IGVFDS0993NTCB

released
{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS0993NTCB/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS0993NTCB",
    "aliases": [
        "jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF2-BinE-PCR1-Rep1_S125",
        "jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF2-BinE-PCR2-Rep1_S131",
        "jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF2-BinE-PCR3-Rep1_S179",
        "jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF2-BinE-PCR4-Rep1_S185"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS0993NTCB](/auxiliary-sets/IGVFDS0993NTCB/) has sequence file(s) [IGVFFI7894YYZC](/sequence-files/IGVFFI7894YYZC/), [IGVFFI8705DNZH](/sequence-files/IGVFFI8705DNZH/), [IGVFFI7395GMMQ](/sequence-files/IGVFFI7395GMMQ/), [IGVFFI9082ISDE](/sequence-files/IGVFFI9082ISDE/) 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/IGVFDS0993NTCB/"
            }
        ]
    },
    "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": "2024-05-14T16:24:22.975926+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/IGVFFI7894YYZC/",
            "accession": "IGVFFI7894YYZC",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF2-BinE-PCR1-Rep1_S125"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:52:19.148644+00:00",
            "file_format": "fastq",
            "file_size": 24225395,
            "href": "/sequence-files/IGVFFI7894YYZC/@@download/IGVFFI7894YYZC.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/a7cf7146-d4c5-46ea-a908-a39386bf4ca5/IGVFFI7894YYZC.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-Auxin0hrs-FF2-BinE-PCR1-Rep1_S125_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI1274LNCV/",
            "accession": "IGVFFI1274LNCV",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF2-BinE-PCR1-Rep1_S125"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:42:55.331019+00:00",
            "file_format": "yaml",
            "file_size": 915,
            "href": "/configuration-files/IGVFFI1274LNCV/@@download/IGVFFI1274LNCV.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/f41132e6-e0e9-4d18-86e1-fba82ddfd04f/IGVFFI1274LNCV.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF2-BinE-PCR1-Rep1_S125.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8705DNZH/",
            "accession": "IGVFFI8705DNZH",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF2-BinE-PCR2-Rep1_S131"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:52:37.012660+00:00",
            "file_format": "fastq",
            "file_size": 23951492,
            "href": "/sequence-files/IGVFFI8705DNZH/@@download/IGVFFI8705DNZH.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/b80efc39-d524-447c-8855-6e8ca0eaf051/IGVFFI8705DNZH.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-Auxin0hrs-FF2-BinE-PCR2-Rep1_S131_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI7395GMMQ/",
            "accession": "IGVFFI7395GMMQ",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF2-BinE-PCR3-Rep1_S179"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:52:55.384991+00:00",
            "file_format": "fastq",
            "file_size": 31056667,
            "href": "/sequence-files/IGVFFI7395GMMQ/@@download/IGVFFI7395GMMQ.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/0e0794bf-c0fa-48ff-a40b-89450e6efbf3/IGVFFI7395GMMQ.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-Auxin0hrs-FF2-BinE-PCR3-Rep1_S179_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9082ISDE/",
            "accession": "IGVFFI9082ISDE",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF2-BinE-PCR4-Rep1_S185"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:53:13.412020+00:00",
            "file_format": "fastq",
            "file_size": 30206781,
            "href": "/sequence-files/IGVFFI9082ISDE/@@download/IGVFFI9082ISDE.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/f61fa0f0-dbf2-4685-9ef8-1f2f194b96af/IGVFFI9082ISDE.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-Auxin0hrs-FF2-BinE-PCR4-Rep1_S185_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI5302WHBP/",
            "accession": "IGVFFI5302WHBP",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF2-BinE-PCR4-Rep1_S185"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:43:36.562343+00:00",
            "file_format": "yaml",
            "file_size": 914,
            "href": "/configuration-files/IGVFFI5302WHBP/@@download/IGVFFI5302WHBP.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/99b249a3-f56c-445d-950d-2c9e68751acd/IGVFFI5302WHBP.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF2-BinE-PCR4-Rep1_S185.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI5240ILIB/",
            "accession": "IGVFFI5240ILIB",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF2-BinE-PCR3-Rep1_S179"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:43:23.243379+00:00",
            "file_format": "yaml",
            "file_size": 914,
            "href": "/configuration-files/IGVFFI5240ILIB/@@download/IGVFFI5240ILIB.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/eeface6f-90f4-4ff4-9adb-d56ebd7199b9/IGVFFI5240ILIB.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF2-BinE-PCR3-Rep1_S179.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI3040ASPY/",
            "accession": "IGVFFI3040ASPY",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF2-BinE-PCR2-Rep1_S131"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:43:09.120633+00:00",
            "file_format": "yaml",
            "file_size": 915,
            "href": "/configuration-files/IGVFFI3040ASPY/@@download/IGVFFI3040ASPY.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/b162e737-2412-4b42-899b-389f4901a51f/IGVFFI3040ASPY.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF2-BinE-PCR2-Rep1_S131.yaml",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS5239VQTN/"
    ],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS6734DXEE/",
            "accession": "IGVFDS6734DXEE",
            "aliases": [
                "jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF2-BinE-PCR1-Rep1_S125",
                "jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF2-BinE-PCR2-Rep1_S131",
                "jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF2-BinE-PCR3-Rep1_S179",
                "jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF2-BinE-PCR4-Rep1_S185"
            ],
            "preferred_assay_title": "CRISPR FlowFISH screen",
            "status": "released"
        }
    ],
    "release_timestamp": "2024-07-10T20:11:50.093856+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM1344KAZA/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM1344KAZA",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF2-BinE-PCR1-Rep1_S125",
                "jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF2-BinE-PCR2-Rep1_S131",
                "jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF2-BinE-PCR3-Rep1_S179",
                "jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF2-BinE-PCR4-Rep1_S185"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS1891GTLU/"
            ],
            "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 FAM3C) 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": "2024-06-01T01:52:19.148644+00:00",
    "summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "bf7513b2-7b56-4eee-b670-14b647e3735b"
}