IGVFDS3611WVHW

released
{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS3611WVHW/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS3611WVHW",
    "aliases": [
        "jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF1-BinE-PCR1-Rep1_S113",
        "jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF1-BinE-PCR2-Rep1_S119",
        "jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF1-BinE-PCR3-Rep1_S167",
        "jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF1-BinE-PCR4-Rep1_S173"
    ],
    "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/"
            }
        ],
        "WARNING": [
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS3611WVHW](/auxiliary-sets/IGVFDS3611WVHW/) has sequence file(s) [IGVFFI8497NPVR](/sequence-files/IGVFFI8497NPVR/), [IGVFFI0840FMQW](/sequence-files/IGVFFI0840FMQW/), [IGVFFI7555FXHU](/sequence-files/IGVFFI7555FXHU/), [IGVFFI0393VYGB](/sequence-files/IGVFFI0393VYGB/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
                "level": 40,
                "level_name": "WARNING",
                "name": "audit_inconsistent_sequencing_kit",
                "path": "/auxiliary-sets/IGVFDS3611WVHW/"
            },
            {
                "category": "missing analysis",
                "detail": "Auxiliary set [IGVFDS3611WVHW](/auxiliary-sets/IGVFDS3611WVHW/) is a raw data set with files, but is not listed in any `input_file_sets` for any analysis sets. Raw data sets with files are expected to be associated with at least one analysis set.",
                "level": 40,
                "level_name": "WARNING",
                "name": "audit_input_file_set_for",
                "path": "/auxiliary-sets/IGVFDS3611WVHW/"
            }
        ]
    },
    "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": "2024-05-14T16:23:54.784069+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/IGVFFI8497NPVR/",
            "accession": "IGVFFI8497NPVR",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF1-BinE-PCR1-Rep1_S113"
            ],
            "content_type": "reads",
            "creation_timestamp": "2024-06-01T01:51:03.804629+00:00",
            "file_format": "fastq",
            "file_size": 18858257,
            "href": "/sequence-files/IGVFFI8497NPVR/@@download/IGVFFI8497NPVR.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/2e730e47-783c-41a9-bcac-943971d7eb30/IGVFFI8497NPVR.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/FAM3C-Auxin0hrs-FF1-BinE-PCR1-Rep1_S113_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI1875AKLE/",
            "accession": "IGVFFI1875AKLE",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF1-BinE-PCR1-Rep1_S113"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:41:59.862244+00:00",
            "file_format": "yaml",
            "file_size": 913,
            "href": "/configuration-files/IGVFFI1875AKLE/@@download/IGVFFI1875AKLE.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/acee7f90-56b8-4d88-9996-42d85077752e/IGVFFI1875AKLE.yaml.gz",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF1-BinE-PCR1-Rep1_S113.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI0840FMQW/",
            "accession": "IGVFFI0840FMQW",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF1-BinE-PCR2-Rep1_S119"
            ],
            "content_type": "reads",
            "creation_timestamp": "2024-06-01T01:51:22.667705+00:00",
            "file_format": "fastq",
            "file_size": 24853329,
            "href": "/sequence-files/IGVFFI0840FMQW/@@download/IGVFFI0840FMQW.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/f43ab3e5-3f39-4f91-866d-03c4f3f0cd44/IGVFFI0840FMQW.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/FAM3C-Auxin0hrs-FF1-BinE-PCR2-Rep1_S119_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI7555FXHU/",
            "accession": "IGVFFI7555FXHU",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF1-BinE-PCR3-Rep1_S167"
            ],
            "content_type": "reads",
            "creation_timestamp": "2024-06-01T01:51:40.927275+00:00",
            "file_format": "fastq",
            "file_size": 24620913,
            "href": "/sequence-files/IGVFFI7555FXHU/@@download/IGVFFI7555FXHU.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/9a1dc410-cde1-4b78-95c5-464e29c0c356/IGVFFI7555FXHU.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/FAM3C-Auxin0hrs-FF1-BinE-PCR3-Rep1_S167_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI0393VYGB/",
            "accession": "IGVFFI0393VYGB",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF1-BinE-PCR4-Rep1_S173"
            ],
            "content_type": "reads",
            "creation_timestamp": "2024-06-01T01:52:00.458588+00:00",
            "file_format": "fastq",
            "file_size": 29643478,
            "href": "/sequence-files/IGVFFI0393VYGB/@@download/IGVFFI0393VYGB.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/fae35da2-9903-466a-9445-de0b7393cb4e/IGVFFI0393VYGB.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/FAM3C-Auxin0hrs-FF1-BinE-PCR4-Rep1_S173_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI0081OFZM/",
            "accession": "IGVFFI0081OFZM",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF1-BinE-PCR2-Rep1_S119"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:42:15.178823+00:00",
            "file_format": "yaml",
            "file_size": 914,
            "href": "/configuration-files/IGVFFI0081OFZM/@@download/IGVFFI0081OFZM.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/8b3d9272-eb90-4386-953e-92b6a1f3cff7/IGVFFI0081OFZM.yaml.gz",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF1-BinE-PCR2-Rep1_S119.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI1460IMUJ/",
            "accession": "IGVFFI1460IMUJ",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF1-BinE-PCR4-Rep1_S173"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:42:41.944823+00:00",
            "file_format": "yaml",
            "file_size": 914,
            "href": "/configuration-files/IGVFFI1460IMUJ/@@download/IGVFFI1460IMUJ.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/48546bdb-1b17-4308-87e7-384983cd1054/IGVFFI1460IMUJ.yaml.gz",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF1-BinE-PCR4-Rep1_S173.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI9021TJZW/",
            "accession": "IGVFFI9021TJZW",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF1-BinE-PCR3-Rep1_S167"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:42:28.524961+00:00",
            "file_format": "yaml",
            "file_size": 915,
            "href": "/configuration-files/IGVFFI9021TJZW/@@download/IGVFFI9021TJZW.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/27360650-8282-4829-862c-7723a93b0989/IGVFFI9021TJZW.yaml.gz",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF1-BinE-PCR3-Rep1_S167.yaml",
            "upload_status": "validated"
        }
    ],
    "input_file_set_for": [],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS5612XEIT/",
            "accession": "IGVFDS5612XEIT",
            "aliases": [
                "jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF1-BinE-PCR1-Rep1_S113",
                "jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF1-BinE-PCR2-Rep1_S119",
                "jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF1-BinE-PCR3-Rep1_S167",
                "jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF1-BinE-PCR4-Rep1_S173"
            ],
            "preferred_assay_title": "CRISPR FlowFISH screen"
        }
    ],
    "release_timestamp": "2024-07-10T20:11:07.720466+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM4222TCYN/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM4222TCYN",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF1-BinE-PCR1-Rep1_S113",
                "jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF1-BinE-PCR2-Rep1_S119",
                "jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF1-BinE-PCR3-Rep1_S167",
                "jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF1-BinE-PCR4-Rep1_S173"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS1891GTLU/"
            ],
            "modifications": [
                "/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 FAM3C) modified with a guide library",
            "taxa": "Homo sapiens"
        }
    ],
    "schema_version": "11",
    "status": "released",
    "submitted_by": {
        "@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
        "title": "Chongyon Park"
    },
    "submitted_files_timestamp": "2024-06-01T01:51:03.804629+00:00",
    "summary": "gRNA sequencing for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "79faf7d1-2e28-4f7c-a9c2-cafd0e17779a"
}