IGVFDS2084ZSSG

released
{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS2084ZSSG/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS2084ZSSG",
    "aliases": [
        "jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin6hrs-FF1-BinF-PCR1-Rep1_S246",
        "jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin6hrs-FF1-BinF-PCR2-Rep1_S252",
        "jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin6hrs-FF1-BinF-PCR3-Rep1_S288",
        "jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin6hrs-FF1-BinF-PCR4-Rep1_S294"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS2084ZSSG](/auxiliary-sets/IGVFDS2084ZSSG/) has sequence file(s) [IGVFFI0753QNVY](/sequence-files/IGVFFI0753QNVY/), [IGVFFI8888QXML](/sequence-files/IGVFFI8888QXML/), [IGVFFI9575XKJG](/sequence-files/IGVFFI9575XKJG/), [IGVFFI3313PFDP](/sequence-files/IGVFFI3313PFDP/) 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/IGVFDS2084ZSSG/"
            }
        ]
    },
    "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": "2024-05-13T22:50:49.539613+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/IGVFFI0753QNVY/",
            "accession": "IGVFFI0753QNVY",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF1-BinF-PCR1-Rep1_S246"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:42:15.781055+00:00",
            "file_format": "fastq",
            "file_size": 19663507,
            "href": "/sequence-files/IGVFFI0753QNVY/@@download/IGVFFI0753QNVY.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/c19e57b0-db9c-490c-901a-865a636575cf/IGVFFI0753QNVY.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-Auxin6hrs-FF1-BinF-PCR1-Rep1_S246_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI8908XMQK/",
            "accession": "IGVFFI8908XMQK",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF1-BinF-PCR1-Rep1_S246"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:30:04.028101+00:00",
            "file_format": "yaml",
            "file_size": 915,
            "href": "/configuration-files/IGVFFI8908XMQK/@@download/IGVFFI8908XMQK.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/b5efd564-73cf-4d58-88d1-d3d51b6b7fb3/IGVFFI8908XMQK.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF1-BinF-PCR1-Rep1_S246.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8888QXML/",
            "accession": "IGVFFI8888QXML",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF1-BinF-PCR2-Rep1_S252"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:42:32.556190+00:00",
            "file_format": "fastq",
            "file_size": 14562870,
            "href": "/sequence-files/IGVFFI8888QXML/@@download/IGVFFI8888QXML.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/49882cd5-7113-4362-9fcc-7836a8a2749e/IGVFFI8888QXML.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-Auxin6hrs-FF1-BinF-PCR2-Rep1_S252_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9575XKJG/",
            "accession": "IGVFFI9575XKJG",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF1-BinF-PCR3-Rep1_S288"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:42:49.899464+00:00",
            "file_format": "fastq",
            "file_size": 29442591,
            "href": "/sequence-files/IGVFFI9575XKJG/@@download/IGVFFI9575XKJG.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/6d3d5fb9-ef30-47a2-a7e8-d7271c939b28/IGVFFI9575XKJG.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-Auxin6hrs-FF1-BinF-PCR3-Rep1_S288_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3313PFDP/",
            "accession": "IGVFFI3313PFDP",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF1-BinF-PCR4-Rep1_S294"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:43:09.564609+00:00",
            "file_format": "fastq",
            "file_size": 31736889,
            "href": "/sequence-files/IGVFFI3313PFDP/@@download/IGVFFI3313PFDP.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/b9964b31-efcb-422b-a903-bcefaa5b618c/IGVFFI3313PFDP.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-Auxin6hrs-FF1-BinF-PCR4-Rep1_S294_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI1849NKLD/",
            "accession": "IGVFFI1849NKLD",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF1-BinF-PCR3-Rep1_S288"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:30:31.954015+00:00",
            "file_format": "yaml",
            "file_size": 914,
            "href": "/configuration-files/IGVFFI1849NKLD/@@download/IGVFFI1849NKLD.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/8c0f735a-d7bf-431c-a2ec-a52f1ad6e85e/IGVFFI1849NKLD.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF1-BinF-PCR3-Rep1_S288.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI5842FKDB/",
            "accession": "IGVFFI5842FKDB",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF1-BinF-PCR4-Rep1_S294"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:30:46.473880+00:00",
            "file_format": "yaml",
            "file_size": 913,
            "href": "/configuration-files/IGVFFI5842FKDB/@@download/IGVFFI5842FKDB.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/5c937862-0e7c-4982-afd3-6b76ad509d16/IGVFFI5842FKDB.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF1-BinF-PCR4-Rep1_S294.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI4334FUHO/",
            "accession": "IGVFFI4334FUHO",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF1-BinF-PCR2-Rep1_S252"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:30:17.908462+00:00",
            "file_format": "yaml",
            "file_size": 914,
            "href": "/configuration-files/IGVFFI4334FUHO/@@download/IGVFFI4334FUHO.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/a7507ebf-4907-4e25-ba1c-bf5c51b0fae9/IGVFFI4334FUHO.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF1-BinF-PCR2-Rep1_S252.yaml",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS1569RNPD/"
    ],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS5981KTQT/",
            "accession": "IGVFDS5981KTQT",
            "aliases": [
                "jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF1-BinF-PCR1-Rep1_S246",
                "jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF1-BinF-PCR2-Rep1_S252",
                "jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF1-BinF-PCR3-Rep1_S288",
                "jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF1-BinF-PCR4-Rep1_S294"
            ],
            "preferred_assay_title": "CRISPR FlowFISH screen",
            "status": "released"
        }
    ],
    "release_timestamp": "2024-07-10T20:09:48.647256+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM7718ZYYQ/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM7718ZYYQ",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF1-BinF-PCR1-Rep1_S246",
                "jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF1-BinF-PCR2-Rep1_S252",
                "jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF1-BinF-PCR3-Rep1_S288",
                "jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF1-BinF-PCR4-Rep1_S294"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS6351FGNG/"
            ],
            "modifications": [
                {
                    "@id": "/degron-modifications/95081d1b-08b4-49ed-b324-e53fc43d8456/",
                    "modality": "degradation",
                    "status": "released"
                },
                {
                    "@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
                    "modality": "interference",
                    "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 CCND1) treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours, modified with AID system targeting RAD21, CRISPRi Sp-dCas9-KOX1-KRAB, transfected with a guide library",
            "taxa": "Homo sapiens",
            "treatments": [
                {
                    "@id": "/treatments/d35868d1-c45b-49ae-8ff3-a9c0c22551c2/",
                    "status": "released",
                    "treatment_term_name": "5-Phenyl-1H-indole-3-acetic acid"
                }
            ]
        }
    ],
    "schema_version": "12",
    "status": "released",
    "submitted_by": {
        "@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
        "title": "Chongyon Park"
    },
    "submitted_files_timestamp": "2024-06-01T01:42:15.781055+00:00",
    "summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "66935e00-cc32-403c-9112-afda3a65e0d0"
}