IGVFDS8492ZWVD

released
{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS8492ZWVD/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS8492ZWVD",
    "aliases": [
        "jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF2-BinB-PCR1-Rep1_S230",
        "jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF2-BinB-PCR2-Rep1_S236",
        "jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF2-BinB-PCR3-Rep1_S272",
        "jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF2-BinB-PCR4-Rep1_S278"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS8492ZWVD](/auxiliary-sets/IGVFDS8492ZWVD/) has sequence file(s) [IGVFFI9565FZNZ](/sequence-files/IGVFFI9565FZNZ/), [IGVFFI6852PRDQ](/sequence-files/IGVFFI6852PRDQ/), [IGVFFI9062PSUL](/sequence-files/IGVFFI9062PSUL/), [IGVFFI1218OAIH](/sequence-files/IGVFFI1218OAIH/) 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/IGVFDS8492ZWVD/"
            }
        ]
    },
    "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": "2024-05-13T22:39:13.252806+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/IGVFFI9565FZNZ/",
            "accession": "IGVFFI9565FZNZ",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF2-BinB-PCR1-Rep1_S230"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:37:11.457096+00:00",
            "file_format": "fastq",
            "file_size": 24958082,
            "href": "/sequence-files/IGVFFI9565FZNZ/@@download/IGVFFI9565FZNZ.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/d5bdc1a2-c59b-4b72-b6ac-313dfeae1621/IGVFFI9565FZNZ.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/CCND1-Auxin0hrs-FF2-BinB-PCR1-Rep1_S230_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI1876ABOL/",
            "accession": "IGVFFI1876ABOL",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF2-BinB-PCR1-Rep1_S230"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:28:58.509236+00:00",
            "file_format": "yaml",
            "file_size": 915,
            "href": "/configuration-files/IGVFFI1876ABOL/@@download/IGVFFI1876ABOL.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/106f2e62-0b84-4c32-bda7-e2125f448903/IGVFFI1876ABOL.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF2-BinB-PCR1-Rep1_S230.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI6852PRDQ/",
            "accession": "IGVFFI6852PRDQ",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF2-BinB-PCR2-Rep1_S236"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:37:29.546554+00:00",
            "file_format": "fastq",
            "file_size": 18602238,
            "href": "/sequence-files/IGVFFI6852PRDQ/@@download/IGVFFI6852PRDQ.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/3aee977e-8eb0-447f-9d7f-d562dc83d26e/IGVFFI6852PRDQ.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/CCND1-Auxin0hrs-FF2-BinB-PCR2-Rep1_S236_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9062PSUL/",
            "accession": "IGVFFI9062PSUL",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF2-BinB-PCR3-Rep1_S272"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:37:47.086105+00:00",
            "file_format": "fastq",
            "file_size": 27474093,
            "href": "/sequence-files/IGVFFI9062PSUL/@@download/IGVFFI9062PSUL.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/652e9561-b44b-44e4-9ee3-99c1f2e5f0a6/IGVFFI9062PSUL.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/CCND1-Auxin0hrs-FF2-BinB-PCR3-Rep1_S272_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI1218OAIH/",
            "accession": "IGVFFI1218OAIH",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF2-BinB-PCR4-Rep1_S278"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:38:05.716965+00:00",
            "file_format": "fastq",
            "file_size": 19641540,
            "href": "/sequence-files/IGVFFI1218OAIH/@@download/IGVFFI1218OAIH.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/b49678e0-ee3f-4cf0-91d3-722b15151e00/IGVFFI1218OAIH.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/CCND1-Auxin0hrs-FF2-BinB-PCR4-Rep1_S278_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI5903GHCI/",
            "accession": "IGVFFI5903GHCI",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF2-BinB-PCR3-Rep1_S272"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:29:26.612999+00:00",
            "file_format": "yaml",
            "file_size": 913,
            "href": "/configuration-files/IGVFFI5903GHCI/@@download/IGVFFI5903GHCI.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/c08387b3-f864-47e2-b34b-ee9b499a6035/IGVFFI5903GHCI.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF2-BinB-PCR3-Rep1_S272.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI3347MQPE/",
            "accession": "IGVFFI3347MQPE",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF2-BinB-PCR4-Rep1_S278"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:29:40.605284+00:00",
            "file_format": "yaml",
            "file_size": 913,
            "href": "/configuration-files/IGVFFI3347MQPE/@@download/IGVFFI3347MQPE.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/41dd722d-d76b-47c8-a9b5-10de4670d312/IGVFFI3347MQPE.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF2-BinB-PCR4-Rep1_S278.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI9158EPYH/",
            "accession": "IGVFFI9158EPYH",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF2-BinB-PCR2-Rep1_S236"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:29:12.774331+00:00",
            "file_format": "yaml",
            "file_size": 913,
            "href": "/configuration-files/IGVFFI9158EPYH/@@download/IGVFFI9158EPYH.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/0b0fe4cd-2941-4cea-9ef6-28aa4af27ecc/IGVFFI9158EPYH.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF2-BinB-PCR2-Rep1_S236.yaml",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS1569RNPD/"
    ],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS3149HCGU/",
            "accession": "IGVFDS3149HCGU",
            "aliases": [
                "jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF2-BinB-PCR1-Rep1_S230",
                "jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF2-BinB-PCR2-Rep1_S236",
                "jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF2-BinB-PCR3-Rep1_S272",
                "jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF2-BinB-PCR4-Rep1_S278"
            ],
            "preferred_assay_title": "CRISPR FlowFISH screen",
            "status": "released"
        }
    ],
    "release_timestamp": "2024-07-10T20:08:37.730861+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM6482UHDK/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM6482UHDK",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF2-BinB-PCR1-Rep1_S230",
                "jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF2-BinB-PCR2-Rep1_S236",
                "jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF2-BinB-PCR3-Rep1_S272",
                "jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF2-BinB-PCR4-Rep1_S278"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS6351FGNG/"
            ],
            "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 B for 10-20% expression of CCND1) 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": "2024-06-01T01:37:11.457096+00:00",
    "summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "6f59ed53-bc21-412d-8d66-15aed8cfdb8e"
}