IGVFDS2403ZERE

released
{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS2403ZERE/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS2403ZERE",
    "aliases": [
        "jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF2-BinD-PCR1-Rep1_S232",
        "jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF2-BinD-PCR2-Rep1_S238",
        "jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF2-BinD-PCR3-Rep1_S274",
        "jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF2-BinD-PCR4-Rep1_S280"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS2403ZERE](/auxiliary-sets/IGVFDS2403ZERE/) has sequence file(s) [IGVFFI9017LLWY](/sequence-files/IGVFFI9017LLWY/), [IGVFFI7774KVKB](/sequence-files/IGVFFI7774KVKB/), [IGVFFI6030SAOG](/sequence-files/IGVFFI6030SAOG/), [IGVFFI8172OMRE](/sequence-files/IGVFFI8172OMRE/) 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/IGVFDS2403ZERE/"
            }
        ]
    },
    "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": "2024-05-13T22:39:15.099118+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/IGVFFI9017LLWY/",
            "accession": "IGVFFI9017LLWY",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF2-BinD-PCR1-Rep1_S232"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:37:17.550617+00:00",
            "file_format": "fastq",
            "file_size": 19145096,
            "href": "/sequence-files/IGVFFI9017LLWY/@@download/IGVFFI9017LLWY.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/f76e5b80-83be-451f-af1c-c2e12a4ea06c/IGVFFI9017LLWY.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/CCND1-Auxin0hrs-FF2-BinD-PCR1-Rep1_S232_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI3301LAMU/",
            "accession": "IGVFFI3301LAMU",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF2-BinD-PCR1-Rep1_S232"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:29:03.395319+00:00",
            "file_format": "yaml",
            "file_size": 915,
            "href": "/configuration-files/IGVFFI3301LAMU/@@download/IGVFFI3301LAMU.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/e136e748-bcda-41c1-946b-f1991edb189a/IGVFFI3301LAMU.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF2-BinD-PCR1-Rep1_S232.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI7774KVKB/",
            "accession": "IGVFFI7774KVKB",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF2-BinD-PCR2-Rep1_S238"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:37:35.348521+00:00",
            "file_format": "fastq",
            "file_size": 18935065,
            "href": "/sequence-files/IGVFFI7774KVKB/@@download/IGVFFI7774KVKB.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/c96f8bd5-5c9f-4e8f-bbfc-5e9b913555f5/IGVFFI7774KVKB.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/CCND1-Auxin0hrs-FF2-BinD-PCR2-Rep1_S238_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI6030SAOG/",
            "accession": "IGVFFI6030SAOG",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF2-BinD-PCR3-Rep1_S274"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:37:53.123405+00:00",
            "file_format": "fastq",
            "file_size": 24245776,
            "href": "/sequence-files/IGVFFI6030SAOG/@@download/IGVFFI6030SAOG.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/93a6bfd4-f546-4268-9d4c-36e2eb5dedc5/IGVFFI6030SAOG.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/CCND1-Auxin0hrs-FF2-BinD-PCR3-Rep1_S274_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8172OMRE/",
            "accession": "IGVFFI8172OMRE",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF2-BinD-PCR4-Rep1_S280"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:38:15.440089+00:00",
            "file_format": "fastq",
            "file_size": 24490365,
            "href": "/sequence-files/IGVFFI8172OMRE/@@download/IGVFFI8172OMRE.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/5df06ec8-2c66-4755-82ca-33d90a801d29/IGVFFI8172OMRE.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/CCND1-Auxin0hrs-FF2-BinD-PCR4-Rep1_S280_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI9558UYBL/",
            "accession": "IGVFFI9558UYBL",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF2-BinD-PCR3-Rep1_S274"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:29:31.272162+00:00",
            "file_format": "yaml",
            "file_size": 912,
            "href": "/configuration-files/IGVFFI9558UYBL/@@download/IGVFFI9558UYBL.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/987616fe-7d14-4324-9ad0-77ae7de1bd76/IGVFFI9558UYBL.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF2-BinD-PCR3-Rep1_S274.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI7568TJSW/",
            "accession": "IGVFFI7568TJSW",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF2-BinD-PCR4-Rep1_S280"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:29:45.264881+00:00",
            "file_format": "yaml",
            "file_size": 914,
            "href": "/configuration-files/IGVFFI7568TJSW/@@download/IGVFFI7568TJSW.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/248276f3-e5c5-42db-b72d-10163dd224b6/IGVFFI7568TJSW.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF2-BinD-PCR4-Rep1_S280.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI7108WMVT/",
            "accession": "IGVFFI7108WMVT",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF2-BinD-PCR2-Rep1_S238"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:29:17.307762+00:00",
            "file_format": "yaml",
            "file_size": 914,
            "href": "/configuration-files/IGVFFI7108WMVT/@@download/IGVFFI7108WMVT.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/021d990e-97f0-4ac5-902c-a9c4e080ec75/IGVFFI7108WMVT.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF2-BinD-PCR2-Rep1_S238.yaml",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS1569RNPD/"
    ],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS2949NCKP/",
            "accession": "IGVFDS2949NCKP",
            "aliases": [
                "jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF2-BinD-PCR1-Rep1_S232",
                "jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF2-BinD-PCR2-Rep1_S238",
                "jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF2-BinD-PCR3-Rep1_S274",
                "jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF2-BinD-PCR4-Rep1_S280"
            ],
            "preferred_assay_title": "CRISPR FlowFISH screen",
            "status": "released"
        }
    ],
    "release_timestamp": "2024-07-10T20:08:50.119317+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM9888RFRZ/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM9888RFRZ",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF2-BinD-PCR1-Rep1_S232",
                "jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF2-BinD-PCR2-Rep1_S238",
                "jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF2-BinD-PCR3-Rep1_S274",
                "jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF2-BinD-PCR4-Rep1_S280"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS6351FGNG/"
            ],
            "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 D for 55-65% expression of CCND1) 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": "2024-06-01T01:37:17.550617+00:00",
    "summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "6c54ecd8-a998-4b9b-b254-2623110a63c9"
}