IGVFDS3290DKIW

released
{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS3290DKIW/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS3290DKIW",
    "aliases": [
        "jesse-engreitz:auxiliary_NOS3_CRISPRi_FF_R2_FFrep1_binB_PCR2_S210"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS3290DKIW](/auxiliary-sets/IGVFDS3290DKIW/) has sequence file(s): [IGVFFI9106HGMS](/sequence-files/IGVFFI9106HGMS/), [IGVFFI6488VKEZ](/sequence-files/IGVFFI6488VKEZ/), [IGVFFI6431VJUM](/sequence-files/IGVFFI6431VJUM/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_missing_seqspec",
                "path": "/auxiliary-sets/IGVFDS3290DKIW/"
            },
            {
                "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/"
            }
        ]
    },
    "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": "2024-04-15T23:17:21.996949+00:00",
    "donors": [
        {
            "@id": "/human-donors/IGVFDO3459DFTW/",
            "accession": "IGVFDO3459DFTW",
            "aliases": [
                "igvf:donor_of_teloHAEC"
            ],
            "sex": "female",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "file_set_type": "gRNA sequencing",
    "files": [
        {
            "@id": "/sequence-files/IGVFFI9106HGMS/",
            "accession": "IGVFFI9106HGMS",
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-04-16T22:02:07.055120+00:00",
            "file_format": "fastq",
            "file_size": 5515339,
            "href": "/sequence-files/IGVFFI9106HGMS/@@download/IGVFFI9106HGMS.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/04/16/931f10be-e3fd-4ece-83fa-7bf895d4b0f2/IGVFFI9106HGMS.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0004205/",
            "status": "released",
            "submitted_file_name": "/Desktop/NOS3/NOS3_CRISPRi_FlowFISH/231215S023-TeloHAEC-P219-Amp_NOS3-BioRep2-FFrep1-BinB-PCRrep2_S210_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI6488VKEZ/",
            "accession": "IGVFFI6488VKEZ",
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-04-16T22:02:05.801280+00:00",
            "file_format": "fastq",
            "file_size": 5722815,
            "href": "/sequence-files/IGVFFI6488VKEZ/@@download/IGVFFI6488VKEZ.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/04/16/43b2c126-ab9b-43fc-b84d-d0eb8b7dfb7f/IGVFFI6488VKEZ.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0004205/",
            "status": "released",
            "submitted_file_name": "/Desktop/NOS3/NOS3_CRISPRi_FlowFISH/231215S023-TeloHAEC-P219-Amp_NOS3-BioRep2-FFrep1-BinB-PCRrep2_S210_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI6431VJUM/",
            "accession": "IGVFFI6431VJUM",
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-04-16T22:02:08.605977+00:00",
            "file_format": "fastq",
            "file_size": 15641943,
            "href": "/sequence-files/IGVFFI6431VJUM/@@download/IGVFFI6431VJUM.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/04/16/d5d07b3d-57e5-4a24-9f0e-4c97e7cf1f4e/IGVFFI6431VJUM.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0004205/",
            "status": "released",
            "submitted_file_name": "/Desktop/NOS3/NOS3_CRISPRi_FlowFISH/231215S023-TeloHAEC-P219-Amp_NOS3-BioRep2-FFrep1-BinB-PCRrep2_S210_R1_001.fastq.gz",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS7917YHKA/"
    ],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS0207ETLT/",
            "accession": "IGVFDS0207ETLT",
            "aliases": [
                "jesse-engreitz:measurement_NOS3_CRISPRi_FF_R2_FFrep1_binB_PCR2_S210"
            ],
            "preferred_assay_title": "CRISPR FlowFISH screen",
            "status": "released"
        }
    ],
    "release_timestamp": "2024-06-22T00:26:50.187586+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM0912IPPR/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM0912IPPR",
            "aliases": [
                "jesse-engreitz:in-vitro-system_NOS3_CRISPRi_FF_R2_FFrep1_binB_PCR2_S210"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS8953DFJK/"
            ],
            "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 B for 26-50% expression of NOS3) modified with CRISPRi Sp-dCas9-KOX1-KRAB, 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": "2024-04-16T22:02:05.801280+00:00",
    "summary": "gRNA sequencing for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting sequence variants, transcription start sites in NOS3",
    "uuid": "73936f54-ae0d-450d-a4e8-aec20e346a39"
}