IGVFDS3171OFHP

released
{
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        "FileSet",
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    ],
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        "term_name": "in vitro CRISPR screen using single-cell RNA-seq"
    },
    "audit": {
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            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS0282GEHF](/auxiliary-sets/IGVFDS0282GEHF/) has sequence file(s) [IGVFFI5080FNQC](/sequence-files/IGVFFI5080FNQC/), [IGVFFI0308CWCN](/sequence-files/IGVFFI0308CWCN/), [IGVFFI1051BZRQ](/sequence-files/IGVFFI1051BZRQ/), [IGVFFI2340RLRP](/sequence-files/IGVFFI2340RLRP/), [IGVFFI7481IACD](/sequence-files/IGVFFI7481IACD/), [IGVFFI7657ATAO](/sequence-files/IGVFFI7657ATAO/), [IGVFFI6529TUVF](/sequence-files/IGVFFI6529TUVF/), [IGVFFI9836SEKG](/sequence-files/IGVFFI9836SEKG/), [IGVFFI1579GEEH](/sequence-files/IGVFFI1579GEEH/), [IGVFFI6069TAYE](/sequence-files/IGVFFI6069TAYE/), [IGVFFI6689KNLG](/sequence-files/IGVFFI6689KNLG/), [IGVFFI1488GZKB](/sequence-files/IGVFFI1488GZKB/) 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/IGVFDS0282GEHF/"
            },
            {
                "category": "missing sequencing kit",
                "detail": "Measurement set [IGVFDS3171OFHP](/measurement-sets/IGVFDS3171OFHP/) has sequence file(s) [IGVFFI2851WWMV](/sequence-files/IGVFFI2851WWMV/), [IGVFFI0493ZORD](/sequence-files/IGVFFI0493ZORD/), [IGVFFI5644SHUR](/sequence-files/IGVFFI5644SHUR/), [IGVFFI0123WFFT](/sequence-files/IGVFFI0123WFFT/), [IGVFFI9133BYDP](/sequence-files/IGVFFI9133BYDP/), [IGVFFI9924ZSNL](/sequence-files/IGVFFI9924ZSNL/), [IGVFFI4406QWXH](/sequence-files/IGVFFI4406QWXH/), [IGVFFI0133FTES](/sequence-files/IGVFFI0133FTES/), [IGVFFI3618MDPB](/sequence-files/IGVFFI3618MDPB/), [IGVFFI5928SCMR](/sequence-files/IGVFFI5928SCMR/), [IGVFFI6981CWAL](/sequence-files/IGVFFI6981CWAL/), [IGVFFI3790XJRX](/sequence-files/IGVFFI3790XJRX/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
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        "@id": "/awards/HG011972/",
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            "@id": "/users/6c75dbfa-635e-4a7a-8ec8-9e51e9c380a4/",
            "title": "Jesse Engreitz"
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        "title": "Stanford Center for Connecting DNA Variants to Function and Phenotype"
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    "creation_timestamp": "2024-05-23T22:48:10.883999+00:00",
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            "taxa": "Homo sapiens"
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            "s3_uri": "s3://igvf-files/2024/06/20/da7a9171-f35d-4589-ab6d-be34de096676/IGVFFI8706AAXI.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/tapseq_seqspec.out.Auxin0hrs-Rep1-S4.rna.yaml.gz",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS5308EMCG/"
    ],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "notes": "The readout 86015c12-b9a6-43ba-9601-5d75aab4d39c was removed from this measurement set.",
    "preferred_assay_title": "TAP-seq",
    "protocols": [
        "https://www.protocols.io/view/crispri-of-regulatory-elements-upon-degron-operati-5jyl82d59l2w/v1"
    ],
    "release_timestamp": "2024-07-10T19:53:21.427662+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM5799ZEJH/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM5799ZEJH",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_TAPseq-Auxin0hrs-Rep1"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                {
                    "@id": "/construct-library-sets/IGVFDS9869EMNE/",
                    "accession": "IGVFDS9869EMNE",
                    "file_set_type": "guide library",
                    "status": "released",
                    "summary": "guide (sgRNA) library targeting accessible genome regions in 29 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 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": "2024-06-03T18:12:28.807286+00:00",
    "summary": "mixed CRISPR TAP-seq integrating a guide (sgRNA) library targeting accessible genome regions in 29 genomic loci",
    "uuid": "b29dea8d-86be-4e17-ba2c-644ec13112a8"
}