IGVFDS0887BEDU

released
{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS0887BEDU/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS0887BEDU",
    "aliases": [
        "jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin6hrs-FF2-BinC-PCR1-Rep1_S147",
        "jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin6hrs-FF2-BinC-PCR2-Rep1_S153",
        "jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin6hrs-FF2-BinC-PCR3-Rep1_S201",
        "jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin6hrs-FF2-BinC-PCR4-Rep1_S207"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS0887BEDU](/auxiliary-sets/IGVFDS0887BEDU/) has sequence file(s) [IGVFFI6284GDRW](/sequence-files/IGVFFI6284GDRW/), [IGVFFI6670CCCW](/sequence-files/IGVFFI6670CCCW/), [IGVFFI4732FGXM](/sequence-files/IGVFFI4732FGXM/), [IGVFFI9975SRBC](/sequence-files/IGVFFI9975SRBC/) 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/IGVFDS0887BEDU/"
            }
        ]
    },
    "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": "2024-05-14T16:51:34.602209+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/IGVFFI6284GDRW/",
            "accession": "IGVFFI6284GDRW",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF2-BinC-PCR1-Rep1_S147"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:54:39.030311+00:00",
            "file_format": "fastq",
            "file_size": 15588192,
            "href": "/sequence-files/IGVFFI6284GDRW/@@download/IGVFFI6284GDRW.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/2c1926a6-e693-46e6-809d-e99a3f20e763/IGVFFI6284GDRW.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-Auxin6hrs-FF2-BinC-PCR1-Rep1_S147_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI9955CJZS/",
            "accession": "IGVFFI9955CJZS",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF2-BinC-PCR1-Rep1_S147"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:44:41.481369+00:00",
            "file_format": "yaml",
            "file_size": 913,
            "href": "/configuration-files/IGVFFI9955CJZS/@@download/IGVFFI9955CJZS.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/e3c701e3-811d-40f0-b21a-7b417b364a63/IGVFFI9955CJZS.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF2-BinC-PCR1-Rep1_S147.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI6670CCCW/",
            "accession": "IGVFFI6670CCCW",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF2-BinC-PCR4-Rep1_S207"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:55:34.312744+00:00",
            "file_format": "fastq",
            "file_size": 6218387,
            "href": "/sequence-files/IGVFFI6670CCCW/@@download/IGVFFI6670CCCW.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/2dfe7547-9ebc-4f6f-99f3-d6547241aad1/IGVFFI6670CCCW.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-Auxin6hrs-FF2-BinC-PCR4-Rep1_S207_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI8571MRWS/",
            "accession": "IGVFFI8571MRWS",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF2-BinC-PCR4-Rep1_S207"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:45:22.967263+00:00",
            "file_format": "yaml",
            "file_size": 912,
            "href": "/configuration-files/IGVFFI8571MRWS/@@download/IGVFFI8571MRWS.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/17a4abdc-c6e7-45b8-a9c8-6a0fe1814ca2/IGVFFI8571MRWS.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF2-BinC-PCR4-Rep1_S207.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI4732FGXM/",
            "accession": "IGVFFI4732FGXM",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF2-BinC-PCR2-Rep1_S153"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:54:57.393409+00:00",
            "file_format": "fastq",
            "file_size": 7486318,
            "href": "/sequence-files/IGVFFI4732FGXM/@@download/IGVFFI4732FGXM.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/1340cce3-01ed-4dfc-a4ad-091685c639f1/IGVFFI4732FGXM.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-Auxin6hrs-FF2-BinC-PCR2-Rep1_S153_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9975SRBC/",
            "accession": "IGVFFI9975SRBC",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF2-BinC-PCR3-Rep1_S201"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:55:15.554298+00:00",
            "file_format": "fastq",
            "file_size": 26528834,
            "href": "/sequence-files/IGVFFI9975SRBC/@@download/IGVFFI9975SRBC.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/8b82bc36-58c8-4314-a10d-0f4885ca9749/IGVFFI9975SRBC.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-Auxin6hrs-FF2-BinC-PCR3-Rep1_S201_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI4903FZPN/",
            "accession": "IGVFFI4903FZPN",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF2-BinC-PCR2-Rep1_S153"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:44:55.973022+00:00",
            "file_format": "yaml",
            "file_size": 914,
            "href": "/configuration-files/IGVFFI4903FZPN/@@download/IGVFFI4903FZPN.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/386ea622-5e72-4d3b-b117-a6a0563c50ea/IGVFFI4903FZPN.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF2-BinC-PCR2-Rep1_S153.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI0190JMYM/",
            "accession": "IGVFFI0190JMYM",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF2-BinC-PCR3-Rep1_S201"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:45:09.635159+00:00",
            "file_format": "yaml",
            "file_size": 913,
            "href": "/configuration-files/IGVFFI0190JMYM/@@download/IGVFFI0190JMYM.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/928bf542-6a10-42af-8a03-7a482ef23d79/IGVFFI0190JMYM.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF2-BinC-PCR3-Rep1_S201.yaml",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS5239VQTN/"
    ],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS3361ABEP/",
            "accession": "IGVFDS3361ABEP",
            "aliases": [
                "jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF2-BinC-PCR1-Rep1_S147",
                "jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF2-BinC-PCR2-Rep1_S153",
                "jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF2-BinC-PCR3-Rep1_S201",
                "jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF2-BinC-PCR4-Rep1_S207"
            ],
            "preferred_assay_title": "CRISPR FlowFISH screen",
            "status": "released"
        }
    ],
    "release_timestamp": "2024-07-10T20:13:03.873576+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM5674HHJF/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM5674HHJF",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF2-BinC-PCR1-Rep1_S147",
                "jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF2-BinC-PCR2-Rep1_S153",
                "jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF2-BinC-PCR3-Rep1_S201",
                "jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF2-BinC-PCR4-Rep1_S207"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS1891GTLU/"
            ],
            "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 C for 35-45% expression of FAM3C) 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": "2024-06-01T01:54:39.030311+00:00",
    "summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "7b6f468d-967a-4649-8f7c-de810c1c4636"
}