IGVFDS4475OZFW

released
{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS4475OZFW/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS4475OZFW",
    "aliases": [
        "jesse-engreitz:measurement_NOS3_CRISPRi_FF_R1_FFrep1_binA_PCR1_S113"
    ],
    "assay_term": {
        "@id": "/assay-terms/OBI_0003661/",
        "status": "released",
        "term_name": "in vitro CRISPR screen using flow cytometry"
    },
    "audit": {
        "ERROR": [
            {
                "category": "missing auxiliary set",
                "detail": "Measurement set [IGVFDS4475OZFW](/measurement-sets/IGVFDS4475OZFW/) links to sample [IGVFSM6792NCMN](/in-vitro-systems/IGVFSM6792NCMN/) which links to auxiliary set [IGVFDS1319ZTHG](/auxiliary-sets/IGVFDS1319ZTHG/) but is not in its `auxiliary_sets`. Measurement sets are expected to link to auxiliary sets if they share the same sample.",
                "level": 60,
                "level_name": "ERROR",
                "name": "audit_missing_auxiliary_set_link",
                "path": "/measurement-sets/IGVFDS4475OZFW/"
            }
        ],
        "INTERNAL_ACTION": [
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS4475OZFW](/measurement-sets/IGVFDS4475OZFW/) has sequence file(s): [IGVFFI7594DBPI](/sequence-files/IGVFFI7594DBPI/), [IGVFFI7155AWTQ](/sequence-files/IGVFFI7155AWTQ/), [IGVFFI3363IMCX](/sequence-files/IGVFFI3363IMCX/) which do not have any `seqspecs`. Sequence files in a file set associated with bulk data are expected to link to a sequence specification file.",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_missing_seqspec",
                "path": "/measurement-sets/IGVFDS4475OZFW/"
            },
            {
                "category": "NTR term ID",
                "detail": "Sample term for [NTR_0000753](/sample-terms/NTR_0000753/) has been newly requested. Ontology terms with a newly requested term ID are expected to have it updated following its addition to the appropriate ontology database.",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_ntr_term_id",
                "path": "/sample-terms/NTR_0000753/"
            }
        ],
        "WARNING": [
            {
                "category": "missing analysis",
                "detail": "Measurement set [IGVFDS4475OZFW](/measurement-sets/IGVFDS4475OZFW/) is a raw data set with files, but is not listed in any `input_file_sets` for any analysis sets. Raw data sets with files are expected to be associated with at least one analysis set.",
                "level": 40,
                "level_name": "WARNING",
                "name": "audit_input_for",
                "path": "/measurement-sets/IGVFDS4475OZFW/"
            },
            {
                "category": "missing auxiliary set",
                "detail": "Measurement set [IGVFDS4475OZFW](/measurement-sets/IGVFDS4475OZFW/) has no cell sorting `auxiliary_sets`. CRISPR-based measurement sets that utilize flow cytometry are expected to link to a cell sorting auxiliary set.",
                "level": 40,
                "level_name": "WARNING",
                "name": "audit_missing_auxiliary_set",
                "path": "/measurement-sets/IGVFDS4475OZFW/"
            },
            {
                "category": "missing nucleic acid delivery",
                "detail": "In vitro system [IGVFSM6792NCMN](/in-vitro-systems/IGVFSM6792NCMN/) 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/IGVFSM6792NCMN/"
            }
        ]
    },
    "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/IGVFDS8953DFJK/",
            "accession": "IGVFDS8953DFJK",
            "file_set_type": "guide library",
            "integrated_content_files": [
                {
                    "@id": "/tabular-files/IGVFFI5833LNWN/",
                    "accession": "IGVFFI5833LNWN",
                    "content_type": "guide RNA sequences",
                    "status": "released",
                    "summary": "GRCh38 guide RNA sequences"
                }
            ],
            "status": "released",
            "summary": "guide (sgRNA) library targeting sequence variants, transcription start sites in NOS3"
        }
    ],
    "control_for": [],
    "creation_timestamp": "2024-04-16T14:54:00.576893+00:00",
    "documents": [
        "/documents/1d492aa4-f111-4220-aeaa-f43a3cbda78b/"
    ],
    "donors": [
        {
            "@id": "/human-donors/IGVFDO3459DFTW/",
            "accession": "IGVFDO3459DFTW",
            "aliases": [
                "igvf:donor_of_teloHAEC"
            ],
            "sex": "female",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "externally_hosted": false,
    "file_set_type": "experimental data",
    "files": [
        {
            "@id": "/sequence-files/IGVFFI7594DBPI/",
            "accession": "IGVFFI7594DBPI",
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-04-16T21:42:46.308185+00:00",
            "file_format": "fastq",
            "file_size": 42443774,
            "href": "/sequence-files/IGVFFI7594DBPI/@@download/IGVFFI7594DBPI.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/04/16/0b881d0b-48c6-4b53-b88f-d894229a7616/IGVFFI7594DBPI.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0004205/",
                "status": "released",
                "term_name": "Illumina MiSeq"
            },
            "status": "released",
            "submitted_file_name": "/Desktop/NOS3/NOS3_CRISPRi_FlowFISH/231215S023-TeloHAEC-P219-Amp_NOS3-BioRep1-FFrep1-BinA-PCRrep1_S113_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI7155AWTQ/",
            "accession": "IGVFFI7155AWTQ",
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-04-16T21:42:44.457483+00:00",
            "file_format": "fastq",
            "file_size": 15049413,
            "href": "/sequence-files/IGVFFI7155AWTQ/@@download/IGVFFI7155AWTQ.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/04/16/331d2a32-356e-4e44-8b86-8af840422f8b/IGVFFI7155AWTQ.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0004205/",
                "status": "released",
                "term_name": "Illumina MiSeq"
            },
            "status": "released",
            "submitted_file_name": "/Desktop/NOS3/NOS3_CRISPRi_FlowFISH/231215S023-TeloHAEC-P219-Amp_NOS3-BioRep1-FFrep1-BinA-PCRrep1_S113_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3363IMCX/",
            "accession": "IGVFFI3363IMCX",
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-04-16T21:42:42.736353+00:00",
            "file_format": "fastq",
            "file_size": 15695081,
            "href": "/sequence-files/IGVFFI3363IMCX/@@download/IGVFFI3363IMCX.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/04/16/961cfd67-4b56-4b9e-82a0-085752e6a47e/IGVFFI3363IMCX.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0004205/",
                "status": "released",
                "term_name": "Illumina MiSeq"
            },
            "status": "released",
            "submitted_file_name": "/Desktop/NOS3/NOS3_CRISPRi_FlowFISH/231215S023-TeloHAEC-P219-Amp_NOS3-BioRep1-FFrep1-BinA-PCRrep1_S113_I1_001.fastq.gz",
            "upload_status": "validated"
        }
    ],
    "input_for": [],
    "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/flowfish-with-primeflow-36wgq3q4olk5/v1"
    ],
    "release_timestamp": "2024-06-22T00:20:33.282857+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM6792NCMN/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM6792NCMN",
            "aliases": [
                "jesse-engreitz:in-vitro-system_NOS3_CRISPRi_FF_R1_FFrep1_binA_PCR1_S113"
            ],
            "classifications": [
                "cell line"
            ],
            "modifications": [
                {
                    "@id": "/crispr-modifications/b4bc725a-8eeb-4180-9789-bece3516c0c1/",
                    "modality": "interference",
                    "status": "released"
                }
            ],
            "sample_terms": [
                {
                    "@id": "/sample-terms/NTR_0000753/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
                        "Item"
                    ],
                    "aliases": [
                        "igvf:TeloHAEC"
                    ],
                    "status": "released",
                    "summary": "TeloHAEC",
                    "term_name": "TeloHAEC"
                }
            ],
            "status": "released",
            "summary": "TeloHAEC cell line, female, Homo sapiens (sorting details: FACS bin A for 0-25% expression of NOS3) modified with CRISPRi Sp-dCas9-KOX1-KRAB, transfected with a guide library",
            "taxa": "Homo sapiens"
        }
    ],
    "schema_version": "23",
    "status": "released",
    "submitted_by": {
        "@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
        "title": "Chongyon Park"
    },
    "submitted_files_timestamp": "2024-04-16T21:42:42.736353+00:00",
    "summary": "CRISPR interference FlowFISH screen sorted on the expression of NOS3 integrating a guide (sgRNA) library targeting sequence variants, transcription start sites in NOS3",
    "targeted_genes": [
        {
            "@id": "/genes/ENSG00000164867/",
            "geneid": "ENSG00000164867",
            "name": "nitric oxide synthase 3",
            "status": "released",
            "symbol": "NOS3",
            "synonyms": [
                "cNOS",
                "constitutive NOS",
                "EC-NOS",
                "nitric oxide synthase, endothelial",
                "eNOS",
                "ECNOS",
                "NOS type III",
                "NOSIII",
                "nitric oxide synthase 3 (endothelial cell)",
                "endothelial NOS"
            ]
        }
    ],
    "uuid": "0bcf33de-f171-4a37-8626-0ed26cac65fd"
}