IGVFDS2426AOQY

released
{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS2426AOQY/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS2426AOQY",
    "aliases": [
        "jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF1-BinA-PCR1-Rep1_S1",
        "jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF1-BinA-PCR2-Rep1_S7",
        "jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF1-BinA-PCR3-Rep1_S55",
        "jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF1-BinA-PCR4-Rep1_S61"
    ],
    "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 [IGVFDS2426AOQY](/auxiliary-sets/IGVFDS2426AOQY/) has sequence file(s) [IGVFFI9023FXEP](/sequence-files/IGVFFI9023FXEP/), [IGVFFI8100KOAD](/sequence-files/IGVFFI8100KOAD/), [IGVFFI0928JDQC](/sequence-files/IGVFFI0928JDQC/), [IGVFFI8198LFFE](/sequence-files/IGVFFI8198LFFE/) 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/IGVFDS2426AOQY/"
            },
            {
                "category": "missing analysis",
                "detail": "Auxiliary set [IGVFDS2426AOQY](/auxiliary-sets/IGVFDS2426AOQY/) 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/IGVFDS2426AOQY/"
            }
        ]
    },
    "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": "2024-05-14T20:30:52.595320+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/IGVFFI9023FXEP/",
            "accession": "IGVFFI9023FXEP",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF1-BinA-PCR1-Rep1_S1"
            ],
            "content_type": "reads",
            "creation_timestamp": "2024-06-01T01:44:33.420710+00:00",
            "file_format": "fastq",
            "file_size": 34325316,
            "href": "/sequence-files/IGVFFI9023FXEP/@@download/IGVFFI9023FXEP.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/887869cd-0f10-4ecb-b525-7f18dac2bb0c/IGVFFI9023FXEP.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/SSFA2-Auxin0hrs-FF1-BinA-PCR1-Rep1_S1_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI0261CXQV/",
            "accession": "IGVFFI0261CXQV",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF1-BinA-PCR1-Rep1_S1"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:37:17.163920+00:00",
            "file_format": "yaml",
            "file_size": 912,
            "href": "/configuration-files/IGVFFI0261CXQV/@@download/IGVFFI0261CXQV.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/1578df4c-01d0-4fe7-803b-22e71d8a6e66/IGVFFI0261CXQV.yaml.gz",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF1-BinA-PCR1-Rep1_S1.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8100KOAD/",
            "accession": "IGVFFI8100KOAD",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF1-BinA-PCR2-Rep1_S7"
            ],
            "content_type": "reads",
            "creation_timestamp": "2024-06-01T01:44:53.552323+00:00",
            "file_format": "fastq",
            "file_size": 23816136,
            "href": "/sequence-files/IGVFFI8100KOAD/@@download/IGVFFI8100KOAD.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/579cc3c4-0751-433f-a9c0-7221966f1378/IGVFFI8100KOAD.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/SSFA2-Auxin0hrs-FF1-BinA-PCR2-Rep1_S7_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI7888TKOX/",
            "accession": "IGVFFI7888TKOX",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF1-BinA-PCR2-Rep1_S7"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:37:31.478357+00:00",
            "file_format": "yaml",
            "file_size": 911,
            "href": "/configuration-files/IGVFFI7888TKOX/@@download/IGVFFI7888TKOX.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/4a73e654-f3ce-4300-93df-c71437957f4a/IGVFFI7888TKOX.yaml.gz",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF1-BinA-PCR2-Rep1_S7.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI0928JDQC/",
            "accession": "IGVFFI0928JDQC",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF1-BinA-PCR3-Rep1_S55"
            ],
            "content_type": "reads",
            "creation_timestamp": "2024-06-01T01:45:12.054732+00:00",
            "file_format": "fastq",
            "file_size": 20434853,
            "href": "/sequence-files/IGVFFI0928JDQC/@@download/IGVFFI0928JDQC.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/bc973919-d275-4f5f-85d9-726a267118c5/IGVFFI0928JDQC.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/SSFA2-Auxin0hrs-FF1-BinA-PCR3-Rep1_S55_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8198LFFE/",
            "accession": "IGVFFI8198LFFE",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF1-BinA-PCR4-Rep1_S61"
            ],
            "content_type": "reads",
            "creation_timestamp": "2024-06-01T01:45:29.856413+00:00",
            "file_format": "fastq",
            "file_size": 21146947,
            "href": "/sequence-files/IGVFFI8198LFFE/@@download/IGVFFI8198LFFE.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/48fdfa97-164c-4131-b266-2d48d07a1415/IGVFFI8198LFFE.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/SSFA2-Auxin0hrs-FF1-BinA-PCR4-Rep1_S61_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI2857XLQE/",
            "accession": "IGVFFI2857XLQE",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF1-BinA-PCR3-Rep1_S55"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:37:46.726765+00:00",
            "file_format": "yaml",
            "file_size": 912,
            "href": "/configuration-files/IGVFFI2857XLQE/@@download/IGVFFI2857XLQE.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/7d98f901-d35b-4858-ba4e-8d05423f39a9/IGVFFI2857XLQE.yaml.gz",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF1-BinA-PCR3-Rep1_S55.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI8878HOHR/",
            "accession": "IGVFFI8878HOHR",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF1-BinA-PCR4-Rep1_S61"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:38:02.070161+00:00",
            "file_format": "yaml",
            "file_size": 913,
            "href": "/configuration-files/IGVFFI8878HOHR/@@download/IGVFFI8878HOHR.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/eb0fd4aa-f39c-4b46-8acc-8567df51aa1c/IGVFFI8878HOHR.yaml.gz",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF1-BinA-PCR4-Rep1_S61.yaml",
            "upload_status": "validated"
        }
    ],
    "input_file_set_for": [],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS7398YKXX/",
            "accession": "IGVFDS7398YKXX",
            "aliases": [
                "jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinA-PCR1-Rep1_S1",
                "jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinA-PCR2-Rep1_S7",
                "jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinA-PCR3-Rep1_S55",
                "jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinA-PCR4-Rep1_S61"
            ],
            "preferred_assay_title": "CRISPR FlowFISH screen"
        }
    ],
    "release_timestamp": "2024-07-10T20:23:41.682522+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM7231THBU/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM7231THBU",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinA-PCR1-Rep1_S1",
                "jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinA-PCR2-Rep1_S7",
                "jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinA-PCR3-Rep1_S55",
                "jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinA-PCR4-Rep1_S61"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS5413RKIA/"
            ],
            "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 A for 0-10% expression of SSFA2) 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": "2024-06-01T01:44:33.420710+00:00",
    "summary": "gRNA sequencing for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "515e8408-7e95-4293-b8fb-59ad469193f0"
}