IGVFDS2978YQVA

released
{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS2978YQVA/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS2978YQVA",
    "aliases": [
        "jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input_AmpliconSequencing"
    ],
    "assay_term": {
        "@id": "/assay-terms/OBI_0003661/",
        "assay_slims": [
            "CRISPR screens"
        ],
        "status": "released",
        "term_name": "in vitro CRISPR screen using flow cytometry"
    },
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing publication",
                "detail": "Measurement set [IGVFDS2978YQVA](/measurement-sets/IGVFDS2978YQVA/) has no `publications`. Released and archived file sets are expected to be associated with a publication.",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_file_set_missing_publication",
                "path": "/measurement-sets/IGVFDS2978YQVA/"
            },
            {
                "category": "missing sequencing kit",
                "detail": "Measurement set [IGVFDS2978YQVA](/measurement-sets/IGVFDS2978YQVA/) has sequence file(s) [IGVFFI4719EJGG](/sequence-files/IGVFFI4719EJGG/), [IGVFFI2343VDQB](/sequence-files/IGVFFI2343VDQB/), [IGVFFI9721QXSH](/sequence-files/IGVFFI9721QXSH/), [IGVFFI9315IHLL](/sequence-files/IGVFFI9315IHLL/), [IGVFFI5662LHGR](/sequence-files/IGVFFI5662LHGR/), [IGVFFI5349UFOZ](/sequence-files/IGVFFI5349UFOZ/), [IGVFFI5374SSMO](/sequence-files/IGVFFI5374SSMO/), [IGVFFI6448TEJG](/sequence-files/IGVFFI6448TEJG/), [IGVFFI3321HMGZ](/sequence-files/IGVFFI3321HMGZ/), [IGVFFI0864LZHT](/sequence-files/IGVFFI0864LZHT/), [IGVFFI6332YPUU](/sequence-files/IGVFFI6332YPUU/), [IGVFFI2391ZMYI](/sequence-files/IGVFFI2391ZMYI/), [IGVFFI6492FHPV](/sequence-files/IGVFFI6492FHPV/), [IGVFFI9323QYVO](/sequence-files/IGVFFI9323QYVO/), [IGVFFI4573MSCD](/sequence-files/IGVFFI4573MSCD/), [IGVFFI7395ZMHL](/sequence-files/IGVFFI7395ZMHL/) which lack specification of a `sequencing_kit`. Sequence files in a file set associated wtih bulk data should specify a sequencing kit.",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_inconsistent_sequencing_kit",
                "path": "/measurement-sets/IGVFDS2978YQVA/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS2978YQVA](/measurement-sets/IGVFDS2978YQVA/) has sequence file(s): [IGVFFI4719EJGG](/sequence-files/IGVFFI4719EJGG/), [IGVFFI2343VDQB](/sequence-files/IGVFFI2343VDQB/), [IGVFFI9721QXSH](/sequence-files/IGVFFI9721QXSH/), [IGVFFI9315IHLL](/sequence-files/IGVFFI9315IHLL/), [IGVFFI5662LHGR](/sequence-files/IGVFFI5662LHGR/), [IGVFFI5349UFOZ](/sequence-files/IGVFFI5349UFOZ/), [IGVFFI5374SSMO](/sequence-files/IGVFFI5374SSMO/), [IGVFFI6448TEJG](/sequence-files/IGVFFI6448TEJG/), [IGVFFI3321HMGZ](/sequence-files/IGVFFI3321HMGZ/), [IGVFFI0864LZHT](/sequence-files/IGVFFI0864LZHT/), [IGVFFI6332YPUU](/sequence-files/IGVFFI6332YPUU/), [IGVFFI2391ZMYI](/sequence-files/IGVFFI2391ZMYI/), [IGVFFI6492FHPV](/sequence-files/IGVFFI6492FHPV/), [IGVFFI9323QYVO](/sequence-files/IGVFFI9323QYVO/), [IGVFFI4573MSCD](/sequence-files/IGVFFI4573MSCD/), [IGVFFI7395ZMHL](/sequence-files/IGVFFI7395ZMHL/) which do not have any `seqspecs`. Sequence files in a file set associated with bulk data are expected to link to a sequence specification file.",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_missing_seqspec",
                "path": "/measurement-sets/IGVFDS2978YQVA/"
            },
            {
                "category": "mismatched status",
                "detail": "Released in vitro system [IGVFSM5940EPFP](/in-vitro-systems/IGVFSM5940EPFP/) has in progress subobject construct library set [IGVFDS6982DESN](/construct-library-sets/IGVFDS6982DESN/).",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_item_status",
                "path": "/in-vitro-systems/IGVFSM5940EPFP/"
            },
            {
                "category": "missing publication",
                "detail": "In vitro system [IGVFSM5940EPFP](/in-vitro-systems/IGVFSM5940EPFP/) has no `publications`. Released and archived samples are expected to be associated with a publication.",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_sample_missing_publication",
                "path": "/in-vitro-systems/IGVFSM5940EPFP/"
            }
        ],
        "NOT_COMPLIANT": [
            {
                "category": "missing control for",
                "detail": "Measurement set [IGVFDS2978YQVA](/measurement-sets/IGVFDS2978YQVA/) has no `control_for`. The `control_file_sets` should be patched on the file sets it serves as a control for and this property, `control_for`, will be reverse calculated. File sets that specify a control type are expected to be a control for other file sets.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_control_for_control_type",
                "path": "/measurement-sets/IGVFDS2978YQVA/"
            }
        ],
        "WARNING": [
            {
                "category": "missing auxiliary set",
                "detail": "Measurement set [IGVFDS2978YQVA](/measurement-sets/IGVFDS2978YQVA/) 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": 40,
                "level_name": "WARNING",
                "name": "audit_missing_auxiliary_set",
                "path": "/measurement-sets/IGVFDS2978YQVA/"
            },
            {
                "category": "missing targeted genes",
                "detail": "Measurement set [IGVFDS2978YQVA](/measurement-sets/IGVFDS2978YQVA/) has no `targeted_genes`. ChIP-seq and CRISPR flow cytometry assays are expected to specify targeted gene(s).",
                "level": 40,
                "level_name": "WARNING",
                "name": "audit_targeted_genes",
                "path": "/measurement-sets/IGVFDS2978YQVA/"
            }
        ]
    },
    "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"
    },
    "construct_library_sets": [
        {
            "@id": "/construct-library-sets/IGVFDS6982DESN/",
            "accession": "IGVFDS6982DESN",
            "file_set_type": "guide library",
            "status": "in progress",
            "summary": "guide (sgRNA) library targeting sequence variants in a genomic locus"
        }
    ],
    "control_file_sets": [
        {
            "@id": "/measurement-sets/IGVFDS5864UGFT/",
            "accession": "IGVFDS5864UGFT",
            "aliases": [
                "jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-THP1-PE2_Exp2_NegControl_AmpliconSequencing"
            ],
            "status": "released"
        }
    ],
    "control_for": [],
    "control_type": "unsorted FACS input",
    "creation_timestamp": "2023-12-01T00:05:32.482942+00:00",
    "data_use_limitation_summaries": [
        "no certificate"
    ],
    "donors": [
        {
            "@id": "/human-donors/IGVFDO7359LVPI/",
            "accession": "IGVFDO7359LVPI",
            "aliases": [
                "igvf:donor_of_THP1"
            ],
            "sex": "male",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "externally_hosted": false,
    "file_set_type": "experimental data",
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            "upload_status": "validated"
        },
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    "protocols": [
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    ],
    "release_timestamp": "2023-12-20T23:06:04.513290+00:00",
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    "summary": "unsorted FACS input CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
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}