IGVFDS5686BCWV

released
{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS5686BCWV/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS5686BCWV",
    "aliases": [
        "jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF2-BinD-PCR1-Rep1_S16",
        "jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF2-BinD-PCR2-Rep1_S22",
        "jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF2-BinD-PCR3-Rep1_S70",
        "jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF2-BinD-PCR4-Rep1_S76"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS5686BCWV](/auxiliary-sets/IGVFDS5686BCWV/) has sequence file(s) [IGVFFI9405VYLM](/sequence-files/IGVFFI9405VYLM/), [IGVFFI0694FRDB](/sequence-files/IGVFFI0694FRDB/), [IGVFFI5037IDTR](/sequence-files/IGVFFI5037IDTR/), [IGVFFI3468FNAC](/sequence-files/IGVFFI3468FNAC/) 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/IGVFDS5686BCWV/"
            }
        ]
    },
    "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": "2024-05-14T20:31:21.040550+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/IGVFFI9405VYLM/",
            "accession": "IGVFFI9405VYLM",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF2-BinD-PCR1-Rep1_S16"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:45:57.001817+00:00",
            "file_format": "fastq",
            "file_size": 9893485,
            "href": "/sequence-files/IGVFFI9405VYLM/@@download/IGVFFI9405VYLM.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/ec1954e0-5f4a-4323-b163-e5e961b13109/IGVFFI9405VYLM.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/SSFA2-Auxin0hrs-FF2-BinD-PCR1-Rep1_S16_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI2268RIAK/",
            "accession": "IGVFFI2268RIAK",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF2-BinD-PCR1-Rep1_S16"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:38:25.260747+00:00",
            "file_format": "yaml",
            "file_size": 914,
            "href": "/configuration-files/IGVFFI2268RIAK/@@download/IGVFFI2268RIAK.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/04b6cbfc-63ef-45d1-9521-f8f7cbf8d4f2/IGVFFI2268RIAK.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF2-BinD-PCR1-Rep1_S16.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI1293UJBT/",
            "accession": "IGVFFI1293UJBT",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF2-BinD-PCR4-Rep1_S76"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:39:35.081047+00:00",
            "file_format": "yaml",
            "file_size": 911,
            "href": "/configuration-files/IGVFFI1293UJBT/@@download/IGVFFI1293UJBT.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/97001486-35cf-4bd9-ab79-fe4963b58091/IGVFFI1293UJBT.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF2-BinD-PCR4-Rep1_S76.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI0694FRDB/",
            "accession": "IGVFFI0694FRDB",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF2-BinD-PCR2-Rep1_S22"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:46:20.261699+00:00",
            "file_format": "fastq",
            "file_size": 11230610,
            "href": "/sequence-files/IGVFFI0694FRDB/@@download/IGVFFI0694FRDB.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/d25b7f78-21d6-4470-a268-846689560eb0/IGVFFI0694FRDB.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/SSFA2-Auxin0hrs-FF2-BinD-PCR2-Rep1_S22_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI5037IDTR/",
            "accession": "IGVFFI5037IDTR",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF2-BinD-PCR3-Rep1_S70"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:46:38.044973+00:00",
            "file_format": "fastq",
            "file_size": 19549369,
            "href": "/sequence-files/IGVFFI5037IDTR/@@download/IGVFFI5037IDTR.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/d2e67756-1145-4771-b2ac-efd20f35b91d/IGVFFI5037IDTR.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/SSFA2-Auxin0hrs-FF2-BinD-PCR3-Rep1_S70_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3468FNAC/",
            "accession": "IGVFFI3468FNAC",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF2-BinD-PCR4-Rep1_S76"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:46:55.904510+00:00",
            "file_format": "fastq",
            "file_size": 23927332,
            "href": "/sequence-files/IGVFFI3468FNAC/@@download/IGVFFI3468FNAC.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/8133d7a0-1d9e-48a7-850d-b8a8b7f811ab/IGVFFI3468FNAC.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/SSFA2-Auxin0hrs-FF2-BinD-PCR4-Rep1_S76_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI2082IHRL/",
            "accession": "IGVFFI2082IHRL",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF2-BinD-PCR2-Rep1_S22"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:38:41.016438+00:00",
            "file_format": "yaml",
            "file_size": 912,
            "href": "/configuration-files/IGVFFI2082IHRL/@@download/IGVFFI2082IHRL.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/896592f4-a109-4ef2-9fa9-95b738b5f6cb/IGVFFI2082IHRL.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF2-BinD-PCR2-Rep1_S22.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI2987ULMD/",
            "accession": "IGVFFI2987ULMD",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF2-BinD-PCR3-Rep1_S70"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:39:19.579088+00:00",
            "file_format": "yaml",
            "file_size": 912,
            "href": "/configuration-files/IGVFFI2987ULMD/@@download/IGVFFI2987ULMD.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/1a969a1a-6004-424e-8581-725ca4921220/IGVFFI2987ULMD.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF2-BinD-PCR3-Rep1_S70.yaml",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS2031CTSP/"
    ],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS5251YUKR/",
            "accession": "IGVFDS5251YUKR",
            "aliases": [
                "jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF2-BinD-PCR1-Rep1_S16",
                "jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF2-BinD-PCR2-Rep1_S22",
                "jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF2-BinD-PCR3-Rep1_S70",
                "jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF2-BinD-PCR4-Rep1_S76"
            ],
            "preferred_assay_title": "CRISPR FlowFISH screen",
            "status": "released"
        }
    ],
    "release_timestamp": "2024-07-10T20:24:47.719907+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM0599CFOW/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM0599CFOW",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF2-BinD-PCR1-Rep1_S16",
                "jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF2-BinD-PCR2-Rep1_S22",
                "jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF2-BinD-PCR3-Rep1_S70",
                "jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF2-BinD-PCR4-Rep1_S76"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS5413RKIA/"
            ],
            "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 D for 55-65% expression of SSFA2) 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": "2024-06-01T01:45:57.001817+00:00",
    "summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "d2c362f2-cd6c-45a0-a44d-50f8dff732f6"
}