IGVFDS0051MRCH

released
{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS0051MRCH/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS0051MRCH",
    "aliases": [
        "jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin6hrs-FF1-BinB-PCR1-Rep1_S242",
        "jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin6hrs-FF1-BinB-PCR2-Rep1_S248",
        "jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin6hrs-FF1-BinB-PCR3-Rep1_S284",
        "jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin6hrs-FF1-BinB-PCR4-Rep1_S290"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS0051MRCH](/auxiliary-sets/IGVFDS0051MRCH/) has sequence file(s) [IGVFFI4348ZUXP](/sequence-files/IGVFFI4348ZUXP/), [IGVFFI0056ZWFB](/sequence-files/IGVFFI0056ZWFB/), [IGVFFI1781YSJE](/sequence-files/IGVFFI1781YSJE/), [IGVFFI8211KHIX](/sequence-files/IGVFFI8211KHIX/) 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/IGVFDS0051MRCH/"
            }
        ]
    },
    "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": "2024-05-13T22:50:43.949177+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/IGVFFI4348ZUXP/",
            "accession": "IGVFFI4348ZUXP",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF1-BinB-PCR1-Rep1_S242"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:42:03.750959+00:00",
            "file_format": "fastq",
            "file_size": 21187778,
            "href": "/sequence-files/IGVFFI4348ZUXP/@@download/IGVFFI4348ZUXP.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/918f39a3-4639-47fb-a14e-4729d40df862/IGVFFI4348ZUXP.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/CCND1-Auxin6hrs-FF1-BinB-PCR1-Rep1_S242_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI6541RIBO/",
            "accession": "IGVFFI6541RIBO",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF1-BinB-PCR1-Rep1_S242"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:29:54.459004+00:00",
            "file_format": "yaml",
            "file_size": 915,
            "href": "/configuration-files/IGVFFI6541RIBO/@@download/IGVFFI6541RIBO.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/8eee4e1c-1f92-412c-acb1-2a58e5765bd8/IGVFFI6541RIBO.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF1-BinB-PCR1-Rep1_S242.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI0056ZWFB/",
            "accession": "IGVFFI0056ZWFB",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF1-BinB-PCR2-Rep1_S248"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:42:21.490730+00:00",
            "file_format": "fastq",
            "file_size": 15476191,
            "href": "/sequence-files/IGVFFI0056ZWFB/@@download/IGVFFI0056ZWFB.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/3f8af430-a4cd-4b6f-9ac6-caca93fce82b/IGVFFI0056ZWFB.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/CCND1-Auxin6hrs-FF1-BinB-PCR2-Rep1_S248_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI1781YSJE/",
            "accession": "IGVFFI1781YSJE",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF1-BinB-PCR3-Rep1_S284"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:42:38.091546+00:00",
            "file_format": "fastq",
            "file_size": 33923038,
            "href": "/sequence-files/IGVFFI1781YSJE/@@download/IGVFFI1781YSJE.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/3541381a-a7d4-4405-8ea4-244223aee743/IGVFFI1781YSJE.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/CCND1-Auxin6hrs-FF1-BinB-PCR3-Rep1_S284_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8211KHIX/",
            "accession": "IGVFFI8211KHIX",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF1-BinB-PCR4-Rep1_S290"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:42:55.899195+00:00",
            "file_format": "fastq",
            "file_size": 23445132,
            "href": "/sequence-files/IGVFFI8211KHIX/@@download/IGVFFI8211KHIX.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/d540256b-ab1d-4792-b9c0-5388c9cd4df6/IGVFFI8211KHIX.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/CCND1-Auxin6hrs-FF1-BinB-PCR4-Rep1_S290_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI8434JLTQ/",
            "accession": "IGVFFI8434JLTQ",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF1-BinB-PCR2-Rep1_S248"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:30:08.700092+00:00",
            "file_format": "yaml",
            "file_size": 915,
            "href": "/configuration-files/IGVFFI8434JLTQ/@@download/IGVFFI8434JLTQ.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/43656b07-a9ab-4829-af23-2074e998d577/IGVFFI8434JLTQ.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF1-BinB-PCR2-Rep1_S248.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI4045SHGK/",
            "accession": "IGVFFI4045SHGK",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF1-BinB-PCR3-Rep1_S284"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:30:22.769115+00:00",
            "file_format": "yaml",
            "file_size": 915,
            "href": "/configuration-files/IGVFFI4045SHGK/@@download/IGVFFI4045SHGK.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/5966239d-b340-48b5-bb4a-e74b887e9bdd/IGVFFI4045SHGK.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF1-BinB-PCR3-Rep1_S284.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI2535ZPBT/",
            "accession": "IGVFFI2535ZPBT",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF1-BinB-PCR4-Rep1_S290"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:30:37.235850+00:00",
            "file_format": "yaml",
            "file_size": 915,
            "href": "/configuration-files/IGVFFI2535ZPBT/@@download/IGVFFI2535ZPBT.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/8986029e-5350-4d78-9a14-df02923f1b0a/IGVFFI2535ZPBT.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF1-BinB-PCR4-Rep1_S290.yaml",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS1569RNPD/"
    ],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS5572SQRK/",
            "accession": "IGVFDS5572SQRK",
            "aliases": [
                "jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF1-BinB-PCR1-Rep1_S242",
                "jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF1-BinB-PCR2-Rep1_S248",
                "jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF1-BinB-PCR3-Rep1_S284",
                "jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF1-BinB-PCR4-Rep1_S290"
            ],
            "preferred_assay_title": "CRISPR FlowFISH screen",
            "status": "released"
        }
    ],
    "release_timestamp": "2024-07-10T20:09:18.397265+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM5255ABUW/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM5255ABUW",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF1-BinB-PCR1-Rep1_S242",
                "jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF1-BinB-PCR2-Rep1_S248",
                "jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF1-BinB-PCR3-Rep1_S284",
                "jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF1-BinB-PCR4-Rep1_S290"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS6351FGNG/"
            ],
            "modifications": [
                {
                    "@id": "/degron-modifications/95081d1b-08b4-49ed-b324-e53fc43d8456/",
                    "modality": "degradation",
                    "status": "released"
                },
                {
                    "@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
                    "modality": "interference",
                    "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 B for 10-20% expression of CCND1) treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours, modified with AID system targeting RAD21, CRISPRi Sp-dCas9-KOX1-KRAB, transfected with a guide library",
            "taxa": "Homo sapiens",
            "treatments": [
                {
                    "@id": "/treatments/d35868d1-c45b-49ae-8ff3-a9c0c22551c2/",
                    "status": "released",
                    "treatment_term_name": "5-Phenyl-1H-indole-3-acetic acid"
                }
            ]
        }
    ],
    "schema_version": "12",
    "status": "released",
    "submitted_by": {
        "@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
        "title": "Chongyon Park"
    },
    "submitted_files_timestamp": "2024-06-01T01:42:03.750959+00:00",
    "summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "265dbac8-d5f4-4d3c-b834-bca5102e6ec0"
}