IGVFDS2965IRTU

released
{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS2965IRTU/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS2965IRTU",
    "aliases": [
        "jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF1-BinD-PCR1-Rep1_S220",
        "jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF1-BinD-PCR2-Rep1_S226",
        "jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF1-BinD-PCR3-Rep1_S262",
        "jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF1-BinD-PCR4-Rep1_S268"
    ],
    "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 [IGVFDS2965IRTU](/auxiliary-sets/IGVFDS2965IRTU/) has sequence file(s) [IGVFFI1781AOFZ](/sequence-files/IGVFFI1781AOFZ/), [IGVFFI9086AHHC](/sequence-files/IGVFFI9086AHHC/), [IGVFFI0907KKUJ](/sequence-files/IGVFFI0907KKUJ/), [IGVFFI9404GXRL](/sequence-files/IGVFFI9404GXRL/) 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/IGVFDS2965IRTU/"
            },
            {
                "category": "missing analysis",
                "detail": "Auxiliary set [IGVFDS2965IRTU](/auxiliary-sets/IGVFDS2965IRTU/) 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/IGVFDS2965IRTU/"
            }
        ]
    },
    "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": "2024-05-13T22:38:48.028312+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/IGVFFI1781AOFZ/",
            "accession": "IGVFFI1781AOFZ",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF1-BinD-PCR1-Rep1_S220"
            ],
            "content_type": "reads",
            "creation_timestamp": "2024-06-01T01:36:05.323690+00:00",
            "file_format": "fastq",
            "file_size": 23853924,
            "href": "/sequence-files/IGVFFI1781AOFZ/@@download/IGVFFI1781AOFZ.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/07b651f1-1ba7-41ba-b6b0-e26e31e77c99/IGVFFI1781AOFZ.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin0hrs-FF1-BinD-PCR1-Rep1_S220_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI7168PSKZ/",
            "accession": "IGVFFI7168PSKZ",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF1-BinD-PCR1-Rep1_S220"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:28:05.671236+00:00",
            "file_format": "yaml",
            "file_size": 914,
            "href": "/configuration-files/IGVFFI7168PSKZ/@@download/IGVFFI7168PSKZ.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/48f35b37-3419-4608-8394-8f2582c6d7cc/IGVFFI7168PSKZ.yaml.gz",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF1-BinD-PCR1-Rep1_S220.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9086AHHC/",
            "accession": "IGVFFI9086AHHC",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF1-BinD-PCR2-Rep1_S226"
            ],
            "content_type": "reads",
            "creation_timestamp": "2024-06-01T01:36:23.174986+00:00",
            "file_format": "fastq",
            "file_size": 22613096,
            "href": "/sequence-files/IGVFFI9086AHHC/@@download/IGVFFI9086AHHC.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/1247aa3a-d668-4e79-84f4-e12a1c3c4553/IGVFFI9086AHHC.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin0hrs-FF1-BinD-PCR2-Rep1_S226_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI0907KKUJ/",
            "accession": "IGVFFI0907KKUJ",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF1-BinD-PCR3-Rep1_S262"
            ],
            "content_type": "reads",
            "creation_timestamp": "2024-06-01T01:36:41.470464+00:00",
            "file_format": "fastq",
            "file_size": 30315346,
            "href": "/sequence-files/IGVFFI0907KKUJ/@@download/IGVFFI0907KKUJ.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/a7a98b1a-9c08-4341-ba00-990a987c698b/IGVFFI0907KKUJ.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin0hrs-FF1-BinD-PCR3-Rep1_S262_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9404GXRL/",
            "accession": "IGVFFI9404GXRL",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF1-BinD-PCR4-Rep1_S268"
            ],
            "content_type": "reads",
            "creation_timestamp": "2024-06-01T01:36:59.616473+00:00",
            "file_format": "fastq",
            "file_size": 27021538,
            "href": "/sequence-files/IGVFFI9404GXRL/@@download/IGVFFI9404GXRL.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/95f3ceb1-5fd9-4ac7-9a17-e47e4aedfdbb/IGVFFI9404GXRL.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin0hrs-FF1-BinD-PCR4-Rep1_S268_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI8614RUON/",
            "accession": "IGVFFI8614RUON",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF1-BinD-PCR3-Rep1_S262"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:28:34.197831+00:00",
            "file_format": "yaml",
            "file_size": 914,
            "href": "/configuration-files/IGVFFI8614RUON/@@download/IGVFFI8614RUON.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/247c4f9a-83cb-4d88-adc3-67f9bb4a185f/IGVFFI8614RUON.yaml.gz",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF1-BinD-PCR3-Rep1_S262.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI2555BDBO/",
            "accession": "IGVFFI2555BDBO",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF1-BinD-PCR4-Rep1_S268"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:28:48.641839+00:00",
            "file_format": "yaml",
            "file_size": 914,
            "href": "/configuration-files/IGVFFI2555BDBO/@@download/IGVFFI2555BDBO.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/3c05c298-11ef-4044-b3a7-cce09cefaeee/IGVFFI2555BDBO.yaml.gz",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF1-BinD-PCR4-Rep1_S268.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI2589FZCK/",
            "accession": "IGVFFI2589FZCK",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF1-BinD-PCR2-Rep1_S226"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:28:20.413329+00:00",
            "file_format": "yaml",
            "file_size": 913,
            "href": "/configuration-files/IGVFFI2589FZCK/@@download/IGVFFI2589FZCK.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/180090c9-a798-4361-a0e3-740dedf0aa51/IGVFFI2589FZCK.yaml.gz",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF1-BinD-PCR2-Rep1_S226.yaml",
            "upload_status": "validated"
        }
    ],
    "input_file_set_for": [],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS6001NZOV/",
            "accession": "IGVFDS6001NZOV",
            "aliases": [
                "jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinD-PCR1-Rep1_S220",
                "jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinD-PCR2-Rep1_S226",
                "jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinD-PCR3-Rep1_S262",
                "jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinD-PCR4-Rep1_S268"
            ],
            "preferred_assay_title": "CRISPR FlowFISH screen"
        }
    ],
    "release_timestamp": "2024-07-10T20:08:11.628028+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM6400EVKX/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM6400EVKX",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinD-PCR1-Rep1_S220",
                "jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinD-PCR2-Rep1_S226",
                "jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinD-PCR3-Rep1_S262",
                "jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinD-PCR4-Rep1_S268"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS6351FGNG/"
            ],
            "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 D for 55-65% expression of CCND1) 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": "2024-06-01T01:36:05.323690+00:00",
    "summary": "gRNA sequencing for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "d51e2829-d6c5-4232-8d51-a0b94111cc14"
}