IGVFDS5128CXIS

released
{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS5128CXIS/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS5128CXIS",
    "aliases": [
        "jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-THP1-PE2_Exp4_NegControl_AmpliconSequencing"
    ],
    "assay_term": {
        "@id": "/assay-terms/OBI_0003661/",
        "term_name": "in vitro CRISPR screen using flow cytometry"
    },
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "mismatched status",
                "detail": "Released measurement set [IGVFDS5128CXIS](/measurement-sets/IGVFDS5128CXIS/) has in progress subobject auxiliary set [IGVFDS3821IGRL](/auxiliary-sets/IGVFDS3821IGRL/).",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_item_status",
                "path": "/measurement-sets/IGVFDS5128CXIS/"
            }
        ],
        "NOT_COMPLIANT": [
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS3821IGRL](/auxiliary-sets/IGVFDS3821IGRL/) has sequence file(s) [IGVFFI5860PVJQ](/sequence-files/IGVFFI5860PVJQ/), [IGVFFI3449WZQF](/sequence-files/IGVFFI3449WZQF/), [IGVFFI1898QYOM](/sequence-files/IGVFFI1898QYOM/), [IGVFFI8823JOUV](/sequence-files/IGVFFI8823JOUV/), [IGVFFI1771FPVE](/sequence-files/IGVFFI1771FPVE/), [IGVFFI8992CXFT](/sequence-files/IGVFFI8992CXFT/), [IGVFFI9984TILJ](/sequence-files/IGVFFI9984TILJ/), [IGVFFI1798AJTL](/sequence-files/IGVFFI1798AJTL/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_inconsistent_sequencing_kit",
                "path": "/auxiliary-sets/IGVFDS3821IGRL/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS3821IGRL](/auxiliary-sets/IGVFDS3821IGRL/) has sequence file(s): [IGVFFI5860PVJQ](/sequence-files/IGVFFI5860PVJQ/), [IGVFFI3449WZQF](/sequence-files/IGVFFI3449WZQF/), [IGVFFI1898QYOM](/sequence-files/IGVFFI1898QYOM/), [IGVFFI8823JOUV](/sequence-files/IGVFFI8823JOUV/), [IGVFFI1771FPVE](/sequence-files/IGVFFI1771FPVE/), [IGVFFI8992CXFT](/sequence-files/IGVFFI8992CXFT/), [IGVFFI9984TILJ](/sequence-files/IGVFFI9984TILJ/), [IGVFFI1798AJTL](/sequence-files/IGVFFI1798AJTL/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_missing_seqspec",
                "path": "/auxiliary-sets/IGVFDS3821IGRL/"
            },
            {
                "category": "missing auxiliary set",
                "detail": "Measurement set [IGVFDS5128CXIS](/measurement-sets/IGVFDS5128CXIS/) has no cell sorting `auxiliary_sets`. CRISPR-based measurement sets that utilize flow cytometry are expected to link to a cell sorting auxiliary set.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_missing_auxiliary_set",
                "path": "/measurement-sets/IGVFDS5128CXIS/"
            },
            {
                "category": "missing targeted genes",
                "detail": "Measurement set [IGVFDS5128CXIS](/measurement-sets/IGVFDS5128CXIS/) has no `targeted_genes`. ChIP-seq and CRISPR flow cytometry assays are expected to specify targeted gene(s).",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_targeted_genes",
                "path": "/measurement-sets/IGVFDS5128CXIS/"
            }
        ],
        "WARNING": [
            {
                "category": "missing analysis",
                "detail": "Auxiliary set [IGVFDS3821IGRL](/auxiliary-sets/IGVFDS3821IGRL/) is a raw data set with files, but is not listed in any `input_file_sets` for any analysis sets. Raw data sets with files are expected to be associated with at least one analysis set.",
                "level": 40,
                "level_name": "WARNING",
                "name": "audit_input_file_set_for",
                "path": "/auxiliary-sets/IGVFDS3821IGRL/"
            }
        ]
    },
    "auxiliary_sets": [
        {
            "@id": "/auxiliary-sets/IGVFDS3821IGRL/",
            "accession": "IGVFDS3821IGRL",
            "aliases": [
                "jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-THP1-PE2_Exp4_NegControl_AmpliconSequencing_AuxiliarySet"
            ],
            "file_set_type": "variant sequencing"
        }
    ],
    "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": [
        {
            "@id": "/measurement-sets/IGVFDS7230BLHQ/",
            "accession": "IGVFDS7230BLHQ",
            "aliases": [
                "jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep3-BinD_AmpliconSequencing"
            ]
        },
        {
            "@id": "/measurement-sets/IGVFDS6069DTLX/",
            "accession": "IGVFDS6069DTLX",
            "aliases": [
                "jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep4-BinB_AmpliconSequencing"
            ]
        },
        {
            "@id": "/measurement-sets/IGVFDS4188FAAP/",
            "accession": "IGVFDS4188FAAP",
            "aliases": [
                "jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep4-FACS_Input_AmpliconSequencing"
            ]
        },
        {
            "@id": "/measurement-sets/IGVFDS3508UNRE/",
            "accession": "IGVFDS3508UNRE",
            "aliases": [
                "jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-BinA_AmpliconSequencing"
            ]
        },
        {
            "@id": "/measurement-sets/IGVFDS0176OXWE/",
            "accession": "IGVFDS0176OXWE",
            "aliases": [
                "jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-BinB_AmpliconSequencing"
            ]
        },
        {
            "@id": "/measurement-sets/IGVFDS5338RAZZ/",
            "accession": "IGVFDS5338RAZZ",
            "aliases": [
                "jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-BinC_AmpliconSequencing"
            ]
        },
        {
            "@id": "/measurement-sets/IGVFDS8099KDSE/",
            "accession": "IGVFDS8099KDSE",
            "aliases": [
                "jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-BinD_AmpliconSequencing"
            ]
        },
        {
            "@id": "/measurement-sets/IGVFDS6957VHOD/",
            "accession": "IGVFDS6957VHOD",
            "aliases": [
                "jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-BinD_AmpliconSequencing"
            ]
        },
        {
            "@id": "/measurement-sets/IGVFDS6252SSYB/",
            "accession": "IGVFDS6252SSYB",
            "aliases": [
                "jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep3-BinB_AmpliconSequencing"
            ]
        },
        {
            "@id": "/measurement-sets/IGVFDS0839SQRJ/",
            "accession": "IGVFDS0839SQRJ",
            "aliases": [
                "jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep3-BinC_AmpliconSequencing"
            ]
        },
        {
            "@id": "/measurement-sets/IGVFDS5795QOPU/",
            "accession": "IGVFDS5795QOPU",
            "aliases": [
                "jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep2-BinA_AmpliconSequencing"
            ]
        },
        {
            "@id": "/measurement-sets/IGVFDS7378QBUS/",
            "accession": "IGVFDS7378QBUS",
            "aliases": [
                "jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep2-BinB_AmpliconSequencing"
            ]
        },
        {
            "@id": "/measurement-sets/IGVFDS8933DNXM/",
            "accession": "IGVFDS8933DNXM",
            "aliases": [
                "jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep3-BinB_AmpliconSequencing"
            ]
        },
        {
            "@id": "/measurement-sets/IGVFDS2940LDCT/",
            "accession": "IGVFDS2940LDCT",
            "aliases": [
                "jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep3-BinC_AmpliconSequencing"
            ]
        },
        {
            "@id": "/measurement-sets/IGVFDS4141QOFR/",
            "accession": "IGVFDS4141QOFR",
            "aliases": [
                "jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep3-BinA_AmpliconSequencing"
            ]
        },
        {
            "@id": "/measurement-sets/IGVFDS6384OLQB/",
            "accession": "IGVFDS6384OLQB",
            "aliases": [
                "jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep3-BinD_AmpliconSequencing"
            ]
        },
        {
            "@id": "/measurement-sets/IGVFDS2294QFQV/",
            "accession": "IGVFDS2294QFQV",
            "aliases": [
                "jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep3-FACS_Input_AmpliconSequencing"
            ]
        },
        {
            "@id": "/measurement-sets/IGVFDS3326NVFS/",
            "accession": "IGVFDS3326NVFS",
            "aliases": [
                "jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep4-BinB_AmpliconSequencing"
            ]
        },
        {
            "@id": "/measurement-sets/IGVFDS4825MNUM/",
            "accession": "IGVFDS4825MNUM",
            "aliases": [
                "jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep4-FACS_Input_AmpliconSequencing"
            ]
        },
        {
            "@id": "/measurement-sets/IGVFDS9395LATB/",
            "accession": "IGVFDS9395LATB",
            "aliases": [
                "jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-BinA_AmpliconSequencing"
            ]
        },
        {
            "@id": "/measurement-sets/IGVFDS0649NZHX/",
            "accession": "IGVFDS0649NZHX",
            "aliases": [
                "jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-BinB_AmpliconSequencing"
            ]
        },
        {
            "@id": "/measurement-sets/IGVFDS9381QGYL/",
            "accession": "IGVFDS9381QGYL",
            "aliases": [
                "jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-BinC_AmpliconSequencing"
            ]
        },
        {
            "@id": "/measurement-sets/IGVFDS9275AQHE/",
            "accession": "IGVFDS9275AQHE",
            "aliases": [
                "jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-BinD_AmpliconSequencing"
            ]
        },
        {
            "@id": "/measurement-sets/IGVFDS2337XGGI/",
            "accession": "IGVFDS2337XGGI",
            "aliases": [
                "jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input_AmpliconSequencing"
            ]
        },
        {
            "@id": "/measurement-sets/IGVFDS4607VBYI/",
            "accession": "IGVFDS4607VBYI",
            "aliases": [
                "jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep2-BinC_AmpliconSequencing"
            ]
        },
        {
            "@id": "/measurement-sets/IGVFDS7805IFYA/",
            "accession": "IGVFDS7805IFYA",
            "aliases": [
                "jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep2-BinD_AmpliconSequencing"
            ]
        },
        {
            "@id": "/measurement-sets/IGVFDS6266PDNX/",
            "accession": "IGVFDS6266PDNX",
            "aliases": [
                "jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep2-FACS_Input_AmpliconSequencing"
            ]
        },
        {
            "@id": "/measurement-sets/IGVFDS3292ERTL/",
            "accession": "IGVFDS3292ERTL",
            "aliases": [
                "jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep3-BinA_AmpliconSequencing"
            ]
        },
        {
            "@id": "/measurement-sets/IGVFDS4811UOUL/",
            "accession": "IGVFDS4811UOUL",
            "aliases": [
                "jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep3-FACS_Input_AmpliconSequencing"
            ]
        },
        {
            "@id": "/measurement-sets/IGVFDS7998ZPYH/",
            "accession": "IGVFDS7998ZPYH",
            "aliases": [
                "jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep4-BinA_AmpliconSequencing"
            ]
        },
        {
            "@id": "/measurement-sets/IGVFDS8163FWZM/",
            "accession": "IGVFDS8163FWZM",
            "aliases": [
                "jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep4-BinC_AmpliconSequencing"
            ]
        },
        {
            "@id": "/measurement-sets/IGVFDS5989CMGV/",
            "accession": "IGVFDS5989CMGV",
            "aliases": [
                "jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep4-BinD_AmpliconSequencing"
            ]
        },
        {
            "@id": "/measurement-sets/IGVFDS8499AVHV/",
            "accession": "IGVFDS8499AVHV",
            "aliases": [
                "jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-FACS_Input_AmpliconSequencing"
            ]
        },
        {
            "@id": "/measurement-sets/IGVFDS4363PDBQ/",
            "accession": "IGVFDS4363PDBQ",
            "aliases": [
                "jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-BinA_AmpliconSequencing"
            ]
        },
        {
            "@id": "/measurement-sets/IGVFDS9880SAMJ/",
            "accession": "IGVFDS9880SAMJ",
            "aliases": [
                "jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-BinB_AmpliconSequencing"
            ]
        },
        {
            "@id": "/measurement-sets/IGVFDS7100AAFY/",
            "accession": "IGVFDS7100AAFY",
            "aliases": [
                "jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-FACS_Input_AmpliconSequencing"
            ]
        },
        {
            "@id": "/measurement-sets/IGVFDS3765SWWC/",
            "accession": "IGVFDS3765SWWC",
            "aliases": [
                "jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep4-BinA_AmpliconSequencing"
            ]
        },
        {
            "@id": "/measurement-sets/IGVFDS2247EEVD/",
            "accession": "IGVFDS2247EEVD",
            "aliases": [
                "jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep4-BinC_AmpliconSequencing"
            ]
        },
        {
            "@id": "/measurement-sets/IGVFDS7957LQTQ/",
            "accession": "IGVFDS7957LQTQ",
            "aliases": [
                "jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep4-BinD_AmpliconSequencing"
            ]
        },
        {
            "@id": "/measurement-sets/IGVFDS0872DEIB/",
            "accession": "IGVFDS0872DEIB",
            "aliases": [
                "jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-BinC_AmpliconSequencing"
            ]
        }
    ],
    "creation_timestamp": "2023-12-13T08:01:35.729249+00:00",
    "donors": [
        {
            "@id": "/human-donors/IGVFDO7359LVPI/",
            "accession": "IGVFDO7359LVPI",
            "aliases": [
                "igvf:donor_of_THP1"
            ],
            "sex": "male",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "file_set_type": "experimental data",
    "files": [],
    "input_file_set_for": [
        "/analysis-sets/IGVFDS4359OODY/"
    ],
    "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": "Variant FlowFISH",
    "protocols": [
        "https://www.protocols.io/view/flowfish-with-primeflow-36wgq3q4olk5/v1"
    ],
    "release_timestamp": "2023-12-20T23:07:56.546430+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM3211UEWZ/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM3211UEWZ",
            "aliases": [
                "jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-THP1-PE2_Exp4_NegControl"
            ],
            "classifications": [
                "cell line"
            ],
            "modifications": [
                {
                    "@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
                    "modality": "prime editing"
                }
            ],
            "sample_terms": [
                {
                    "@id": "/sample-terms/EFO_0001253/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
                        "Item"
                    ],
                    "aliases": [
                        "igvf:THP-1"
                    ],
                    "status": "released",
                    "summary": "THP-1",
                    "term_name": "THP-1"
                }
            ],
            "status": "released",
            "summary": "THP-1 cell line, male, Homo sapiens",
            "taxa": "Homo sapiens"
        }
    ],
    "schema_version": "22",
    "status": "released",
    "submitted_by": {
        "@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
        "title": "Michael Montgomery"
    },
    "submitted_files_timestamp": "2023-12-13T08:17:19.736198+00:00",
    "summary": "prime editing Variant FlowFISH",
    "uuid": "fb47792f-c0be-488b-84bd-c23a65c154a1"
}