IGVFDS6376TFTJ

released
{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS6376TFTJ/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS6376TFTJ",
    "aliases": [
        "jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR1-Rep1_S217",
        "jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR2-Rep1_S223",
        "jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR3-Rep1_S259",
        "jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR4-Rep1_S265"
    ],
    "assay_term": {
        "@id": "/assay-terms/OBI_0003661/",
        "status": "released",
        "term_name": "in vitro CRISPR screen using flow cytometry"
    },
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS0319JZYS](/auxiliary-sets/IGVFDS0319JZYS/) has sequence file(s) [IGVFFI3927LCXN](/sequence-files/IGVFFI3927LCXN/), [IGVFFI8797POIP](/sequence-files/IGVFFI8797POIP/), [IGVFFI4291ESKX](/sequence-files/IGVFFI4291ESKX/), [IGVFFI1384RCQE](/sequence-files/IGVFFI1384RCQE/) 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/IGVFDS0319JZYS/"
            }
        ],
        "WARNING": [
            {
                "category": "missing files",
                "detail": "Measurement set [IGVFDS6376TFTJ](/measurement-sets/IGVFDS6376TFTJ/) has no `files`. File sets are expected to have files.",
                "level": 40,
                "level_name": "WARNING",
                "name": "audit_no_files",
                "path": "/measurement-sets/IGVFDS6376TFTJ/"
            }
        ]
    },
    "auxiliary_sets": [
        {
            "@id": "/auxiliary-sets/IGVFDS5464XLTY/",
            "accession": "IGVFDS5464XLTY",
            "aliases": [
                "jesse-engreitz:auxiliary_sortparams_CRUDO_CCND1_Auxin0hrs-FF1"
            ],
            "file_set_type": "cell sorting",
            "status": "released"
        },
        {
            "@id": "/auxiliary-sets/IGVFDS0319JZYS/",
            "accession": "IGVFDS0319JZYS",
            "aliases": [
                "jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR1-Rep1_S217",
                "jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR2-Rep1_S223",
                "jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR3-Rep1_S259",
                "jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR4-Rep1_S265"
            ],
            "file_set_type": "gRNA sequencing",
            "status": "released"
        }
    ],
    "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": "2024-05-13T22:07:21.499963+00:00",
    "documents": [
        "/documents/74d53b9c-ab1d-42e3-b679-d3a00ae3d842/"
    ],
    "donors": [
        {
            "@id": "/human-donors/IGVFDO0384OZRW/",
            "accession": "IGVFDO0384OZRW",
            "aliases": [
                "igvf:donor_of_HCT116"
            ],
            "sex": "male",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "externally_hosted": false,
    "file_set_type": "experimental data",
    "files": [],
    "input_for": [
        "/analysis-sets/IGVFDS1569RNPD/"
    ],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "notes": "The readout 2e41e624-f6c7-4f0c-a07e-bc36cefdca39 was removed from this measurement set.",
    "preferred_assay_title": "CRISPR FlowFISH screen",
    "protocols": [
        "https://www.protocols.io/view/crispri-of-regulatory-elements-upon-degron-operati-5jyl82d59l2w/v1"
    ],
    "release_timestamp": "2024-07-10T19:37:41.161637+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM9315IOJD/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM9315IOJD",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR1-Rep1_S217",
                "jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR2-Rep1_S223",
                "jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR3-Rep1_S259",
                "jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR4-Rep1_S265"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                {
                    "@id": "/construct-library-sets/IGVFDS6351FGNG/",
                    "accession": "IGVFDS6351FGNG",
                    "file_set_type": "guide library",
                    "status": "released",
                    "summary": "guide (sgRNA) library targeting accessible genome regions in many genomic loci"
                }
            ],
            "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 A for 0-10% expression of CCND1) modified with CRISPRi Sp-dCas9-KOX1-KRAB, inactive AID system targeting RAD21, transfected with a guide library",
            "taxa": "Homo sapiens"
        }
    ],
    "schema_version": "23",
    "status": "released",
    "submitted_by": {
        "@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
        "title": "Chongyon Park"
    },
    "submitted_files_timestamp": "2024-06-01T01:35:55.762873+00:00",
    "summary": "mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "targeted_genes": [
        {
            "@id": "/genes/ENSG00000110092/",
            "geneid": "ENSG00000110092",
            "name": "cyclin D1",
            "status": "released",
            "symbol": "CCND1",
            "synonyms": [
                "BCL1",
                "PRAD1",
                "D11S287E",
                "B-cell CLL/lymphoma 1",
                "PRAD1 oncogene",
                "BCL-1 oncogene",
                "G1/S-specific cyclin-D1",
                "B-cell lymphoma 1 protein",
                "U21B31"
            ]
        }
    ],
    "uuid": "a1ccc6cc-d9a8-4e7b-ae1a-1da5a7d76123"
}