IGVFDS3673BXYO

released
{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS3673BXYO/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS3673BXYO",
    "aliases": [
        "jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF3-BinE-PCR1_S29",
        "jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF3-BinE-PCR2_S35",
        "jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF3-BinE-PCR3_S125",
        "jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF3-BinE-PCR4_S131"
    ],
    "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 [IGVFDS3673BXYO](/auxiliary-sets/IGVFDS3673BXYO/) has sequence file(s) [IGVFFI1262UZWR](/sequence-files/IGVFFI1262UZWR/), [IGVFFI7056URWW](/sequence-files/IGVFFI7056URWW/), [IGVFFI8116SREE](/sequence-files/IGVFFI8116SREE/), [IGVFFI4420MMWA](/sequence-files/IGVFFI4420MMWA/) 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/IGVFDS3673BXYO/"
            },
            {
                "category": "missing analysis",
                "detail": "Auxiliary set [IGVFDS3673BXYO](/auxiliary-sets/IGVFDS3673BXYO/) 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/IGVFDS3673BXYO/"
            }
        ]
    },
    "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": "2024-05-16T17:42:01.204541+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/IGVFFI1262UZWR/",
            "accession": "IGVFFI1262UZWR",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF3-BinE-PCR1_S29"
            ],
            "content_type": "reads",
            "creation_timestamp": "2024-06-01T02:17:36.651541+00:00",
            "file_format": "fastq",
            "file_size": 8054235,
            "href": "/sequence-files/IGVFFI1262UZWR/@@download/IGVFFI1262UZWR.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/14a6f507-a79c-45b3-95de-705ad09e624b/IGVFFI1262UZWR.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF3-BinE-PCR1_S29_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI1204XAGV/",
            "accession": "IGVFFI1204XAGV",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF3-BinE-PCR1_S29"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T22:07:38.167567+00:00",
            "file_format": "yaml",
            "file_size": 903,
            "href": "/configuration-files/IGVFFI1204XAGV/@@download/IGVFFI1204XAGV.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/e882493e-903c-4908-8696-f468aaa17851/IGVFFI1204XAGV.yaml.gz",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF3-BinE-PCR1_S29.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI7056URWW/",
            "accession": "IGVFFI7056URWW",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF3-BinE-PCR3_S125"
            ],
            "content_type": "reads",
            "creation_timestamp": "2024-06-01T02:18:12.720454+00:00",
            "file_format": "fastq",
            "file_size": 15620018,
            "href": "/sequence-files/IGVFFI7056URWW/@@download/IGVFFI7056URWW.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/24bfb3dc-36eb-4a7f-a124-67cb9b7d66f2/IGVFFI7056URWW.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF3-BinE-PCR3_S125_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI1263XHMB/",
            "accession": "IGVFFI1263XHMB",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF3-BinE-PCR4_S131"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T22:08:17.780766+00:00",
            "file_format": "yaml",
            "file_size": 902,
            "href": "/configuration-files/IGVFFI1263XHMB/@@download/IGVFFI1263XHMB.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/52380662-eca1-4964-9ed8-ced9bd4a5e8d/IGVFFI1263XHMB.yaml.gz",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF3-BinE-PCR4_S131.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8116SREE/",
            "accession": "IGVFFI8116SREE",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF3-BinE-PCR4_S131"
            ],
            "content_type": "reads",
            "creation_timestamp": "2024-06-01T02:18:31.280501+00:00",
            "file_format": "fastq",
            "file_size": 20036420,
            "href": "/sequence-files/IGVFFI8116SREE/@@download/IGVFFI8116SREE.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/b0f9a0f9-20b5-4732-9f12-c76124d298ba/IGVFFI8116SREE.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF3-BinE-PCR4_S131_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI4420MMWA/",
            "accession": "IGVFFI4420MMWA",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF3-BinE-PCR2_S35"
            ],
            "content_type": "reads",
            "creation_timestamp": "2024-06-01T02:17:54.767308+00:00",
            "file_format": "fastq",
            "file_size": 12422630,
            "href": "/sequence-files/IGVFFI4420MMWA/@@download/IGVFFI4420MMWA.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/82c96975-e983-4f43-8c1b-78ec9ad54732/IGVFFI4420MMWA.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF3-BinE-PCR2_S35_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI6946JJKZ/",
            "accession": "IGVFFI6946JJKZ",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF3-BinE-PCR3_S125"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T22:08:04.499774+00:00",
            "file_format": "yaml",
            "file_size": 903,
            "href": "/configuration-files/IGVFFI6946JJKZ/@@download/IGVFFI6946JJKZ.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/1e15d39a-523f-46d2-b2ff-f3b42b83ab44/IGVFFI6946JJKZ.yaml.gz",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF3-BinE-PCR3_S125.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI7018BVOW/",
            "accession": "IGVFFI7018BVOW",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF3-BinE-PCR2_S35"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T22:07:51.305025+00:00",
            "file_format": "yaml",
            "file_size": 902,
            "href": "/configuration-files/IGVFFI7018BVOW/@@download/IGVFFI7018BVOW.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/d904a362-5731-40d9-b340-a7e456df80cb/IGVFFI7018BVOW.yaml.gz",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF3-BinE-PCR2_S35.yaml",
            "upload_status": "validated"
        }
    ],
    "input_file_set_for": [],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS9498BKLC/",
            "accession": "IGVFDS9498BKLC",
            "aliases": [
                "jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF3-BinE-PCR1_S29",
                "jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF3-BinE-PCR2_S35",
                "jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF3-BinE-PCR3_S125",
                "jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF3-BinE-PCR4_S131"
            ],
            "preferred_assay_title": "CRISPR FlowFISH screen"
        }
    ],
    "release_timestamp": "2024-07-10T20:15:24.858522+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM0596STHT/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM0596STHT",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF3-BinE-PCR1_S29",
                "jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF3-BinE-PCR2_S35",
                "jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF3-BinE-PCR3_S125",
                "jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF3-BinE-PCR4_S131"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS7846UISG/"
            ],
            "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 KITLG) 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": "2024-06-01T02:17:36.651541+00:00",
    "summary": "gRNA sequencing for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "b1ab4e0a-e9d8-49cb-868f-11aa22bfd3da"
}