IGVFDS6282WCIA

released
{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS6282WCIA/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS6282WCIA",
    "aliases": [
        "jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF2-BinE-PCR1-Rep1_S233",
        "jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF2-BinE-PCR2-Rep1_S239",
        "jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF2-BinE-PCR3-Rep1_S275",
        "jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF2-BinE-PCR4-Rep1_S281"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS6282WCIA](/auxiliary-sets/IGVFDS6282WCIA/) has sequence file(s) [IGVFFI4637QKGZ](/sequence-files/IGVFFI4637QKGZ/), [IGVFFI6534BXXG](/sequence-files/IGVFFI6534BXXG/), [IGVFFI4232HLWS](/sequence-files/IGVFFI4232HLWS/), [IGVFFI2737UPLU](/sequence-files/IGVFFI2737UPLU/) 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/IGVFDS6282WCIA/"
            }
        ]
    },
    "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": "2024-05-13T22:39:16.530545+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/IGVFFI4637QKGZ/",
            "accession": "IGVFFI4637QKGZ",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF2-BinE-PCR1-Rep1_S233"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:37:20.701469+00:00",
            "file_format": "fastq",
            "file_size": 29405205,
            "href": "/sequence-files/IGVFFI4637QKGZ/@@download/IGVFFI4637QKGZ.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/042cff1c-f9c7-401c-974a-da3664b59376/IGVFFI4637QKGZ.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-Auxin0hrs-FF2-BinE-PCR1-Rep1_S233_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI2698LUYO/",
            "accession": "IGVFFI2698LUYO",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF2-BinE-PCR1-Rep1_S233"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:29:05.800223+00:00",
            "file_format": "yaml",
            "file_size": 915,
            "href": "/configuration-files/IGVFFI2698LUYO/@@download/IGVFFI2698LUYO.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/ef796ab8-5ea9-422b-a850-e2c16801d071/IGVFFI2698LUYO.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF2-BinE-PCR1-Rep1_S233.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI6534BXXG/",
            "accession": "IGVFFI6534BXXG",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF2-BinE-PCR2-Rep1_S239"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:37:38.303413+00:00",
            "file_format": "fastq",
            "file_size": 18504941,
            "href": "/sequence-files/IGVFFI6534BXXG/@@download/IGVFFI6534BXXG.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/01fa316e-8746-4183-a0e7-273f62338de0/IGVFFI6534BXXG.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-Auxin0hrs-FF2-BinE-PCR2-Rep1_S239_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI4232HLWS/",
            "accession": "IGVFFI4232HLWS",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF2-BinE-PCR3-Rep1_S275"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:37:55.962582+00:00",
            "file_format": "fastq",
            "file_size": 32150955,
            "href": "/sequence-files/IGVFFI4232HLWS/@@download/IGVFFI4232HLWS.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/27886f37-a435-4b71-aef5-161328022c2f/IGVFFI4232HLWS.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-Auxin0hrs-FF2-BinE-PCR3-Rep1_S275_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI2737UPLU/",
            "accession": "IGVFFI2737UPLU",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF2-BinE-PCR4-Rep1_S281"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:41:54.276520+00:00",
            "file_format": "fastq",
            "file_size": 25032339,
            "href": "/sequence-files/IGVFFI2737UPLU/@@download/IGVFFI2737UPLU.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/57d4bcbf-ea4b-48f6-9150-75785f0cb55c/IGVFFI2737UPLU.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-Auxin0hrs-FF2-BinE-PCR4-Rep1_S281_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI0884PTAR/",
            "accession": "IGVFFI0884PTAR",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF2-BinE-PCR2-Rep1_S239"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:29:19.605413+00:00",
            "file_format": "yaml",
            "file_size": 914,
            "href": "/configuration-files/IGVFFI0884PTAR/@@download/IGVFFI0884PTAR.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/de333ec7-d958-436a-b0d8-0c82fed01d5f/IGVFFI0884PTAR.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF2-BinE-PCR2-Rep1_S239.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI9590CNGN/",
            "accession": "IGVFFI9590CNGN",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF2-BinE-PCR4-Rep1_S281"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:29:47.582235+00:00",
            "file_format": "yaml",
            "file_size": 915,
            "href": "/configuration-files/IGVFFI9590CNGN/@@download/IGVFFI9590CNGN.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/f3398629-3486-42ce-b5b9-de96d7aeb7ee/IGVFFI9590CNGN.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF2-BinE-PCR4-Rep1_S281.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI2548FNWF/",
            "accession": "IGVFFI2548FNWF",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF2-BinE-PCR3-Rep1_S275"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:29:33.621814+00:00",
            "file_format": "yaml",
            "file_size": 914,
            "href": "/configuration-files/IGVFFI2548FNWF/@@download/IGVFFI2548FNWF.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/a6755d98-3357-407d-a32d-4a52f2c931c2/IGVFFI2548FNWF.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF2-BinE-PCR3-Rep1_S275.yaml",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS1569RNPD/"
    ],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS5565SKCZ/",
            "accession": "IGVFDS5565SKCZ",
            "aliases": [
                "jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF2-BinE-PCR1-Rep1_S233",
                "jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF2-BinE-PCR2-Rep1_S239",
                "jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF2-BinE-PCR3-Rep1_S275",
                "jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF2-BinE-PCR4-Rep1_S281"
            ],
            "preferred_assay_title": "CRISPR FlowFISH screen",
            "status": "released"
        }
    ],
    "notes": "The origninal alias jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF2-BinE-PCR4-Rep1_S2817 was changed to jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF2-BinE-PCR4-Rep1_S281",
    "release_timestamp": "2024-07-10T20:08:57.462015+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM0671URTU/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM0671URTU",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF2-BinE-PCR1-Rep1_S233",
                "jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF2-BinE-PCR2-Rep1_S239",
                "jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF2-BinE-PCR3-Rep1_S275",
                "jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF2-BinE-PCR4-Rep1_S281"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS6351FGNG/"
            ],
            "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 E for 80-90% expression of CCND1) 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": "2024-06-01T01:37:20.701469+00:00",
    "summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "79e0557f-59bb-4aa4-84ae-6d33041f3996"
}