IGVFDS6281UOJN

released
{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS6281UOJN/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS6281UOJN",
    "aliases": [
        "jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF3-BinF-PCR1_S30",
        "jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF3-BinF-PCR2_S36",
        "jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF3-BinF-PCR3_S126",
        "jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF3-BinF-PCR4_S132"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS6281UOJN](/auxiliary-sets/IGVFDS6281UOJN/) has sequence file(s) [IGVFFI1150JCHT](/sequence-files/IGVFFI1150JCHT/), [IGVFFI1402KSIW](/sequence-files/IGVFFI1402KSIW/), [IGVFFI8461PESG](/sequence-files/IGVFFI8461PESG/), [IGVFFI1359HHUE](/sequence-files/IGVFFI1359HHUE/) 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/IGVFDS6281UOJN/"
            }
        ]
    },
    "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": "2024-05-16T17:42:02.955270+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/IGVFFI1150JCHT/",
            "accession": "IGVFFI1150JCHT",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF3-BinF-PCR1_S30"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T02:17:39.461501+00:00",
            "file_format": "fastq",
            "file_size": 12726879,
            "href": "/sequence-files/IGVFFI1150JCHT/@@download/IGVFFI1150JCHT.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/a3bf18b1-ae51-49ef-b4eb-4b6333194aa8/IGVFFI1150JCHT.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-FF3-BinF-PCR1_S30_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI4265GEQC/",
            "accession": "IGVFFI4265GEQC",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF3-BinF-PCR1_S30"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T22:07:40.336209+00:00",
            "file_format": "yaml",
            "file_size": 901,
            "href": "/configuration-files/IGVFFI4265GEQC/@@download/IGVFFI4265GEQC.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/f5aee5c0-a565-4b78-bc74-5dcc4cddd3d7/IGVFFI4265GEQC.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF3-BinF-PCR1_S30.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI1402KSIW/",
            "accession": "IGVFFI1402KSIW",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF3-BinF-PCR4_S132"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T02:18:37.897313+00:00",
            "file_format": "fastq",
            "file_size": 20561098,
            "href": "/sequence-files/IGVFFI1402KSIW/@@download/IGVFFI1402KSIW.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/84596e94-1e29-4049-9787-cfd61e28f5ec/IGVFFI1402KSIW.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-FF3-BinF-PCR4_S132_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI8549VEWO/",
            "accession": "IGVFFI8549VEWO",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF3-BinF-PCR4_S132"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T22:08:19.954150+00:00",
            "file_format": "yaml",
            "file_size": 903,
            "href": "/configuration-files/IGVFFI8549VEWO/@@download/IGVFFI8549VEWO.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/6d8d5d64-a4d0-47a7-b97c-691ab6b85dab/IGVFFI8549VEWO.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF3-BinF-PCR4_S132.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8461PESG/",
            "accession": "IGVFFI8461PESG",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF3-BinF-PCR2_S36"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T02:17:57.746625+00:00",
            "file_format": "fastq",
            "file_size": 8943891,
            "href": "/sequence-files/IGVFFI8461PESG/@@download/IGVFFI8461PESG.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/98635695-ddcf-4a47-8660-bd6e220b521b/IGVFFI8461PESG.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-FF3-BinF-PCR2_S36_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI1359HHUE/",
            "accession": "IGVFFI1359HHUE",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF3-BinF-PCR3_S126"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T02:18:15.672424+00:00",
            "file_format": "fastq",
            "file_size": 27179584,
            "href": "/sequence-files/IGVFFI1359HHUE/@@download/IGVFFI1359HHUE.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/dff0393e-fa3d-4588-ab17-ad64dfd42d10/IGVFFI1359HHUE.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-FF3-BinF-PCR3_S126_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI5393CUFG/",
            "accession": "IGVFFI5393CUFG",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF3-BinF-PCR2_S36"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T22:07:53.508073+00:00",
            "file_format": "yaml",
            "file_size": 901,
            "href": "/configuration-files/IGVFFI5393CUFG/@@download/IGVFFI5393CUFG.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/f452fa10-19ed-41c8-8be4-56004e3d1c91/IGVFFI5393CUFG.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF3-BinF-PCR2_S36.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI4893JIOO/",
            "accession": "IGVFFI4893JIOO",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF3-BinF-PCR3_S126"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T22:08:06.662117+00:00",
            "file_format": "yaml",
            "file_size": 903,
            "href": "/configuration-files/IGVFFI4893JIOO/@@download/IGVFFI4893JIOO.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/1491fc12-14a1-421d-9eba-4cc71534fcb7/IGVFFI4893JIOO.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF3-BinF-PCR3_S126.yaml",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS6482AXWW/"
    ],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS0600IKJB/",
            "accession": "IGVFDS0600IKJB",
            "aliases": [
                "jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF3-BinF-PCR1_S30",
                "jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF3-BinF-PCR2_S36",
                "jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF3-BinF-PCR3_S126",
                "jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF3-BinF-PCR4_S132"
            ],
            "preferred_assay_title": "CRISPR FlowFISH screen",
            "status": "released"
        }
    ],
    "release_timestamp": "2024-07-10T20:15:31.247984+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM7141IWGF/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM7141IWGF",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF3-BinF-PCR1_S30",
                "jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF3-BinF-PCR2_S36",
                "jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF3-BinF-PCR3_S126",
                "jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF3-BinF-PCR4_S132"
            ],
            "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": "2024-06-01T02:17:39.461501+00:00",
    "summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "a5e7f61b-173a-46da-a9b0-8baa2f646e0b"
}