IGVFDS7308SSJS

released
{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS7308SSJS/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS7308SSJS",
    "aliases": [
        "jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin6hrs-FF1-BinC-PCR1-Rep1_S135",
        "jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin6hrs-FF1-BinC-PCR2-Rep1_S141",
        "jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin6hrs-FF1-BinC-PCR3-Rep1_S189",
        "jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin6hrs-FF1-BinC-PCR4-Rep1_S195"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS7308SSJS](/auxiliary-sets/IGVFDS7308SSJS/) has sequence file(s) [IGVFFI6247BYIS](/sequence-files/IGVFFI6247BYIS/), [IGVFFI3369KHSA](/sequence-files/IGVFFI3369KHSA/), [IGVFFI1726SABC](/sequence-files/IGVFFI1726SABC/), [IGVFFI6913STDU](/sequence-files/IGVFFI6913STDU/) 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/IGVFDS7308SSJS/"
            }
        ]
    },
    "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": "2024-05-14T16:51:09.241024+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/IGVFFI6247BYIS/",
            "accession": "IGVFFI6247BYIS",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF1-BinC-PCR1-Rep1_S135"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:53:25.766652+00:00",
            "file_format": "fastq",
            "file_size": 29711268,
            "href": "/sequence-files/IGVFFI6247BYIS/@@download/IGVFFI6247BYIS.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/2a0b544b-46ea-46ce-89ba-5b98e428a7ff/IGVFFI6247BYIS.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/FAM3C-Auxin6hrs-FF1-BinC-PCR1-Rep1_S135_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI5075XAJF/",
            "accession": "IGVFFI5075XAJF",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF1-BinC-PCR1-Rep1_S135"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:43:46.260593+00:00",
            "file_format": "yaml",
            "file_size": 914,
            "href": "/configuration-files/IGVFFI5075XAJF/@@download/IGVFFI5075XAJF.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/7e871baa-8987-4315-a75c-bdeeab9bba1c/IGVFFI5075XAJF.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF1-BinC-PCR1-Rep1_S135.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3369KHSA/",
            "accession": "IGVFFI3369KHSA",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF1-BinC-PCR3-Rep1_S189"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:54:02.268396+00:00",
            "file_format": "fastq",
            "file_size": 36565907,
            "href": "/sequence-files/IGVFFI3369KHSA/@@download/IGVFFI3369KHSA.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/dc931aad-094d-4b6b-9664-7e90d96cd996/IGVFFI3369KHSA.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/FAM3C-Auxin6hrs-FF1-BinC-PCR3-Rep1_S189_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI1726SABC/",
            "accession": "IGVFFI1726SABC",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF1-BinC-PCR2-Rep1_S141"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:53:43.806938+00:00",
            "file_format": "fastq",
            "file_size": 28363430,
            "href": "/sequence-files/IGVFFI1726SABC/@@download/IGVFFI1726SABC.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/90d7aa70-ede7-4c04-95ea-155ba6679eb4/IGVFFI1726SABC.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/FAM3C-Auxin6hrs-FF1-BinC-PCR2-Rep1_S141_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI6913STDU/",
            "accession": "IGVFFI6913STDU",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF1-BinC-PCR4-Rep1_S195"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:54:21.051992+00:00",
            "file_format": "fastq",
            "file_size": 34740332,
            "href": "/sequence-files/IGVFFI6913STDU/@@download/IGVFFI6913STDU.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/53daa44c-9477-49d4-845f-c37accb68d82/IGVFFI6913STDU.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/FAM3C-Auxin6hrs-FF1-BinC-PCR4-Rep1_S195_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI7035ZSAZ/",
            "accession": "IGVFFI7035ZSAZ",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF1-BinC-PCR2-Rep1_S141"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:44:00.243453+00:00",
            "file_format": "yaml",
            "file_size": 913,
            "href": "/configuration-files/IGVFFI7035ZSAZ/@@download/IGVFFI7035ZSAZ.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/132b2353-fab5-4dca-8175-8ada3bc8c289/IGVFFI7035ZSAZ.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF1-BinC-PCR2-Rep1_S141.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI9615WQQN/",
            "accession": "IGVFFI9615WQQN",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF1-BinC-PCR3-Rep1_S189"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:44:13.901272+00:00",
            "file_format": "yaml",
            "file_size": 913,
            "href": "/configuration-files/IGVFFI9615WQQN/@@download/IGVFFI9615WQQN.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/e725308b-5862-4d61-beac-6b248fed4487/IGVFFI9615WQQN.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF1-BinC-PCR3-Rep1_S189.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI9344XDPG/",
            "accession": "IGVFFI9344XDPG",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF1-BinC-PCR4-Rep1_S195"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:44:27.724170+00:00",
            "file_format": "yaml",
            "file_size": 913,
            "href": "/configuration-files/IGVFFI9344XDPG/@@download/IGVFFI9344XDPG.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/6d6bc907-f34d-4c7e-84e2-1d42a519032a/IGVFFI9344XDPG.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF1-BinC-PCR4-Rep1_S195.yaml",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS5239VQTN/"
    ],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS6992SRVM/",
            "accession": "IGVFDS6992SRVM",
            "aliases": [
                "jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF1-BinC-PCR1-Rep1_S135",
                "jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF1-BinC-PCR2-Rep1_S141",
                "jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF1-BinC-PCR3-Rep1_S189",
                "jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF1-BinC-PCR4-Rep1_S195"
            ],
            "preferred_assay_title": "CRISPR FlowFISH screen",
            "status": "released"
        }
    ],
    "release_timestamp": "2024-07-10T20:12:18.893684+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM5752WTYA/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM5752WTYA",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF1-BinC-PCR1-Rep1_S135",
                "jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF1-BinC-PCR2-Rep1_S141",
                "jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF1-BinC-PCR3-Rep1_S189",
                "jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF1-BinC-PCR4-Rep1_S195"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS1891GTLU/"
            ],
            "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 C for 35-45% expression of FAM3C) 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": "2024-06-01T01:53:25.766652+00:00",
    "summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "9d8a202f-fdda-4049-b271-f68fe6b19689"
}