IGVFDS4721YEEW

released
{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS4721YEEW/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS4721YEEW",
    "aliases": [
        "jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF2-BinE-PCR1-Rep1_S17",
        "jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF2-BinE-PCR2-Rep1_S23",
        "jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF2-BinE-PCR3-Rep1_S71",
        "jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF2-BinE-PCR4-Rep1_S77"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS4721YEEW](/auxiliary-sets/IGVFDS4721YEEW/) has sequence file(s) [IGVFFI7752CYYJ](/sequence-files/IGVFFI7752CYYJ/), [IGVFFI4315EDNJ](/sequence-files/IGVFFI4315EDNJ/), [IGVFFI6094QETO](/sequence-files/IGVFFI6094QETO/), [IGVFFI8646GHGN](/sequence-files/IGVFFI8646GHGN/) 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/IGVFDS4721YEEW/"
            }
        ]
    },
    "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": "2024-05-14T20:31:21.906143+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/IGVFFI7752CYYJ/",
            "accession": "IGVFFI7752CYYJ",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF2-BinE-PCR1-Rep1_S17"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:46:03.633426+00:00",
            "file_format": "fastq",
            "file_size": 9130239,
            "href": "/sequence-files/IGVFFI7752CYYJ/@@download/IGVFFI7752CYYJ.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/f1725405-7e26-42d5-b449-13f52bea58cf/IGVFFI7752CYYJ.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-Auxin0hrs-FF2-BinE-PCR1-Rep1_S17_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI3316VTMT/",
            "accession": "IGVFFI3316VTMT",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF2-BinE-PCR1-Rep1_S17"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:38:28.029318+00:00",
            "file_format": "yaml",
            "file_size": 913,
            "href": "/configuration-files/IGVFFI3316VTMT/@@download/IGVFFI3316VTMT.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/85fd1a9d-04d6-4a83-9ae4-9dbe29db0e20/IGVFFI3316VTMT.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF2-BinE-PCR1-Rep1_S17.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI4315EDNJ/",
            "accession": "IGVFFI4315EDNJ",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF2-BinE-PCR2-Rep1_S23"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:46:23.222743+00:00",
            "file_format": "fastq",
            "file_size": 19460589,
            "href": "/sequence-files/IGVFFI4315EDNJ/@@download/IGVFFI4315EDNJ.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/3c140bbf-4f16-40be-be23-b5e996d0cbda/IGVFFI4315EDNJ.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-Auxin0hrs-FF2-BinE-PCR2-Rep1_S23_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI6094QETO/",
            "accession": "IGVFFI6094QETO",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF2-BinE-PCR3-Rep1_S71"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:46:40.966016+00:00",
            "file_format": "fastq",
            "file_size": 14344858,
            "href": "/sequence-files/IGVFFI6094QETO/@@download/IGVFFI6094QETO.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/3e20f801-835d-4a18-9032-209ef76b7075/IGVFFI6094QETO.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-Auxin0hrs-FF2-BinE-PCR3-Rep1_S71_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8646GHGN/",
            "accession": "IGVFFI8646GHGN",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF2-BinE-PCR4-Rep1_S77"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:46:58.883877+00:00",
            "file_format": "fastq",
            "file_size": 20050660,
            "href": "/sequence-files/IGVFFI8646GHGN/@@download/IGVFFI8646GHGN.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/5523ffb8-5160-446b-963a-418279843f0b/IGVFFI8646GHGN.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-Auxin0hrs-FF2-BinE-PCR4-Rep1_S77_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI4784OLOD/",
            "accession": "IGVFFI4784OLOD",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF2-BinE-PCR3-Rep1_S71"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:39:22.214545+00:00",
            "file_format": "yaml",
            "file_size": 912,
            "href": "/configuration-files/IGVFFI4784OLOD/@@download/IGVFFI4784OLOD.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/43cbe569-08db-4c7f-9ebb-95d2a903aa3d/IGVFFI4784OLOD.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF2-BinE-PCR3-Rep1_S71.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI0392HWSG/",
            "accession": "IGVFFI0392HWSG",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF2-BinE-PCR4-Rep1_S77"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:39:38.091137+00:00",
            "file_format": "yaml",
            "file_size": 911,
            "href": "/configuration-files/IGVFFI0392HWSG/@@download/IGVFFI0392HWSG.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/cf53b9cb-581f-4582-bbea-090e206a46b2/IGVFFI0392HWSG.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF2-BinE-PCR4-Rep1_S77.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI5168BJYX/",
            "accession": "IGVFFI5168BJYX",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF2-BinE-PCR2-Rep1_S23"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:38:43.507832+00:00",
            "file_format": "yaml",
            "file_size": 913,
            "href": "/configuration-files/IGVFFI5168BJYX/@@download/IGVFFI5168BJYX.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/ed0867b0-4f40-443f-8095-2a179f68bd71/IGVFFI5168BJYX.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF2-BinE-PCR2-Rep1_S23.yaml",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS2031CTSP/"
    ],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS8098OGBN/",
            "accession": "IGVFDS8098OGBN",
            "aliases": [
                "jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF2-BinE-PCR1-Rep1_S17",
                "jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF2-BinE-PCR2-Rep1_S23",
                "jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF2-BinE-PCR3-Rep1_S71",
                "jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF2-BinE-PCR4-Rep1_S77"
            ],
            "preferred_assay_title": "CRISPR FlowFISH screen",
            "status": "released"
        }
    ],
    "release_timestamp": "2024-07-10T20:24:54.299714+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM9097DRIA/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM9097DRIA",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF2-BinE-PCR1-Rep1_S17",
                "jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF2-BinE-PCR2-Rep1_S23",
                "jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF2-BinE-PCR3-Rep1_S71",
                "jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF2-BinE-PCR4-Rep1_S77"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS5413RKIA/"
            ],
            "modifications": [
                {
                    "@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
                    "modality": "interference",
                    "status": "released"
                },
                {
                    "@id": "/degron-modifications/2e8d10cc-fc98-44d5-a7d9-e2892e16c98a/",
                    "modality": "degradation",
                    "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 E for 80-90% expression of SSFA2) modified with CRISPRi Sp-dCas9-KOX1-KRAB, inactive AID system targeting RAD21, transfected with a guide library",
            "taxa": "Homo sapiens"
        }
    ],
    "schema_version": "12",
    "status": "released",
    "submitted_by": {
        "@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
        "title": "Chongyon Park"
    },
    "submitted_files_timestamp": "2024-06-01T01:46:03.633426+00:00",
    "summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "e1d0b00e-9916-4c5b-9451-df9e051ed838"
}