IGVFDS2850LCWI

released
{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS2850LCWI/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS2850LCWI",
    "aliases": [
        "jesse-engreitz:auxiliary_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinF-PCR1_S6",
        "jesse-engreitz:auxiliary_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinF-PCR2_S102",
        "jesse-engreitz:auxiliary_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinF-PCR3_S198",
        "jesse-engreitz:auxiliary_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinF-PCR4_S294"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS2850LCWI](/auxiliary-sets/IGVFDS2850LCWI/) has sequence file(s) [IGVFFI3706DIIS](/sequence-files/IGVFFI3706DIIS/), [IGVFFI1185QZTN](/sequence-files/IGVFFI1185QZTN/), [IGVFFI5243ZITD](/sequence-files/IGVFFI5243ZITD/), [IGVFFI5705VZDO](/sequence-files/IGVFFI5705VZDO/) 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/IGVFDS2850LCWI/"
            }
        ]
    },
    "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": "2024-05-06T23:13:30.854808+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/IGVFFI3706DIIS/",
            "accession": "IGVFFI3706DIIS",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinF-PCR1_S6"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:24:52.604345+00:00",
            "file_format": "fastq",
            "file_size": 2386043,
            "href": "/sequence-files/IGVFFI3706DIIS/@@download/IGVFFI3706DIIS.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/89def70c-55ca-4878-934a-abff7fb08ffb/IGVFFI3706DIIS.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/210301B002-CohesinFF/fastq/CCND1-Auxin6hrs-FF1-BinF-PCR1_S6_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI8851ZPDX/",
            "accession": "IGVFFI8851ZPDX",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinF-PCR1_S6"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:23:05.209946+00:00",
            "file_format": "yaml",
            "file_size": 906,
            "href": "/configuration-files/IGVFFI8851ZPDX/@@download/IGVFFI8851ZPDX.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/5c748d96-94a4-4dba-9697-f23f81e0e261/IGVFFI8851ZPDX.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin6hrs-FF1-BinF-PCR1_S6.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI1185QZTN/",
            "accession": "IGVFFI1185QZTN",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinF-PCR2_S102"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:25:08.876707+00:00",
            "file_format": "fastq",
            "file_size": 2949646,
            "href": "/sequence-files/IGVFFI1185QZTN/@@download/IGVFFI1185QZTN.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/958be19b-e16b-4675-8ca8-d9fe31289887/IGVFFI1185QZTN.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/210301B002-CohesinFF/fastq/CCND1-Auxin6hrs-FF1-BinF-PCR2_S102_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI5243ZITD/",
            "accession": "IGVFFI5243ZITD",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinF-PCR3_S198"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:25:24.889588+00:00",
            "file_format": "fastq",
            "file_size": 3289690,
            "href": "/sequence-files/IGVFFI5243ZITD/@@download/IGVFFI5243ZITD.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/a2365a59-3a2f-4313-9ba1-40510a005f41/IGVFFI5243ZITD.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/210301B002-CohesinFF/fastq/CCND1-Auxin6hrs-FF1-BinF-PCR3_S198_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI5705VZDO/",
            "accession": "IGVFFI5705VZDO",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinF-PCR4_S294"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:25:40.430198+00:00",
            "file_format": "fastq",
            "file_size": 2578702,
            "href": "/sequence-files/IGVFFI5705VZDO/@@download/IGVFFI5705VZDO.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/07d52b45-2ff8-4287-8235-1a7219a20949/IGVFFI5705VZDO.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/210301B002-CohesinFF/fastq/CCND1-Auxin6hrs-FF1-BinF-PCR4_S294_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI6893TRQO/",
            "accession": "IGVFFI6893TRQO",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinF-PCR2_S102"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:23:18.957181+00:00",
            "file_format": "yaml",
            "file_size": 910,
            "href": "/configuration-files/IGVFFI6893TRQO/@@download/IGVFFI6893TRQO.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/0d209287-25c9-4f63-beea-4152ec6c39fc/IGVFFI6893TRQO.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin6hrs-FF1-BinF-PCR2_S102.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI1848XHZT/",
            "accession": "IGVFFI1848XHZT",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinF-PCR3_S198"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:23:32.494764+00:00",
            "file_format": "yaml",
            "file_size": 910,
            "href": "/configuration-files/IGVFFI1848XHZT/@@download/IGVFFI1848XHZT.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/abb18ba0-39f9-4767-add3-8e8570bd93c1/IGVFFI1848XHZT.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin6hrs-FF1-BinF-PCR3_S198.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI7044YYIY/",
            "accession": "IGVFFI7044YYIY",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinF-PCR4_S294"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:23:46.211814+00:00",
            "file_format": "yaml",
            "file_size": 910,
            "href": "/configuration-files/IGVFFI7044YYIY/@@download/IGVFFI7044YYIY.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/77b66746-a2c4-47a4-abba-696f2f49308a/IGVFFI7044YYIY.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin6hrs-FF1-BinF-PCR4_S294.yaml",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS2982SJGW/"
    ],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS2079MGOR/",
            "accession": "IGVFDS2079MGOR",
            "aliases": [
                "jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinF-PCR1_S6",
                "jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinF-PCR2_S102",
                "jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinF-PCR3_S198",
                "jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinF-PCR4_S294"
            ],
            "preferred_assay_title": "CRISPR FlowFISH screen",
            "status": "released"
        }
    ],
    "release_timestamp": "2024-07-10T20:23:34.320597+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM0904FNLS/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM0904FNLS",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinF-PCR1_S6",
                "jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinF-PCR2_S102",
                "jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinF-PCR3_S198",
                "jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinF-PCR4_S294"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS0392OWNZ/"
            ],
            "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": "2024-06-01T01:24:52.604345+00:00",
    "summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in 36 genomic loci",
    "uuid": "1706472d-ab14-45b0-b000-6200b737d70a"
}