IGVFDS8772YTOP

released
{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS8772YTOP/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS8772YTOP",
    "aliases": [
        "jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF1-BinF-PCR1_S6",
        "jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF1-BinF-PCR2_S12",
        "jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF1-BinF-PCR3_S102",
        "jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF1-BinF-PCR4_S108"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS8772YTOP](/auxiliary-sets/IGVFDS8772YTOP/) has sequence file(s) [IGVFFI6575LYZN](/sequence-files/IGVFFI6575LYZN/), [IGVFFI1910QCOP](/sequence-files/IGVFFI1910QCOP/), [IGVFFI7770QKUY](/sequence-files/IGVFFI7770QKUY/), [IGVFFI3880FPSK](/sequence-files/IGVFFI3880FPSK/) 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/IGVFDS8772YTOP/"
            }
        ]
    },
    "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": "2024-05-16T17:41:07.373627+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/IGVFFI6575LYZN/",
            "accession": "IGVFFI6575LYZN",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF1-BinF-PCR1_S6"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T02:10:27.221651+00:00",
            "file_format": "fastq",
            "file_size": 20442777,
            "href": "/sequence-files/IGVFFI6575LYZN/@@download/IGVFFI6575LYZN.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/b4defe1a-4c01-4616-8e48-91b24f734f41/IGVFFI6575LYZN.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-FF1-BinF-PCR1_S6_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI8582UZLK/",
            "accession": "IGVFFI8582UZLK",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF1-BinF-PCR1_S6"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T22:05:52.442076+00:00",
            "file_format": "yaml",
            "file_size": 902,
            "href": "/configuration-files/IGVFFI8582UZLK/@@download/IGVFFI8582UZLK.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/6c4670fd-06f5-4a7f-910d-54b4d2073030/IGVFFI8582UZLK.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF1-BinF-PCR1_S6.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI1910QCOP/",
            "accession": "IGVFFI1910QCOP",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF1-BinF-PCR3_S102"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T02:11:07.268875+00:00",
            "file_format": "fastq",
            "file_size": 38522468,
            "href": "/sequence-files/IGVFFI1910QCOP/@@download/IGVFFI1910QCOP.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/48867b74-44ca-4b5f-9fa7-9f99164aa891/IGVFFI1910QCOP.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-FF1-BinF-PCR3_S102_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI7770QKUY/",
            "accession": "IGVFFI7770QKUY",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF1-BinF-PCR4_S108"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T02:14:26.364740+00:00",
            "file_format": "fastq",
            "file_size": 44307926,
            "href": "/sequence-files/IGVFFI7770QKUY/@@download/IGVFFI7770QKUY.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/8bcdf0c8-2be2-446e-9da5-86b984d2db15/IGVFFI7770QKUY.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-FF1-BinF-PCR4_S108_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3880FPSK/",
            "accession": "IGVFFI3880FPSK",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF1-BinF-PCR2_S12"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T02:10:49.254748+00:00",
            "file_format": "fastq",
            "file_size": 15427391,
            "href": "/sequence-files/IGVFFI3880FPSK/@@download/IGVFFI3880FPSK.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/a8376b5f-7bb3-439a-b441-8ab5607abb3d/IGVFFI3880FPSK.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-FF1-BinF-PCR2_S12_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI1199IUIN/",
            "accession": "IGVFFI1199IUIN",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF1-BinF-PCR2_S12"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T22:06:05.952559+00:00",
            "file_format": "yaml",
            "file_size": 901,
            "href": "/configuration-files/IGVFFI1199IUIN/@@download/IGVFFI1199IUIN.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/29d519de-2697-4f9f-92c6-a47dce07add3/IGVFFI1199IUIN.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF1-BinF-PCR2_S12.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI0059WNTR/",
            "accession": "IGVFFI0059WNTR",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF1-BinF-PCR3_S102"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T22:06:19.359333+00:00",
            "file_format": "yaml",
            "file_size": 902,
            "href": "/configuration-files/IGVFFI0059WNTR/@@download/IGVFFI0059WNTR.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/2b61137f-8665-44a6-abec-7caeba4b818d/IGVFFI0059WNTR.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF1-BinF-PCR3_S102.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI7676KGCV/",
            "accession": "IGVFFI7676KGCV",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF1-BinF-PCR4_S108"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T22:06:32.856796+00:00",
            "file_format": "yaml",
            "file_size": 904,
            "href": "/configuration-files/IGVFFI7676KGCV/@@download/IGVFFI7676KGCV.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/5e09aac3-5770-4ca0-bcc4-ed52f679cb30/IGVFFI7676KGCV.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF1-BinF-PCR4_S108.yaml",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS6482AXWW/"
    ],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS7789CCCR/",
            "accession": "IGVFDS7789CCCR",
            "aliases": [
                "jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF1-BinF-PCR1_S6",
                "jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF1-BinF-PCR2_S12",
                "jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF1-BinF-PCR3_S102",
                "jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF1-BinF-PCR4_S108"
            ],
            "preferred_assay_title": "CRISPR FlowFISH screen",
            "status": "released"
        }
    ],
    "release_timestamp": "2024-07-10T20:14:06.047463+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM9117BTSA/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM9117BTSA",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF1-BinF-PCR1_S6",
                "jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF1-BinF-PCR2_S12",
                "jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF1-BinF-PCR3_S102",
                "jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF1-BinF-PCR4_S108"
            ],
            "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 F for 80-100% 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": "2024-06-01T02:10:27.221651+00:00",
    "summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "3941d1f1-bdc9-4966-bb87-beba3b801cf4"
}