IGVFDS8403DDLC

released
{
    "@context": "/terms/",
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    ],
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        "status": "released",
        "term_name": "in vitro CRISPR screen using single-cell RNA-seq"
    },
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS4057PFBU](/auxiliary-sets/IGVFDS4057PFBU/) has sequence file(s) [IGVFFI3454BUML](/sequence-files/IGVFFI3454BUML/), [IGVFFI3968OUXL](/sequence-files/IGVFFI3968OUXL/), [IGVFFI4244AIHE](/sequence-files/IGVFFI4244AIHE/), [IGVFFI6509IKAK](/sequence-files/IGVFFI6509IKAK/), [IGVFFI7745NNEZ](/sequence-files/IGVFFI7745NNEZ/), [IGVFFI4261MKPE](/sequence-files/IGVFFI4261MKPE/), [IGVFFI2009UHTY](/sequence-files/IGVFFI2009UHTY/), [IGVFFI7212KPPW](/sequence-files/IGVFFI7212KPPW/), [IGVFFI2734JVZP](/sequence-files/IGVFFI2734JVZP/), [IGVFFI3142LWDR](/sequence-files/IGVFFI3142LWDR/), [IGVFFI6662ZMLA](/sequence-files/IGVFFI6662ZMLA/), [IGVFFI8620YJXA](/sequence-files/IGVFFI8620YJXA/) 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/IGVFDS4057PFBU/"
            },
            {
                "category": "missing sequencing kit",
                "detail": "Measurement set [IGVFDS8403DDLC](/measurement-sets/IGVFDS8403DDLC/) has sequence file(s) [IGVFFI9534FGRQ](/sequence-files/IGVFFI9534FGRQ/), [IGVFFI5460ASSY](/sequence-files/IGVFFI5460ASSY/), [IGVFFI4839QVTC](/sequence-files/IGVFFI4839QVTC/), [IGVFFI8111MPTE](/sequence-files/IGVFFI8111MPTE/), [IGVFFI2837YQLJ](/sequence-files/IGVFFI2837YQLJ/), [IGVFFI6606YZTP](/sequence-files/IGVFFI6606YZTP/), [IGVFFI5238KZBQ](/sequence-files/IGVFFI5238KZBQ/), [IGVFFI3272DDWD](/sequence-files/IGVFFI3272DDWD/), [IGVFFI1090FYAA](/sequence-files/IGVFFI1090FYAA/), [IGVFFI9275BZMG](/sequence-files/IGVFFI9275BZMG/), [IGVFFI9043ACMD](/sequence-files/IGVFFI9043ACMD/), [IGVFFI3461WBDK](/sequence-files/IGVFFI3461WBDK/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
                "level": 30,
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                "name": "audit_inconsistent_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": "2024-05-23T22:48:14.733164+00:00",
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            "taxa": "Homo sapiens"
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            "creation_timestamp": "2024-06-20T17:16:52.002958+00:00",
            "file_format": "yaml",
            "file_size": 1045,
            "href": "/configuration-files/IGVFFI2982KSVM/@@download/IGVFFI2982KSVM.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/20/75badb6c-c57f-4f0f-af2e-1ba0e7ca9c5e/IGVFFI2982KSVM.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/tapseq_seqspec.out.Auxin6hrs-Rep2-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": "2024-07-10T19:53:43.373893+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM8511JOMW/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM8511JOMW",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_TAPseq-Auxin6hrs-Rep2"
            ],
            "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": "/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 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": "23",
    "status": "released",
    "submitted_by": {
        "@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
        "title": "Chongyon Park"
    },
    "submitted_files_timestamp": "2024-06-03T19:12:44.938830+00:00",
    "summary": "mixed CRISPR TAP-seq integrating a guide (sgRNA) library targeting accessible genome regions in 29 genomic loci",
    "uuid": "cb574488-7b6d-4b8e-ba92-0e930e94e429"
}