IGVFDS7753HONE

released
{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS7753HONE/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS7753HONE",
    "aliases": [
        "jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF2-BinE-PCR1_S17",
        "jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF2-BinE-PCR2_S23",
        "jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF2-BinE-PCR3_S113",
        "jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF2-BinE-PCR4_S119"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS7753HONE](/auxiliary-sets/IGVFDS7753HONE/) has sequence file(s) [IGVFFI6004KUNG](/sequence-files/IGVFFI6004KUNG/), [IGVFFI4888REEW](/sequence-files/IGVFFI4888REEW/), [IGVFFI4302EURY](/sequence-files/IGVFFI4302EURY/), [IGVFFI7967STOK](/sequence-files/IGVFFI7967STOK/) 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/IGVFDS7753HONE/"
            }
        ]
    },
    "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": "2024-05-16T17:41:32.612056+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/IGVFFI6004KUNG/",
            "accession": "IGVFFI6004KUNG",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF2-BinE-PCR1_S17"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T02:14:41.760588+00:00",
            "file_format": "fastq",
            "file_size": 2872205,
            "href": "/sequence-files/IGVFFI6004KUNG/@@download/IGVFFI6004KUNG.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/8f9fd099-3ad8-40cb-b90c-0e0a6895e9b1/IGVFFI6004KUNG.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF2-BinE-PCR1_S17_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI3756GQZG/",
            "accession": "IGVFFI3756GQZG",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF2-BinE-PCR1_S17"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T22:06:44.114700+00:00",
            "file_format": "yaml",
            "file_size": 901,
            "href": "/configuration-files/IGVFFI3756GQZG/@@download/IGVFFI3756GQZG.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/7007c891-0fb3-490e-b65d-93c6ac0a4490/IGVFFI3756GQZG.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF2-BinE-PCR1_S17.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI4888REEW/",
            "accession": "IGVFFI4888REEW",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF2-BinE-PCR4_S119"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T02:17:19.211616+00:00",
            "file_format": "fastq",
            "file_size": 16205238,
            "href": "/sequence-files/IGVFFI4888REEW/@@download/IGVFFI4888REEW.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/d2527f18-21cd-400a-a556-6088ed44fd7e/IGVFFI4888REEW.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF2-BinE-PCR4_S119_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI6848VWFJ/",
            "accession": "IGVFFI6848VWFJ",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF2-BinE-PCR2_S23"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T22:06:57.740616+00:00",
            "file_format": "yaml",
            "file_size": 903,
            "href": "/configuration-files/IGVFFI6848VWFJ/@@download/IGVFFI6848VWFJ.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/6900f5d2-bf26-4f71-81b3-15a8fa3b081c/IGVFFI6848VWFJ.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF2-BinE-PCR2_S23.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI4302EURY/",
            "accession": "IGVFFI4302EURY",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF2-BinE-PCR2_S23"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T02:14:59.272481+00:00",
            "file_format": "fastq",
            "file_size": 7422037,
            "href": "/sequence-files/IGVFFI4302EURY/@@download/IGVFFI4302EURY.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/8a05be0b-8807-40b2-a306-46e2bba950dc/IGVFFI4302EURY.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF2-BinE-PCR2_S23_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI7967STOK/",
            "accession": "IGVFFI7967STOK",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF2-BinE-PCR3_S113"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T02:17:01.141538+00:00",
            "file_format": "fastq",
            "file_size": 11451670,
            "href": "/sequence-files/IGVFFI7967STOK/@@download/IGVFFI7967STOK.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/ae17dcb3-ba2e-4f80-9f73-5ed95b8e18c8/IGVFFI7967STOK.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF2-BinE-PCR3_S113_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI3445KTGV/",
            "accession": "IGVFFI3445KTGV",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF2-BinE-PCR4_S119"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T22:07:24.525471+00:00",
            "file_format": "yaml",
            "file_size": 903,
            "href": "/configuration-files/IGVFFI3445KTGV/@@download/IGVFFI3445KTGV.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/e8f48e4c-6ff5-4bff-a426-790c7e3f6bf0/IGVFFI3445KTGV.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF2-BinE-PCR4_S119.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI8709FCAZ/",
            "accession": "IGVFFI8709FCAZ",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF2-BinE-PCR3_S113"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T22:07:11.250180+00:00",
            "file_format": "yaml",
            "file_size": 903,
            "href": "/configuration-files/IGVFFI8709FCAZ/@@download/IGVFFI8709FCAZ.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/6b5f57d8-0176-4150-a2ff-145b5ebbf07a/IGVFFI8709FCAZ.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF2-BinE-PCR3_S113.yaml",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS6482AXWW/"
    ],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS8133FFMV/",
            "accession": "IGVFDS8133FFMV",
            "aliases": [
                "jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF2-BinE-PCR1_S17",
                "jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF2-BinE-PCR2_S23",
                "jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF2-BinE-PCR3_S113",
                "jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF2-BinE-PCR4_S119"
            ],
            "preferred_assay_title": "CRISPR FlowFISH screen",
            "status": "released"
        }
    ],
    "release_timestamp": "2024-07-10T20:14:42.667983+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM9074NPMT/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM9074NPMT",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinE-PCR1_S17",
                "jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinE-PCR2_S23",
                "jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinE-PCR3_S113",
                "jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinE-PCR4_S119"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS7846UISG/"
            ],
            "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 (sorting details: FACS bin E for 80-90% expression of KITLG) modified with CRISPRi Sp-dCas9-KOX1-KRAB, inactive AID system targeting RAD21, transfected with a guide library",
            "taxa": "Homo sapiens"
        }
    ],
    "schema_version": "12",
    "status": "released",
    "submitted_by": {
        "@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
        "title": "Chongyon Park"
    },
    "submitted_files_timestamp": "2024-06-01T02:14:41.760588+00:00",
    "summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "975c4ee3-ffed-461f-968e-f614591cecda"
}