IGVFDS7007ZSGW

released
{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS7007ZSGW/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS7007ZSGW",
    "aliases": [
        "jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin6hrs-FF2-BinA-PCR1-Rep1_S37",
        "jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin6hrs-FF2-BinA-PCR2-Rep1_S43",
        "jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin6hrs-FF2-BinA-PCR3-Rep1_S91",
        "jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin6hrs-FF2-BinA-PCR4-Rep1_S97"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS7007ZSGW](/auxiliary-sets/IGVFDS7007ZSGW/) has sequence file(s) [IGVFFI9973DZYW](/sequence-files/IGVFFI9973DZYW/), [IGVFFI6480QLXO](/sequence-files/IGVFFI6480QLXO/), [IGVFFI0058RTZN](/sequence-files/IGVFFI0058RTZN/), [IGVFFI8730IUFZ](/sequence-files/IGVFFI8730IUFZ/) 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/IGVFDS7007ZSGW/"
            }
        ]
    },
    "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": "2024-05-14T21:06:42.987979+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/IGVFFI9973DZYW/",
            "accession": "IGVFFI9973DZYW",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin6hrs-FF2-BinA-PCR1-Rep1_S37"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:48:18.486834+00:00",
            "file_format": "fastq",
            "file_size": 7864454,
            "href": "/sequence-files/IGVFFI9973DZYW/@@download/IGVFFI9973DZYW.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/4c3e2645-91d6-41c3-ac5b-5dab73dc9b79/IGVFFI9973DZYW.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/SSFA2-Auxin6hrs-FF2-BinA-PCR1-Rep1_S37_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI3768XAAB/",
            "accession": "IGVFFI3768XAAB",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin6hrs-FF2-BinA-PCR1-Rep1_S37"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:40:45.426965+00:00",
            "file_format": "yaml",
            "file_size": 915,
            "href": "/configuration-files/IGVFFI3768XAAB/@@download/IGVFFI3768XAAB.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/0f68d729-5885-469b-8a06-7f196dffac1e/IGVFFI3768XAAB.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin6hrs-FF2-BinA-PCR1-Rep1_S37.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI6480QLXO/",
            "accession": "IGVFFI6480QLXO",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin6hrs-FF2-BinA-PCR2-Rep1_S43"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:48:36.228122+00:00",
            "file_format": "fastq",
            "file_size": 8538820,
            "href": "/sequence-files/IGVFFI6480QLXO/@@download/IGVFFI6480QLXO.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/8690f808-e208-4e4a-96cd-21b150fa5717/IGVFFI6480QLXO.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/SSFA2-Auxin6hrs-FF2-BinA-PCR2-Rep1_S43_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI0058RTZN/",
            "accession": "IGVFFI0058RTZN",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin6hrs-FF2-BinA-PCR3-Rep1_S91"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:48:53.106959+00:00",
            "file_format": "fastq",
            "file_size": 13916900,
            "href": "/sequence-files/IGVFFI0058RTZN/@@download/IGVFFI0058RTZN.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/89ccf062-4c99-4426-9c6b-4a9c458e7570/IGVFFI0058RTZN.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/SSFA2-Auxin6hrs-FF2-BinA-PCR3-Rep1_S91_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI6560RWUV/",
            "accession": "IGVFFI6560RWUV",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin6hrs-FF2-BinA-PCR3-Rep1_S91"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:41:16.783129+00:00",
            "file_format": "yaml",
            "file_size": 913,
            "href": "/configuration-files/IGVFFI6560RWUV/@@download/IGVFFI6560RWUV.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/14b9f801-f43a-4723-8615-c549889ec116/IGVFFI6560RWUV.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin6hrs-FF2-BinA-PCR3-Rep1_S91.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8730IUFZ/",
            "accession": "IGVFFI8730IUFZ",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin6hrs-FF2-BinA-PCR4-Rep1_S97"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:49:11.407478+00:00",
            "file_format": "fastq",
            "file_size": 12391583,
            "href": "/sequence-files/IGVFFI8730IUFZ/@@download/IGVFFI8730IUFZ.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/82500dee-1bc2-4dbc-a52b-e9227fa5ca01/IGVFFI8730IUFZ.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/SSFA2-Auxin6hrs-FF2-BinA-PCR4-Rep1_S97_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI9194KAOF/",
            "accession": "IGVFFI9194KAOF",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin6hrs-FF2-BinA-PCR4-Rep1_S97"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:41:32.139853+00:00",
            "file_format": "yaml",
            "file_size": 914,
            "href": "/configuration-files/IGVFFI9194KAOF/@@download/IGVFFI9194KAOF.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/9c58b4a9-0d94-45c1-ae68-7137db8bfeff/IGVFFI9194KAOF.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin6hrs-FF2-BinA-PCR4-Rep1_S97.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI7652SENN/",
            "accession": "IGVFFI7652SENN",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin6hrs-FF2-BinA-PCR2-Rep1_S43"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:41:01.230119+00:00",
            "file_format": "yaml",
            "file_size": 914,
            "href": "/configuration-files/IGVFFI7652SENN/@@download/IGVFFI7652SENN.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/f24df06a-8316-4f0e-ac2e-4998ebaced01/IGVFFI7652SENN.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin6hrs-FF2-BinA-PCR2-Rep1_S43.yaml",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS2031CTSP/"
    ],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS4988ZVEF/",
            "accession": "IGVFDS4988ZVEF",
            "aliases": [
                "jesse-engreitz:measurement_CRUDO_SSFA2-Auxin6hrs-FF2-BinA-PCR1-Rep1_S37",
                "jesse-engreitz:measurement_CRUDO_SSFA2-Auxin6hrs-FF2-BinA-PCR2-Rep1_S43",
                "jesse-engreitz:measurement_CRUDO_SSFA2-Auxin6hrs-FF2-BinA-PCR3-Rep1_S91",
                "jesse-engreitz:measurement_CRUDO_SSFA2-Auxin6hrs-FF2-BinA-PCR4-Rep1_S97"
            ],
            "preferred_assay_title": "CRISPR FlowFISH screen",
            "status": "released"
        }
    ],
    "release_timestamp": "2024-07-10T20:25:52.238345+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM2476YZDG/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM2476YZDG",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF2-BinA-PCR1-Rep1_S37",
                "jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF2-BinA-PCR2-Rep1_S43",
                "jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF2-BinA-PCR3-Rep1_S91",
                "jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF2-BinA-PCR4-Rep1_S97"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS5413RKIA/"
            ],
            "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 A for 0-10% expression of SSFA2) 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": "2024-06-01T01:48:18.486834+00:00",
    "summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "6220b022-10a6-46c8-a49d-de68969a5f1c"
}