IGVFDS3199FLOT

released
{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS3199FLOT/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS3199FLOT",
    "aliases": [
        "jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF1-BinA-PCR1_S1",
        "jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF1-BinA-PCR2_S7",
        "jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF1-BinA-PCR3_S97",
        "jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF1-BinA-PCR4_S103"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS3199FLOT](/auxiliary-sets/IGVFDS3199FLOT/) has sequence file(s) [IGVFFI9053ATLK](/sequence-files/IGVFFI9053ATLK/), [IGVFFI3274GRZY](/sequence-files/IGVFFI3274GRZY/), [IGVFFI2171OGJO](/sequence-files/IGVFFI2171OGJO/), [IGVFFI9605MXIW](/sequence-files/IGVFFI9605MXIW/) 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/IGVFDS3199FLOT/"
            }
        ]
    },
    "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": "2024-05-16T17:41:00.833329+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/IGVFFI9053ATLK/",
            "accession": "IGVFFI9053ATLK",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF1-BinA-PCR1_S1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T02:10:11.339608+00:00",
            "file_format": "fastq",
            "file_size": 10662322,
            "href": "/sequence-files/IGVFFI9053ATLK/@@download/IGVFFI9053ATLK.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/2ffb14a1-4976-4f07-9d8b-2b1ac7da8848/IGVFFI9053ATLK.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF1-BinA-PCR1_S1_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI8642JEKZ/",
            "accession": "IGVFFI8642JEKZ",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF1-BinA-PCR1_S1"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T22:05:27.129924+00:00",
            "file_format": "yaml",
            "file_size": 900,
            "href": "/configuration-files/IGVFFI8642JEKZ/@@download/IGVFFI8642JEKZ.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/b49bc8c0-8ece-45ad-866c-a87b53780364/IGVFFI8642JEKZ.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF1-BinA-PCR1_S1.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3274GRZY/",
            "accession": "IGVFFI3274GRZY",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF1-BinA-PCR4_S103"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T02:11:10.226683+00:00",
            "file_format": "fastq",
            "file_size": 20053603,
            "href": "/sequence-files/IGVFFI3274GRZY/@@download/IGVFFI3274GRZY.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/90ae2cb4-44ec-473d-8e7f-d041642ab65c/IGVFFI3274GRZY.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF1-BinA-PCR4_S103_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI2171OGJO/",
            "accession": "IGVFFI2171OGJO",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF1-BinA-PCR2_S7"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T02:10:30.356025+00:00",
            "file_format": "fastq",
            "file_size": 8424943,
            "href": "/sequence-files/IGVFFI2171OGJO/@@download/IGVFFI2171OGJO.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/8c93e09f-6315-48be-a9a5-760c1ee09024/IGVFFI2171OGJO.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF1-BinA-PCR2_S7_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI8677QAFW/",
            "accession": "IGVFFI8677QAFW",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF1-BinA-PCR3_S97"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T22:06:08.193076+00:00",
            "file_format": "yaml",
            "file_size": 902,
            "href": "/configuration-files/IGVFFI8677QAFW/@@download/IGVFFI8677QAFW.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/f559802a-e29a-4055-8dd7-57e4bd29b6ed/IGVFFI8677QAFW.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF1-BinA-PCR3_S97.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI4323OUFB/",
            "accession": "IGVFFI4323OUFB",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF1-BinA-PCR4_S103"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T22:06:21.523457+00:00",
            "file_format": "yaml",
            "file_size": 904,
            "href": "/configuration-files/IGVFFI4323OUFB/@@download/IGVFFI4323OUFB.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/bdf95efb-ed69-4006-979c-4866ade46c1f/IGVFFI4323OUFB.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF1-BinA-PCR4_S103.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9605MXIW/",
            "accession": "IGVFFI9605MXIW",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF1-BinA-PCR3_S97"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T02:10:52.072437+00:00",
            "file_format": "fastq",
            "file_size": 36290095,
            "href": "/sequence-files/IGVFFI9605MXIW/@@download/IGVFFI9605MXIW.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/03ddcdcd-6ff3-4326-953b-d55ac9f7d0dc/IGVFFI9605MXIW.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF1-BinA-PCR3_S97_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI8363ADQK/",
            "accession": "IGVFFI8363ADQK",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF1-BinA-PCR2_S7"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T22:05:54.683371+00:00",
            "file_format": "yaml",
            "file_size": 900,
            "href": "/configuration-files/IGVFFI8363ADQK/@@download/IGVFFI8363ADQK.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/0ea6d0f8-a3c1-40c2-b6c2-10325701ac3f/IGVFFI8363ADQK.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF1-BinA-PCR2_S7.yaml",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS6482AXWW/"
    ],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS9168ZKDC/",
            "accession": "IGVFDS9168ZKDC",
            "aliases": [
                "jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF1-BinA-PCR1_S1",
                "jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF1-BinA-PCR2_S7",
                "jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF1-BinA-PCR3_S97",
                "jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF1-BinA-PCR4_S103"
            ],
            "preferred_assay_title": "CRISPR FlowFISH screen",
            "status": "released"
        }
    ],
    "release_timestamp": "2024-07-10T20:13:31.315752+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM8111MLZW/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM8111MLZW",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF1-BinA-PCR1_S1",
                "jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF1-BinA-PCR2_S7",
                "jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF1-BinA-PCR3_S97",
                "jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF1-BinA-PCR4_S103"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS7846UISG/"
            ],
            "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 KITLG) 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": "2024-06-01T02:10:11.339608+00:00",
    "summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "17e83993-00ef-41b6-af08-0d1828865ffa"
}