IGVFDS4010VNGF

released
{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS4010VNGF/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS4010VNGF",
    "aliases": [
        "jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF2-BinB-PCR1-Rep1_S122",
        "jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF2-BinB-PCR2-Rep1_S128",
        "jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF2-BinB-PCR3-Rep1_S176",
        "jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF2-BinB-PCR4-Rep1_S182"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS4010VNGF](/auxiliary-sets/IGVFDS4010VNGF/) has sequence file(s) [IGVFFI4161WIYC](/sequence-files/IGVFFI4161WIYC/), [IGVFFI5330ZBZF](/sequence-files/IGVFFI5330ZBZF/), [IGVFFI6786VTNX](/sequence-files/IGVFFI6786VTNX/), [IGVFFI0237YEQF](/sequence-files/IGVFFI0237YEQF/) 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/IGVFDS4010VNGF/"
            }
        ]
    },
    "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": "2024-05-14T16:24:19.367918+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/IGVFFI4161WIYC/",
            "accession": "IGVFFI4161WIYC",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF2-BinB-PCR1-Rep1_S122"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:52:09.910992+00:00",
            "file_format": "fastq",
            "file_size": 15031923,
            "href": "/sequence-files/IGVFFI4161WIYC/@@download/IGVFFI4161WIYC.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/a3a66435-bad2-4ea4-b510-e3a7709e76a4/IGVFFI4161WIYC.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/FAM3C-Auxin0hrs-FF2-BinB-PCR1-Rep1_S122_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI8739NONQ/",
            "accession": "IGVFFI8739NONQ",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF2-BinB-PCR1-Rep1_S122"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:42:48.825129+00:00",
            "file_format": "yaml",
            "file_size": 914,
            "href": "/configuration-files/IGVFFI8739NONQ/@@download/IGVFFI8739NONQ.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/7595ec06-0f54-482c-b261-4e4b14f7e418/IGVFFI8739NONQ.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF2-BinB-PCR1-Rep1_S122.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI5330ZBZF/",
            "accession": "IGVFFI5330ZBZF",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF2-BinB-PCR2-Rep1_S128"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:52:28.220317+00:00",
            "file_format": "fastq",
            "file_size": 13261753,
            "href": "/sequence-files/IGVFFI5330ZBZF/@@download/IGVFFI5330ZBZF.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/eb458fc3-1f12-4329-b7b5-59f39c61c0e8/IGVFFI5330ZBZF.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/FAM3C-Auxin0hrs-FF2-BinB-PCR2-Rep1_S128_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI6786VTNX/",
            "accession": "IGVFFI6786VTNX",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF2-BinB-PCR3-Rep1_S176"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:52:46.255837+00:00",
            "file_format": "fastq",
            "file_size": 25060691,
            "href": "/sequence-files/IGVFFI6786VTNX/@@download/IGVFFI6786VTNX.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/e342dd20-bb98-4939-9231-6fb3157dd5a0/IGVFFI6786VTNX.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/FAM3C-Auxin0hrs-FF2-BinB-PCR3-Rep1_S176_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI0237YEQF/",
            "accession": "IGVFFI0237YEQF",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF2-BinB-PCR4-Rep1_S182"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:53:04.498696+00:00",
            "file_format": "fastq",
            "file_size": 22293288,
            "href": "/sequence-files/IGVFFI0237YEQF/@@download/IGVFFI0237YEQF.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/4793a8ad-18c3-4cac-8b3e-56c405d82d32/IGVFFI0237YEQF.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/FAM3C-Auxin0hrs-FF2-BinB-PCR4-Rep1_S182_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI3135DSDD/",
            "accession": "IGVFFI3135DSDD",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF2-BinB-PCR4-Rep1_S182"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:43:29.934271+00:00",
            "file_format": "yaml",
            "file_size": 915,
            "href": "/configuration-files/IGVFFI3135DSDD/@@download/IGVFFI3135DSDD.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/0388b421-978f-4f84-8334-ad3fe4bad3ff/IGVFFI3135DSDD.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF2-BinB-PCR4-Rep1_S182.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI2775UGHY/",
            "accession": "IGVFFI2775UGHY",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF2-BinB-PCR2-Rep1_S128"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:43:02.488282+00:00",
            "file_format": "yaml",
            "file_size": 915,
            "href": "/configuration-files/IGVFFI2775UGHY/@@download/IGVFFI2775UGHY.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/36624d58-64f2-4f30-b001-49115769d501/IGVFFI2775UGHY.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF2-BinB-PCR2-Rep1_S128.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI5430OQAY/",
            "accession": "IGVFFI5430OQAY",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF2-BinB-PCR3-Rep1_S176"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:43:16.719372+00:00",
            "file_format": "yaml",
            "file_size": 913,
            "href": "/configuration-files/IGVFFI5430OQAY/@@download/IGVFFI5430OQAY.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/09445a76-3b78-40eb-be23-6ea949669e94/IGVFFI5430OQAY.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF2-BinB-PCR3-Rep1_S176.yaml",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS5239VQTN/"
    ],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS6663FDTV/",
            "accession": "IGVFDS6663FDTV",
            "aliases": [
                "jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF2-BinB-PCR1-Rep1_S122",
                "jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF2-BinB-PCR2-Rep1_S128",
                "jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF2-BinB-PCR3-Rep1_S176",
                "jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF2-BinB-PCR4-Rep1_S182"
            ],
            "preferred_assay_title": "CRISPR FlowFISH screen",
            "status": "released"
        }
    ],
    "release_timestamp": "2024-07-10T20:11:29.314895+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM3569TFCR/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM3569TFCR",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF2-BinB-PCR1-Rep1_S122",
                "jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF2-BinB-PCR2-Rep1_S128",
                "jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF2-BinB-PCR3-Rep1_S176",
                "jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF2-BinB-PCR4-Rep1_S182"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS1891GTLU/"
            ],
            "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 FAM3C) 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": "2024-06-01T01:52:09.910992+00:00",
    "summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "e2c5af2d-b057-4f9c-89f7-a292eb43a8a3"
}