IGVFDS8871HVZU

released
{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS8871HVZU/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS8871HVZU",
    "aliases": [
        "jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF1-BinA-PCR1-Rep1_S109",
        "jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF1-BinA-PCR2-Rep1_S115",
        "jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF1-BinA-PCR3-Rep1_S163",
        "jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF1-BinA-PCR4-Rep1_S169"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS8871HVZU](/auxiliary-sets/IGVFDS8871HVZU/) has sequence file(s) [IGVFFI4047DOQR](/sequence-files/IGVFFI4047DOQR/), [IGVFFI5610GEDM](/sequence-files/IGVFFI5610GEDM/), [IGVFFI8800QUFB](/sequence-files/IGVFFI8800QUFB/), [IGVFFI3269HFXQ](/sequence-files/IGVFFI3269HFXQ/) 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/IGVFDS8871HVZU/"
            }
        ]
    },
    "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": "2024-05-14T16:23:49.600771+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/IGVFFI4047DOQR/",
            "accession": "IGVFFI4047DOQR",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF1-BinA-PCR1-Rep1_S109"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:50:49.609086+00:00",
            "file_format": "fastq",
            "file_size": 33957548,
            "href": "/sequence-files/IGVFFI4047DOQR/@@download/IGVFFI4047DOQR.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/bb35b7fb-9499-4639-8753-cd3f35af1a33/IGVFFI4047DOQR.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-Auxin0hrs-FF1-BinA-PCR1-Rep1_S109_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI7993DQGZ/",
            "accession": "IGVFFI7993DQGZ",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF1-BinA-PCR1-Rep1_S109"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:41:49.365610+00:00",
            "file_format": "yaml",
            "file_size": 913,
            "href": "/configuration-files/IGVFFI7993DQGZ/@@download/IGVFFI7993DQGZ.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/8bc82b03-ad8a-4ff2-8d93-91aedc556a4e/IGVFFI7993DQGZ.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF1-BinA-PCR1-Rep1_S109.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI5610GEDM/",
            "accession": "IGVFFI5610GEDM",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF1-BinA-PCR2-Rep1_S115"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:51:10.148422+00:00",
            "file_format": "fastq",
            "file_size": 24342273,
            "href": "/sequence-files/IGVFFI5610GEDM/@@download/IGVFFI5610GEDM.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/bd623ad6-8f1f-452f-87b9-a6793c76e1bf/IGVFFI5610GEDM.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-Auxin0hrs-FF1-BinA-PCR2-Rep1_S115_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8800QUFB/",
            "accession": "IGVFFI8800QUFB",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF1-BinA-PCR3-Rep1_S163"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:51:28.642686+00:00",
            "file_format": "fastq",
            "file_size": 32923471,
            "href": "/sequence-files/IGVFFI8800QUFB/@@download/IGVFFI8800QUFB.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/56b3e603-2e3d-4076-84ad-9797ffd0b5e7/IGVFFI8800QUFB.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-Auxin0hrs-FF1-BinA-PCR3-Rep1_S163_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3269HFXQ/",
            "accession": "IGVFFI3269HFXQ",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF1-BinA-PCR4-Rep1_S169"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:51:47.738838+00:00",
            "file_format": "fastq",
            "file_size": 29829564,
            "href": "/sequence-files/IGVFFI3269HFXQ/@@download/IGVFFI3269HFXQ.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/82ad45b8-4345-4f90-9fcb-2b774f6f5abc/IGVFFI3269HFXQ.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-Auxin0hrs-FF1-BinA-PCR4-Rep1_S169_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI0611SUFM/",
            "accession": "IGVFFI0611SUFM",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF1-BinA-PCR4-Rep1_S169"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:42:33.082332+00:00",
            "file_format": "yaml",
            "file_size": 915,
            "href": "/configuration-files/IGVFFI0611SUFM/@@download/IGVFFI0611SUFM.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/8466861c-db64-4520-b916-70c93b67b543/IGVFFI0611SUFM.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF1-BinA-PCR4-Rep1_S169.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI7093PHJH/",
            "accession": "IGVFFI7093PHJH",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF1-BinA-PCR2-Rep1_S115"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:42:05.036938+00:00",
            "file_format": "yaml",
            "file_size": 914,
            "href": "/configuration-files/IGVFFI7093PHJH/@@download/IGVFFI7093PHJH.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/a6041667-4d7c-4cc2-ad98-dd9911432087/IGVFFI7093PHJH.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF1-BinA-PCR2-Rep1_S115.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI0987YOBQ/",
            "accession": "IGVFFI0987YOBQ",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF1-BinA-PCR3-Rep1_S163"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:42:19.953519+00:00",
            "file_format": "yaml",
            "file_size": 913,
            "href": "/configuration-files/IGVFFI0987YOBQ/@@download/IGVFFI0987YOBQ.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/3dcc9ff0-f038-409d-b30d-6b1a3030e8d4/IGVFFI0987YOBQ.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF1-BinA-PCR3-Rep1_S163.yaml",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS5239VQTN/"
    ],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS6095WNVW/",
            "accession": "IGVFDS6095WNVW",
            "aliases": [
                "jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF1-BinA-PCR1-Rep1_S109",
                "jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF1-BinA-PCR2-Rep1_S115",
                "jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF1-BinA-PCR3-Rep1_S163",
                "jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF1-BinA-PCR4-Rep1_S169"
            ],
            "preferred_assay_title": "CRISPR FlowFISH screen",
            "status": "released"
        }
    ],
    "release_timestamp": "2024-07-10T20:10:38.272539+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM5410WZKF/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM5410WZKF",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF1-BinA-PCR1-Rep1_S109",
                "jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF1-BinA-PCR2-Rep1_S115",
                "jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF1-BinA-PCR3-Rep1_S163",
                "jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF1-BinA-PCR4-Rep1_S169"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS1891GTLU/"
            ],
            "modifications": [
                {
                    "@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
                    "modality": "interference",
                    "status": "released"
                },
                {
                    "@id": "/degron-modifications/2e8d10cc-fc98-44d5-a7d9-e2892e16c98a/",
                    "modality": "degradation",
                    "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 A for 0-10% expression of FAM3C) modified with CRISPRi Sp-dCas9-KOX1-KRAB, inactive AID system targeting RAD21, transfected with a guide library",
            "taxa": "Homo sapiens"
        }
    ],
    "schema_version": "12",
    "status": "released",
    "submitted_by": {
        "@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
        "title": "Chongyon Park"
    },
    "submitted_files_timestamp": "2024-06-01T01:50:49.609086+00:00",
    "summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "e895b5f3-32d2-4196-a1d8-b75cbedf24e1"
}