IGVFDS5041NPBP

released
{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS5041NPBP/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS5041NPBP",
    "aliases": [
        "jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF4-BinF-PCR1_S42",
        "jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF4-BinF-PCR2_S48",
        "jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF4-BinF-PCR3_S138",
        "jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF4-BinF-PCR4_S144"
    ],
    "assay_term": {
        "@id": "/assay-terms/OBI_0003661/",
        "assay_slims": [
            "CRISPR screens"
        ],
        "status": "released",
        "term_name": "in vitro CRISPR screen using flow cytometry"
    },
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing publication",
                "detail": "In vitro system [IGVFSM1131LTFK](/in-vitro-systems/IGVFSM1131LTFK/) has no `publications`. Released and archived samples are expected to be associated with a publication.",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_sample_missing_publication",
                "path": "/in-vitro-systems/IGVFSM1131LTFK/"
            },
            {
                "category": "missing publication",
                "detail": "Auxiliary set [IGVFDS4590CBRM](/auxiliary-sets/IGVFDS4590CBRM/) has no `publications`. Released and archived file sets are expected to be associated with a publication.",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_file_set_missing_publication",
                "path": "/auxiliary-sets/IGVFDS4590CBRM/"
            },
            {
                "category": "missing publication",
                "detail": "Measurement set [IGVFDS5041NPBP](/measurement-sets/IGVFDS5041NPBP/) has no `publications`. Released and archived file sets are expected to be associated with a publication.",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_file_set_missing_publication",
                "path": "/measurement-sets/IGVFDS5041NPBP/"
            },
            {
                "category": "missing sequencing kit",
                "detail": "Measurement set [IGVFDS5041NPBP](/measurement-sets/IGVFDS5041NPBP/) has sequence file(s) [IGVFFI7703FLHW](/sequence-files/IGVFFI7703FLHW/), [IGVFFI1945MHRX](/sequence-files/IGVFFI1945MHRX/), [IGVFFI2786CBJE](/sequence-files/IGVFFI2786CBJE/), [IGVFFI6557KAII](/sequence-files/IGVFFI6557KAII/) which lack specification of a `sequencing_kit`. Sequence files in a file set associated wtih bulk data should specify a sequencing kit.",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_inconsistent_sequencing_kit",
                "path": "/measurement-sets/IGVFDS5041NPBP/"
            }
        ],
        "WARNING": [
            {
                "category": "missing nucleic acid delivery",
                "detail": "In vitro system [IGVFSM1131LTFK](/in-vitro-systems/IGVFSM1131LTFK/) has `construct_library_sets` but is missing `nucleic_acid_delivery`. Samples linked to construct library sets are expected to specify nucleic acid delivery method.",
                "level": 40,
                "level_name": "WARNING",
                "name": "audit_missing_nucleic_acid_delivery",
                "path": "/in-vitro-systems/IGVFSM1131LTFK/"
            }
        ]
    },
    "auxiliary_sets": [
        {
            "@id": "/auxiliary-sets/IGVFDS4590CBRM/",
            "accession": "IGVFDS4590CBRM",
            "aliases": [
                "jesse-engreitz:auxiliary_sortparams_CRUDO_KITLG-Auxin0hrs-FF4"
            ],
            "file_set_type": "cell sorting",
            "status": "released"
        }
    ],
    "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"
    },
    "construct_library_sets": [
        {
            "@id": "/construct-library-sets/IGVFDS7846UISG/",
            "accession": "IGVFDS7846UISG",
            "file_set_type": "guide library",
            "integrated_content_files": [
                {
                    "@id": "/tabular-files/IGVFFI5995VHKI/",
                    "accession": "IGVFFI5995VHKI",
                    "content_type": "guide RNA sequences",
                    "status": "released",
                    "summary": "guide RNA sequences"
                }
            ],
            "status": "released",
            "summary": "guide (sgRNA) library targeting accessible genome regions in many genomic loci"
        }
    ],
    "control_for": [],
    "creation_timestamp": "2024-05-16T17:33:47.521629+00:00",
    "documents": [
        "/documents/74d53b9c-ab1d-42e3-b679-d3a00ae3d842/"
    ],
    "donors": [
        {
            "@id": "/human-donors/IGVFDO0384OZRW/",
            "accession": "IGVFDO0384OZRW",
            "aliases": [
                "igvf:donor_of_HCT116"
            ],
            "sex": "male",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "externally_hosted": false,
    "file_set_type": "experimental data",
    "files": [
        {
            "@id": "/configuration-files/IGVFFI2418FKKK/",
            "accession": "IGVFFI2418FKKK",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF4-BinF-PCR3_S138"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T22:09:01.513661+00:00",
            "file_format": "yaml",
            "file_size": 904,
            "href": "/configuration-files/IGVFFI2418FKKK/@@download/IGVFFI2418FKKK.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/f3b0be57-c5c1-42fc-8b1a-fb7dd7873c43/IGVFFI2418FKKK.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF4-BinF-PCR3_S138.yaml",
            "upload_status": "validation exempted"
        },
        {
            "@id": "/configuration-files/IGVFFI9623WQKP/",
            "accession": "IGVFFI9623WQKP",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF4-BinF-PCR4_S144"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T22:09:16.017288+00:00",
            "file_format": "yaml",
            "file_size": 903,
            "href": "/configuration-files/IGVFFI9623WQKP/@@download/IGVFFI9623WQKP.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/804a8ae9-8b35-4316-a599-a34eb8d75769/IGVFFI9623WQKP.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF4-BinF-PCR4_S144.yaml",
            "upload_status": "validation exempted"
        },
        {
            "@id": "/configuration-files/IGVFFI7142EQVW/",
            "accession": "IGVFFI7142EQVW",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF4-BinF-PCR2_S48"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T22:08:47.140772+00:00",
            "file_format": "yaml",
            "file_size": 901,
            "href": "/configuration-files/IGVFFI7142EQVW/@@download/IGVFFI7142EQVW.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/f251631a-e414-4884-b565-efce814984ea/IGVFFI7142EQVW.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF4-BinF-PCR2_S48.yaml",
            "upload_status": "validation exempted"
        },
        {
            "@id": "/configuration-files/IGVFFI9051FMRX/",
            "accession": "IGVFFI9051FMRX",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF4-BinF-PCR1_S42"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T22:08:33.163423+00:00",
            "file_format": "yaml",
            "file_size": 901,
            "href": "/configuration-files/IGVFFI9051FMRX/@@download/IGVFFI9051FMRX.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/44c59408-f2b7-46d0-a859-f6f157057539/IGVFFI9051FMRX.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF4-BinF-PCR1_S42.yaml",
            "upload_status": "validation exempted"
        },
        {
            "@id": "/sequence-files/IGVFFI7703FLHW/",
            "accession": "IGVFFI7703FLHW",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF4-BinF-PCR4_S144"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T02:19:53.630489+00:00",
            "file_format": "fastq",
            "file_size": 19854914,
            "href": "/sequence-files/IGVFFI7703FLHW/@@download/IGVFFI7703FLHW.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/1c3645f2-ac1c-4777-90c1-add3dbc2ff25/IGVFFI7703FLHW.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0008565/",
                "status": "released",
                "term_name": "Illumina HiSeq 2500"
            },
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF4-BinF-PCR4_S144_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI1945MHRX/",
            "accession": "IGVFFI1945MHRX",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF4-BinF-PCR3_S138"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T02:19:33.505336+00:00",
            "file_format": "fastq",
            "file_size": 28520131,
            "href": "/sequence-files/IGVFFI1945MHRX/@@download/IGVFFI1945MHRX.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/b3e464d5-026c-4e10-943d-cdd3b5c91b77/IGVFFI1945MHRX.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0008565/",
                "status": "released",
                "term_name": "Illumina HiSeq 2500"
            },
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF4-BinF-PCR3_S138_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI2786CBJE/",
            "accession": "IGVFFI2786CBJE",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF4-BinF-PCR2_S48"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T02:19:15.191152+00:00",
            "file_format": "fastq",
            "file_size": 10504766,
            "href": "/sequence-files/IGVFFI2786CBJE/@@download/IGVFFI2786CBJE.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/90653a57-9bcd-4c7e-afcc-97c7c2f63d90/IGVFFI2786CBJE.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0008565/",
                "status": "released",
                "term_name": "Illumina HiSeq 2500"
            },
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF4-BinF-PCR2_S48_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI6557KAII/",
            "accession": "IGVFFI6557KAII",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF4-BinF-PCR1_S42"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T02:18:56.081838+00:00",
            "file_format": "fastq",
            "file_size": 9120671,
            "href": "/sequence-files/IGVFFI6557KAII/@@download/IGVFFI6557KAII.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/137220dd-40c7-46b8-bcf2-c0d0629d3877/IGVFFI6557KAII.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0008565/",
                "status": "released",
                "term_name": "Illumina HiSeq 2500"
            },
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF4-BinF-PCR1_S42_R1_001.fastq.gz",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS6482AXWW/"
    ],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "notes": "The readout 2e41e624-f6c7-4f0c-a07e-bc36cefdca39 was removed from this measurement set.",
    "preferred_assay_title": "CRISPR FlowFISH screen",
    "protocols": [
        "https://www.protocols.io/view/crispri-of-regulatory-elements-upon-degron-operati-5jyl82d59l2w/v1"
    ],
    "release_timestamp": "2024-07-10T19:43:59.522004+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM1131LTFK/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM1131LTFK",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF4-BinF-PCR1_S42",
                "jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF4-BinF-PCR2_S48",
                "jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF4-BinF-PCR3_S138",
                "jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF4-BinF-PCR4_S144"
            ],
            "classifications": [
                "cell line"
            ],
            "institutional_certificates": [],
            "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": "Homo sapiens (male) HCT116 cell line (sorting details: FACS bin F for 80-100% 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": "26",
    "status": "released",
    "submitted_by": {
        "@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
        "title": "Chongyon Park"
    },
    "submitted_files_timestamp": "2024-06-01T02:18:56.081838+00:00",
    "summary": "mixed CRISPR FlowFISH screen sorted on the expression of KITLG integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "targeted_genes": [
        {
            "@id": "/genes/ENSG00000049130/",
            "geneid": "ENSG00000049130",
            "name": "KIT ligand",
            "status": "released",
            "symbol": "KITLG",
            "synonyms": [
                "SF",
                "WS2F",
                "Kitl",
                "FPH2",
                "SCF",
                "KL-1",
                "DFNA69",
                "familial progressive hyperpigmentation 2",
                "mast cell growth factor",
                "DCUA",
                "kit ligand",
                "c-Kit ligand",
                "SLF",
                "steel factor",
                "KITLG",
                "SHEP7",
                "stem cell factor",
                "KIT ligand",
                "FPHH",
                "MGF"
            ]
        }
    ],
    "uuid": "fe1a8271-fd7e-454e-ae2c-187f1d46d77d"
}