IGVFDS4045JTCH

released
{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS4045JTCH/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS4045JTCH",
    "aliases": [
        "jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF4-BinC-PCR1_S87",
        "jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF4-BinC-PCR2_S93",
        "jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF4-BinC-PCR3_S183",
        "jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF4-BinC-PCR4_S189"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS4045JTCH](/auxiliary-sets/IGVFDS4045JTCH/) has sequence file(s) [IGVFFI4285CCHK](/sequence-files/IGVFFI4285CCHK/), [IGVFFI8374AEMS](/sequence-files/IGVFFI8374AEMS/), [IGVFFI5521JTXL](/sequence-files/IGVFFI5521JTXL/), [IGVFFI2065WSYF](/sequence-files/IGVFFI2065WSYF/) 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/IGVFDS4045JTCH/"
            }
        ]
    },
    "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": "2024-05-16T18:01:20.925098+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/IGVFFI4285CCHK/",
            "accession": "IGVFFI4285CCHK",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF4-BinC-PCR1_S87"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-03T15:27:56.504553+00:00",
            "file_format": "fastq",
            "file_size": 5489268,
            "href": "/sequence-files/IGVFFI4285CCHK/@@download/IGVFFI4285CCHK.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/03/6eccaf1b-f19b-4e9a-b11b-9213b337a44e/IGVFFI4285CCHK.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-FF4-BinC-PCR1_S87_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI2881HWLY/",
            "accession": "IGVFFI2881HWLY",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF4-BinC-PCR1_S87"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T22:12:21.901121+00:00",
            "file_format": "yaml",
            "file_size": 901,
            "href": "/configuration-files/IGVFFI2881HWLY/@@download/IGVFFI2881HWLY.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/bead906b-7e73-49ae-8d57-66d797a76439/IGVFFI2881HWLY.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF4-BinC-PCR1_S87.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8374AEMS/",
            "accession": "IGVFFI8374AEMS",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF4-BinC-PCR2_S93"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-03T15:28:12.613341+00:00",
            "file_format": "fastq",
            "file_size": 5005733,
            "href": "/sequence-files/IGVFFI8374AEMS/@@download/IGVFFI8374AEMS.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/03/879f25c4-e69f-4b0b-b3ed-6308c7daccbe/IGVFFI8374AEMS.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-FF4-BinC-PCR2_S93_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI5521JTXL/",
            "accession": "IGVFFI5521JTXL",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF4-BinC-PCR3_S183"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-03T15:28:28.987250+00:00",
            "file_format": "fastq",
            "file_size": 13306864,
            "href": "/sequence-files/IGVFFI5521JTXL/@@download/IGVFFI5521JTXL.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/03/be2daa09-7de5-4ac4-ba17-b75a31dedfbc/IGVFFI5521JTXL.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-FF4-BinC-PCR3_S183_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI2065WSYF/",
            "accession": "IGVFFI2065WSYF",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF4-BinC-PCR4_S189"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-03T15:28:45.407230+00:00",
            "file_format": "fastq",
            "file_size": 11175898,
            "href": "/sequence-files/IGVFFI2065WSYF/@@download/IGVFFI2065WSYF.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/03/924e15f9-ca81-4bf7-9cf7-282bc22008e2/IGVFFI2065WSYF.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-FF4-BinC-PCR4_S189_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI0861YUMY/",
            "accession": "IGVFFI0861YUMY",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF4-BinC-PCR2_S93"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T22:12:36.519906+00:00",
            "file_format": "yaml",
            "file_size": 901,
            "href": "/configuration-files/IGVFFI0861YUMY/@@download/IGVFFI0861YUMY.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/93fed33e-e63d-4d29-bf94-384449cd4883/IGVFFI0861YUMY.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF4-BinC-PCR2_S93.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI9429EELR/",
            "accession": "IGVFFI9429EELR",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF4-BinC-PCR3_S183"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T22:12:51.231676+00:00",
            "file_format": "yaml",
            "file_size": 903,
            "href": "/configuration-files/IGVFFI9429EELR/@@download/IGVFFI9429EELR.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/ce5c28fa-b06e-4530-8d6e-3fb002833f3f/IGVFFI9429EELR.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF4-BinC-PCR3_S183.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI1481CPMA/",
            "accession": "IGVFFI1481CPMA",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF4-BinC-PCR4_S189"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T22:13:05.903003+00:00",
            "file_format": "yaml",
            "file_size": 904,
            "href": "/configuration-files/IGVFFI1481CPMA/@@download/IGVFFI1481CPMA.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/6820bd03-7cd8-4968-998e-bfddf81b7518/IGVFFI1481CPMA.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF4-BinC-PCR4_S189.yaml",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS6482AXWW/"
    ],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS0360KHPL/",
            "accession": "IGVFDS0360KHPL",
            "aliases": [
                "jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF4-BinC-PCR1_S87",
                "jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF4-BinC-PCR2_S93",
                "jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF4-BinC-PCR3_S183",
                "jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF4-BinC-PCR4_S189"
            ],
            "preferred_assay_title": "CRISPR FlowFISH screen",
            "status": "released"
        }
    ],
    "release_timestamp": "2024-07-10T20:18:43.846993+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM7739FHWE/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM7739FHWE",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF4-BinC-PCR1_S87",
                "jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF4-BinC-PCR2_S93",
                "jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF4-BinC-PCR3_S183",
                "jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF4-BinC-PCR4_S189"
            ],
            "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 C for 35-45% 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": "2024-06-03T15:27:56.504553+00:00",
    "summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "e39c6262-36d4-4106-9163-34c36c3eeb7a"
}