IGVFDS6870QBVM

released
{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS6870QBVM/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS6870QBVM",
    "aliases": [
        "jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF2-BinC-PCR1-Rep1_S15",
        "jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF2-BinC-PCR2-Rep1_S21",
        "jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF2-BinC-PCR3-Rep1_S69",
        "jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF2-BinC-PCR4-Rep1_S75"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS6870QBVM](/auxiliary-sets/IGVFDS6870QBVM/) has sequence file(s) [IGVFFI3952UPLD](/sequence-files/IGVFFI3952UPLD/), [IGVFFI5250HUCB](/sequence-files/IGVFFI5250HUCB/), [IGVFFI3227NNAQ](/sequence-files/IGVFFI3227NNAQ/), [IGVFFI8622TDNM](/sequence-files/IGVFFI8622TDNM/) 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/IGVFDS6870QBVM/"
            }
        ]
    },
    "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": "2024-05-14T20:31:20.203361+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/IGVFFI3952UPLD/",
            "accession": "IGVFFI3952UPLD",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF2-BinC-PCR1-Rep1_S15"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:45:53.847312+00:00",
            "file_format": "fastq",
            "file_size": 10849000,
            "href": "/sequence-files/IGVFFI3952UPLD/@@download/IGVFFI3952UPLD.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/dbad0f22-1fd8-4b58-b661-6ffecce5e1de/IGVFFI3952UPLD.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-FF2-BinC-PCR1-Rep1_S15_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI7304ZIDV/",
            "accession": "IGVFFI7304ZIDV",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF2-BinC-PCR1-Rep1_S15"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:38:22.733909+00:00",
            "file_format": "yaml",
            "file_size": 913,
            "href": "/configuration-files/IGVFFI7304ZIDV/@@download/IGVFFI7304ZIDV.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/45dafe10-cc14-47ba-be08-9df070501866/IGVFFI7304ZIDV.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF2-BinC-PCR1-Rep1_S15.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI5250HUCB/",
            "accession": "IGVFFI5250HUCB",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF2-BinC-PCR2-Rep1_S21"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:46:15.727706+00:00",
            "file_format": "fastq",
            "file_size": 15820281,
            "href": "/sequence-files/IGVFFI5250HUCB/@@download/IGVFFI5250HUCB.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/2f41b100-9878-4c19-9a4d-eec07d690cb1/IGVFFI5250HUCB.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-FF2-BinC-PCR2-Rep1_S21_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3227NNAQ/",
            "accession": "IGVFFI3227NNAQ",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF2-BinC-PCR3-Rep1_S69"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:46:34.986333+00:00",
            "file_format": "fastq",
            "file_size": 20511350,
            "href": "/sequence-files/IGVFFI3227NNAQ/@@download/IGVFFI3227NNAQ.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/8037516d-443c-4325-a655-3ce9d33cbfee/IGVFFI3227NNAQ.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-FF2-BinC-PCR3-Rep1_S69_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8622TDNM/",
            "accession": "IGVFFI8622TDNM",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF2-BinC-PCR4-Rep1_S75"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:46:52.829493+00:00",
            "file_format": "fastq",
            "file_size": 18707865,
            "href": "/sequence-files/IGVFFI8622TDNM/@@download/IGVFFI8622TDNM.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/f7e7249d-8f13-4cd1-80b6-6a173dc1cdf8/IGVFFI8622TDNM.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-FF2-BinC-PCR4-Rep1_S75_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI9956XLRB/",
            "accession": "IGVFFI9956XLRB",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF2-BinC-PCR2-Rep1_S21"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:38:38.329827+00:00",
            "file_format": "yaml",
            "file_size": 912,
            "href": "/configuration-files/IGVFFI9956XLRB/@@download/IGVFFI9956XLRB.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/a49fe185-b57b-479b-ac0e-20c207debad4/IGVFFI9956XLRB.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF2-BinC-PCR2-Rep1_S21.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI2564WQBV/",
            "accession": "IGVFFI2564WQBV",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF2-BinC-PCR3-Rep1_S69"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:39:16.887824+00:00",
            "file_format": "yaml",
            "file_size": 912,
            "href": "/configuration-files/IGVFFI2564WQBV/@@download/IGVFFI2564WQBV.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/ac60fe2b-9bef-492f-999f-ceeb4e6e4828/IGVFFI2564WQBV.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF2-BinC-PCR3-Rep1_S69.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI2975BGQX/",
            "accession": "IGVFFI2975BGQX",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF2-BinC-PCR4-Rep1_S75"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:39:32.374733+00:00",
            "file_format": "yaml",
            "file_size": 913,
            "href": "/configuration-files/IGVFFI2975BGQX/@@download/IGVFFI2975BGQX.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/ee30c74a-1e96-4a58-a8ed-4c66c2be8ca8/IGVFFI2975BGQX.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF2-BinC-PCR4-Rep1_S75.yaml",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS2031CTSP/"
    ],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS6103MEVT/",
            "accession": "IGVFDS6103MEVT",
            "aliases": [
                "jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF2-BinC-PCR1-Rep1_S15",
                "jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF2-BinC-PCR2-Rep1_S21",
                "jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF2-BinC-PCR3-Rep1_S69",
                "jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF2-BinC-PCR4-Rep1_S75"
            ],
            "preferred_assay_title": "CRISPR FlowFISH screen",
            "status": "released"
        }
    ],
    "release_timestamp": "2024-07-10T20:24:40.367999+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM8438GPDC/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM8438GPDC",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF2-BinC-PCR1-Rep1_S15",
                "jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF2-BinC-PCR2-Rep1_S21",
                "jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF2-BinC-PCR3-Rep1_S69",
                "jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF2-BinC-PCR4-Rep1_S75"
            ],
            "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 C for 35-45% 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": "2024-06-01T01:45:53.847312+00:00",
    "summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "0a89a59c-95d7-4ccf-a75d-9afb1d89d739"
}