IGVFDS1369IMLU

released
{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS1369IMLU/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS1369IMLU",
    "aliases": [
        "jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR1-Rep1_S6",
        "jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR2-Rep1_S12",
        "jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR3-Rep1_S60",
        "jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR4-Rep1_S66"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS1369IMLU](/auxiliary-sets/IGVFDS1369IMLU/) has sequence file(s) [IGVFFI1019WGYS](/sequence-files/IGVFFI1019WGYS/), [IGVFFI8263MWWS](/sequence-files/IGVFFI8263MWWS/), [IGVFFI3575WNTZ](/sequence-files/IGVFFI3575WNTZ/), [IGVFFI9696NSTM](/sequence-files/IGVFFI9696NSTM/) 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/IGVFDS1369IMLU/"
            }
        ]
    },
    "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": "2024-05-14T20:30:56.982423+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/IGVFFI1019WGYS/",
            "accession": "IGVFFI1019WGYS",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR1-Rep1_S6"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:44:50.372423+00:00",
            "file_format": "fastq",
            "file_size": 29169256,
            "href": "/sequence-files/IGVFFI1019WGYS/@@download/IGVFFI1019WGYS.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/6a0ef93b-d83f-43b4-84e3-f59c08f4fed4/IGVFFI1019WGYS.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/SSFA2-Auxin0hrs-FF1-BinF-PCR1-Rep1_S6_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI5738MQSZ/",
            "accession": "IGVFFI5738MQSZ",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR1-Rep1_S6"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:37:29.158263+00:00",
            "file_format": "yaml",
            "file_size": 912,
            "href": "/configuration-files/IGVFFI5738MQSZ/@@download/IGVFFI5738MQSZ.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/f7f901d8-d2e9-42c6-82d0-51f2cce9a8b0/IGVFFI5738MQSZ.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF1-BinF-PCR1-Rep1_S6.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8263MWWS/",
            "accession": "IGVFFI8263MWWS",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR2-Rep1_S12"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:45:09.229837+00:00",
            "file_format": "fastq",
            "file_size": 35207176,
            "href": "/sequence-files/IGVFFI8263MWWS/@@download/IGVFFI8263MWWS.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/bd0e67cf-a11f-413e-8b04-c75912dd7f59/IGVFFI8263MWWS.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/SSFA2-Auxin0hrs-FF1-BinF-PCR2-Rep1_S12_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3575WNTZ/",
            "accession": "IGVFFI3575WNTZ",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR3-Rep1_S60"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:45:26.802479+00:00",
            "file_format": "fastq",
            "file_size": 27117255,
            "href": "/sequence-files/IGVFFI3575WNTZ/@@download/IGVFFI3575WNTZ.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/3aeb7dac-ca1b-42a4-9d93-933052b2d191/IGVFFI3575WNTZ.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/SSFA2-Auxin0hrs-FF1-BinF-PCR3-Rep1_S60_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9696NSTM/",
            "accession": "IGVFFI9696NSTM",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR4-Rep1_S66"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:45:44.683382+00:00",
            "file_format": "fastq",
            "file_size": 24887465,
            "href": "/sequence-files/IGVFFI9696NSTM/@@download/IGVFFI9696NSTM.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/e87543cb-09a8-41be-9333-8f0db40080d6/IGVFFI9696NSTM.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/SSFA2-Auxin0hrs-FF1-BinF-PCR4-Rep1_S66_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI8013LHCK/",
            "accession": "IGVFFI8013LHCK",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR3-Rep1_S60"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:37:59.510511+00:00",
            "file_format": "yaml",
            "file_size": 914,
            "href": "/configuration-files/IGVFFI8013LHCK/@@download/IGVFFI8013LHCK.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/3dcfa6d0-8d12-4599-ad28-bd5a6a274728/IGVFFI8013LHCK.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF1-BinF-PCR3-Rep1_S60.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI3817IEYP/",
            "accession": "IGVFFI3817IEYP",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR4-Rep1_S66"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:38:15.142296+00:00",
            "file_format": "yaml",
            "file_size": 912,
            "href": "/configuration-files/IGVFFI3817IEYP/@@download/IGVFFI3817IEYP.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/00f9a3e6-6de5-4623-a80e-7ececd0a32cc/IGVFFI3817IEYP.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF1-BinF-PCR4-Rep1_S66.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI5161XQVK/",
            "accession": "IGVFFI5161XQVK",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR2-Rep1_S12"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:37:44.068688+00:00",
            "file_format": "yaml",
            "file_size": 913,
            "href": "/configuration-files/IGVFFI5161XQVK/@@download/IGVFFI5161XQVK.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/62ede40d-3c8a-440b-a003-7570bfc03728/IGVFFI5161XQVK.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF1-BinF-PCR2-Rep1_S12.yaml",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS2031CTSP/"
    ],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS0674KOZU/",
            "accession": "IGVFDS0674KOZU",
            "aliases": [
                "jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR1-Rep1_S6",
                "jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR2-Rep1_S12",
                "jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR3-Rep1_S60",
                "jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR4-Rep1_S66"
            ],
            "preferred_assay_title": "CRISPR FlowFISH screen",
            "status": "released"
        }
    ],
    "release_timestamp": "2024-07-10T20:24:18.378086+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM4326ZGNE/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM4326ZGNE",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR1-Rep1_S6",
                "jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR2-Rep1_S12",
                "jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR3-Rep1_S60",
                "jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR4-Rep1_S66"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS5413RKIA/"
            ],
            "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 F for 80-100% expression of SSFA2) 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": "2024-06-01T01:44:50.372423+00:00",
    "summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "c3dea016-4963-4c35-aaaf-07e383b1418e"
}