IGVFDS5497GDIR

released
{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS5497GDIR/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS5497GDIR",
    "aliases": [
        "jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin6hrs-FF2-BinE-PCR1-Rep1_S41",
        "jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin6hrs-FF2-BinE-PCR2-Rep1_S47",
        "jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin6hrs-FF2-BinE-PCR3-Rep1_S95",
        "jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin6hrs-FF2-BinE-PCR4-Rep1_S101"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "mismatched status",
                "detail": "Released human donor [IGVFDO0384OZRW](/human-donors/IGVFDO0384OZRW/) has in progress subobject publication [155f24ce-5c2c-4400-8651-da9447eaca25](/publications/155f24ce-5c2c-4400-8651-da9447eaca25/).",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_item_status",
                "path": "/human-donors/IGVFDO0384OZRW/"
            },
            {
                "category": "mismatched status",
                "detail": "Released in vitro system [IGVFSM1662MZZB](/in-vitro-systems/IGVFSM1662MZZB/) has in progress subobject treatment [d35868d1-c45b-49ae-8ff3-a9c0c22551c2](/treatments/d35868d1-c45b-49ae-8ff3-a9c0c22551c2/).",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_item_status",
                "path": "/in-vitro-systems/IGVFSM1662MZZB/"
            }
        ],
        "NOT_COMPLIANT": [
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS5497GDIR](/auxiliary-sets/IGVFDS5497GDIR/) has sequence file(s) [IGVFFI1256JDZP](/sequence-files/IGVFFI1256JDZP/), [IGVFFI7228DOIR](/sequence-files/IGVFFI7228DOIR/), [IGVFFI1967IIXO](/sequence-files/IGVFFI1967IIXO/), [IGVFFI4668DAZM](/sequence-files/IGVFFI4668DAZM/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_inconsistent_sequencing_kit",
                "path": "/auxiliary-sets/IGVFDS5497GDIR/"
            }
        ]
    },
    "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": "2024-05-14T21:06:46.751582+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/IGVFFI1256JDZP/",
            "accession": "IGVFFI1256JDZP",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin6hrs-FF2-BinE-PCR1-Rep1_S41"
            ],
            "content_type": "reads",
            "creation_timestamp": "2024-06-01T01:48:30.148497+00:00",
            "file_format": "fastq",
            "file_size": 10784945,
            "href": "/sequence-files/IGVFFI1256JDZP/@@download/IGVFFI1256JDZP.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/1db04a65-b305-4e6a-badf-fe0cb5236f84/IGVFFI1256JDZP.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/SSFA2-Auxin6hrs-FF2-BinE-PCR1-Rep1_S41_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI1367YZPA/",
            "accession": "IGVFFI1367YZPA",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin6hrs-FF2-BinE-PCR1-Rep1_S41"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:40:55.492275+00:00",
            "file_format": "yaml",
            "file_size": 913,
            "href": "/configuration-files/IGVFFI1367YZPA/@@download/IGVFFI1367YZPA.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/fdc35a23-a98d-4a6a-83a2-d33c00e30d9e/IGVFFI1367YZPA.yaml.gz",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin6hrs-FF2-BinE-PCR1-Rep1_S41.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI7228DOIR/",
            "accession": "IGVFFI7228DOIR",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin6hrs-FF2-BinE-PCR3-Rep1_S95"
            ],
            "content_type": "reads",
            "creation_timestamp": "2024-06-01T01:49:05.184677+00:00",
            "file_format": "fastq",
            "file_size": 20486641,
            "href": "/sequence-files/IGVFFI7228DOIR/@@download/IGVFFI7228DOIR.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/88671496-8d97-49dd-9ba2-1032ea972fa6/IGVFFI7228DOIR.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/SSFA2-Auxin6hrs-FF2-BinE-PCR3-Rep1_S95_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI6763TOPA/",
            "accession": "IGVFFI6763TOPA",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin6hrs-FF2-BinE-PCR3-Rep1_S95"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:41:27.240815+00:00",
            "file_format": "yaml",
            "file_size": 912,
            "href": "/configuration-files/IGVFFI6763TOPA/@@download/IGVFFI6763TOPA.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/d656b880-b879-4f71-a8f9-a66bdbee3b85/IGVFFI6763TOPA.yaml.gz",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin6hrs-FF2-BinE-PCR3-Rep1_S95.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI1967IIXO/",
            "accession": "IGVFFI1967IIXO",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin6hrs-FF2-BinE-PCR2-Rep1_S47"
            ],
            "content_type": "reads",
            "creation_timestamp": "2024-06-01T01:48:47.770983+00:00",
            "file_format": "fastq",
            "file_size": 2191720,
            "href": "/sequence-files/IGVFFI1967IIXO/@@download/IGVFFI1967IIXO.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/9f5b2c0f-2022-4ea0-8056-acf819ce90a3/IGVFFI1967IIXO.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/SSFA2-Auxin6hrs-FF2-BinE-PCR2-Rep1_S47_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI4668DAZM/",
            "accession": "IGVFFI4668DAZM",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin6hrs-FF2-BinE-PCR4-Rep1_S101"
            ],
            "content_type": "reads",
            "creation_timestamp": "2024-06-01T01:49:24.127826+00:00",
            "file_format": "fastq",
            "file_size": 2093063,
            "href": "/sequence-files/IGVFFI4668DAZM/@@download/IGVFFI4668DAZM.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/32626f42-94b0-4627-aff9-625476711673/IGVFFI4668DAZM.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/SSFA2-Auxin6hrs-FF2-BinE-PCR4-Rep1_S101_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI9275HAUL/",
            "accession": "IGVFFI9275HAUL",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin6hrs-FF2-BinE-PCR4-Rep1_S101"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:41:42.794086+00:00",
            "file_format": "yaml",
            "file_size": 915,
            "href": "/configuration-files/IGVFFI9275HAUL/@@download/IGVFFI9275HAUL.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/78f3d2af-9755-43d4-a463-be570ae004c8/IGVFFI9275HAUL.yaml.gz",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin6hrs-FF2-BinE-PCR4-Rep1_S101.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI1493AADV/",
            "accession": "IGVFFI1493AADV",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin6hrs-FF2-BinE-PCR2-Rep1_S47"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:41:11.685764+00:00",
            "file_format": "yaml",
            "file_size": 913,
            "href": "/configuration-files/IGVFFI1493AADV/@@download/IGVFFI1493AADV.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/7fb563d0-77c6-4076-9f18-36a14afded3a/IGVFFI1493AADV.yaml.gz",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin6hrs-FF2-BinE-PCR2-Rep1_S47.yaml",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS2031CTSP/"
    ],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS9337ZLNA/",
            "accession": "IGVFDS9337ZLNA",
            "aliases": [
                "jesse-engreitz:measurement_CRUDO_SSFA2-Auxin6hrs-FF2-BinE-PCR1-Rep1_S41",
                "jesse-engreitz:measurement_CRUDO_SSFA2-Auxin6hrs-FF2-BinE-PCR2-Rep1_S47",
                "jesse-engreitz:measurement_CRUDO_SSFA2-Auxin6hrs-FF2-BinE-PCR3-Rep1_S95",
                "jesse-engreitz:measurement_CRUDO_SSFA2-Auxin6hrs-FF2-BinE-PCR4-Rep1_S101"
            ],
            "preferred_assay_title": "CRISPR FlowFISH screen"
        }
    ],
    "release_timestamp": "2024-07-10T20:26:20.854058+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM1662MZZB/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM1662MZZB",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF2-BinE-PCR1-Rep1_S41",
                "jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF2-BinE-PCR2-Rep1_S47",
                "jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF2-BinE-PCR3-Rep1_S95",
                "jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF2-BinE-PCR4-Rep1_S101"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS5413RKIA/"
            ],
            "modifications": [
                "/degron-modifications/95081d1b-08b4-49ed-b324-e53fc43d8456/",
                "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/"
            ],
            "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 E for 80-90% 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": [
                "/treatments/d35868d1-c45b-49ae-8ff3-a9c0c22551c2/"
            ]
        }
    ],
    "schema_version": "11",
    "status": "released",
    "submitted_by": {
        "@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
        "title": "Chongyon Park"
    },
    "submitted_files_timestamp": "2024-06-01T01:48:30.148497+00:00",
    "summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "76723b8c-aef2-4436-8713-a03738fe2c23"
}