IGVFDS2086YDNO

released
{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS2086YDNO/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS2086YDNO",
    "aliases": [
        "jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF1-BinA-PCR1_S49",
        "jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF1-BinA-PCR2_S55",
        "jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF1-BinA-PCR3_S145",
        "jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF1-BinA-PCR4_S151"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS2086YDNO](/auxiliary-sets/IGVFDS2086YDNO/) has sequence file(s) [IGVFFI6411ZRDE](/sequence-files/IGVFFI6411ZRDE/), [IGVFFI9315VFMT](/sequence-files/IGVFFI9315VFMT/), [IGVFFI2101KHOH](/sequence-files/IGVFFI2101KHOH/), [IGVFFI8335UTTJ](/sequence-files/IGVFFI8335UTTJ/) 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/IGVFDS2086YDNO/"
            }
        ]
    },
    "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": "2024-05-16T17:58:54.936910+00:00",
    "donors": [
        {
            "@id": "/human-donors/IGVFDO0384OZRW/",
            "accession": "IGVFDO0384OZRW",
            "aliases": [
                "igvf:donor_of_HCT116"
            ],
            "sex": "male",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "file_set_type": "gRNA sequencing",
    "files": [
        {
            "@id": "/sequence-files/IGVFFI6411ZRDE/",
            "accession": "IGVFFI6411ZRDE",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF1-BinA-PCR1_S49"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T02:19:56.748397+00:00",
            "file_format": "fastq",
            "file_size": 11164702,
            "href": "/sequence-files/IGVFFI6411ZRDE/@@download/IGVFFI6411ZRDE.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/058fb837-83b6-4c6f-aa8b-59241add2d18/IGVFFI6411ZRDE.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF1-BinA-PCR1_S49_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI0901ITUC/",
            "accession": "IGVFFI0901ITUC",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF1-BinA-PCR1_S49"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T22:09:18.336327+00:00",
            "file_format": "yaml",
            "file_size": 903,
            "href": "/configuration-files/IGVFFI0901ITUC/@@download/IGVFFI0901ITUC.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/05c50283-db8e-4fa1-b123-1499d2fc2dbb/IGVFFI0901ITUC.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF1-BinA-PCR1_S49.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9315VFMT/",
            "accession": "IGVFFI9315VFMT",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF1-BinA-PCR3_S145"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T02:20:37.436735+00:00",
            "file_format": "fastq",
            "file_size": 25312994,
            "href": "/sequence-files/IGVFFI9315VFMT/@@download/IGVFFI9315VFMT.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/553b5cd2-e3d5-4615-a5e6-c3160b9e2113/IGVFFI9315VFMT.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF1-BinA-PCR3_S145_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI2101KHOH/",
            "accession": "IGVFFI2101KHOH",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF1-BinA-PCR2_S55"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T02:20:16.661412+00:00",
            "file_format": "fastq",
            "file_size": 7121098,
            "href": "/sequence-files/IGVFFI2101KHOH/@@download/IGVFFI2101KHOH.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/bcd1b250-72c0-4803-a923-974b92d2ce81/IGVFFI2101KHOH.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF1-BinA-PCR2_S55_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8335UTTJ/",
            "accession": "IGVFFI8335UTTJ",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF1-BinA-PCR4_S151"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T02:20:55.444582+00:00",
            "file_format": "fastq",
            "file_size": 19453121,
            "href": "/sequence-files/IGVFFI8335UTTJ/@@download/IGVFFI8335UTTJ.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/28652d54-f5e3-4b2d-bdb1-01593b2276e9/IGVFFI8335UTTJ.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF1-BinA-PCR4_S151_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI2519BAOP/",
            "accession": "IGVFFI2519BAOP",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF1-BinA-PCR4_S151"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T22:10:03.708778+00:00",
            "file_format": "yaml",
            "file_size": 902,
            "href": "/configuration-files/IGVFFI2519BAOP/@@download/IGVFFI2519BAOP.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/f2948797-08ea-4bda-86d7-ce0265e556a4/IGVFFI2519BAOP.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF1-BinA-PCR4_S151.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI1495XMKJ/",
            "accession": "IGVFFI1495XMKJ",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF1-BinA-PCR2_S55"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T22:09:33.858069+00:00",
            "file_format": "yaml",
            "file_size": 902,
            "href": "/configuration-files/IGVFFI1495XMKJ/@@download/IGVFFI1495XMKJ.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/b83b3244-af65-4059-bf1f-1270ea8d3ba4/IGVFFI1495XMKJ.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF1-BinA-PCR2_S55.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI1838QYEH/",
            "accession": "IGVFFI1838QYEH",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF1-BinA-PCR3_S145"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T22:09:48.811023+00:00",
            "file_format": "yaml",
            "file_size": 903,
            "href": "/configuration-files/IGVFFI1838QYEH/@@download/IGVFFI1838QYEH.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/f6a9caec-7bb3-441a-a27d-706009db62d6/IGVFFI1838QYEH.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF1-BinA-PCR3_S145.yaml",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS6482AXWW/"
    ],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS1505VYUV/",
            "accession": "IGVFDS1505VYUV",
            "aliases": [
                "jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF1-BinA-PCR1_S49",
                "jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF1-BinA-PCR2_S55",
                "jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF1-BinA-PCR3_S145",
                "jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF1-BinA-PCR4_S151"
            ],
            "preferred_assay_title": "CRISPR FlowFISH screen",
            "status": "released"
        }
    ],
    "release_timestamp": "2024-07-10T20:16:20.905833+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM6859FEHH/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM6859FEHH",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF1-BinA-PCR1_S49",
                "jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF1-BinA-PCR2_S55",
                "jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF1-BinA-PCR3_S145",
                "jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF1-BinA-PCR4_S151"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS7846UISG/"
            ],
            "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 (sorting details: FACS bin A for 0-10% expression of KITLG) 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": "12",
    "status": "released",
    "submitted_by": {
        "@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
        "title": "Chongyon Park"
    },
    "submitted_files_timestamp": "2024-06-01T02:19:56.748397+00:00",
    "summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "2305767d-d7ea-42c8-a7cd-b9c734509091"
}