href": "/sequence-files/IGVFFI8303KMQH/@@download/IGVFFI8303KMQH.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/aeebe66c-e6a6-493d-bb62-4c4b8cc7af8f/IGVFFI8303KMQH.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-FF1-BinD-PCR3-Rep1_S190_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI0003GKTA/",
            "accession": "IGVFFI0003GKTA",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR4-Rep1_S196"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:54:24.045661+00:00",
            "file_format": "fastq",
            "file_size": 27878556,
            "href": "/sequence-files/IGVFFI0003GKTA/@@download/IGVFFI0003GKTA.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/3ced79d6-a73c-471f-a681-db8b71db0241/IGVFFI0003GKTA.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-FF1-BinD-PCR4-Rep1_S196_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI0910MBLA/",
            "accession": "IGVFFI0910MBLA",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR4-Rep1_S196"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:44:29.977867+00:00",
            "file_format": "yaml",
            "file_size": 912,
            "href": "/configuration-files/IGVFFI0910MBLA/@@download/IGVFFI0910MBLA.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/15103a88-96d8-494c-a62b-4372c55c5801/IGVFFI0910MBLA.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF1-BinD-PCR4-Rep1_S196.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI9546POQT/",
            "accession": "IGVFFI9546POQT",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR2-Rep1_S142"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:44:02.557487+00:00",
            "file_format": "yaml",
            "file_size": 914,
            "href": "/configuration-files/IGVFFI9546POQT/@@download/IGVFFI9546POQT.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/b699eadb-d44c-42db-a9c7-a696db179ec6/IGVFFI9546POQT.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF1-BinD-PCR2-Rep1_S142.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI6470EGGF/",
            "accession": "IGVFFI6470EGGF",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR3-Rep1_S190"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:44:16.301247+00:00",
            "file_format": "yaml",
            "file_size": 914,
            "href": "/configuration-files/IGVFFI6470EGGF/@@download/IGVFFI6470EGGF.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/4bf8edef-bc26-4857-ad1f-6a0a5732f3ff/IGVFFI6470EGGF.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF1-BinD-PCR3-Rep1_S190.yaml",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS5239VQTN/"
    ],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS2315UDUR/",
            "accession": "IGVFDS2315UDUR",
            "aliases": [
                "jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR1-Rep1_S136",
                "jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR2-Rep1_S142",
                "jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR3-Rep1_S190",
                "jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR4-Rep1_S196"
            ],
            "preferred_assay_title": "CRISPR FlowFISH screen",
            "status": "released"
        }
    ],
    "release_timestamp": "2024-07-10T20:12:26.448816+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM6928JPHO/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM6928JPHO",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR1-Rep1_S136",
                "jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR2-Rep1_S142",
                "jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR3-Rep1_S190",
                "jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR4-Rep1_S196"
            ],
            "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 D for 55-65% 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": "2024-06-01T01:53:28.759279+00:00",
    "summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "34e5d3e5-3fa4-40c4-a530-ef50ded623a9"
}