IGVFDS2192NCTH

released
{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS2192NCTH/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS2192NCTH",
    "aliases": [
        "jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinD_AmpliconSequencing"
    ],
    "assay_term": {
        "@id": "/assay-terms/OBI_0003133/",
        "term_name": "cas mediated mutagenesis"
    },
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "mismatched status",
                "detail": "Released in vitro system [IGVFSM4221WRQS](/in-vitro-systems/IGVFSM4221WRQS/) has in progress subobject construct library set [IGVFDS6377KNCH](/construct-library-sets/IGVFDS6377KNCH/).",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_item_status",
                "path": "/in-vitro-systems/IGVFSM4221WRQS/"
            }
        ],
        "NOT_COMPLIANT": [
            {
                "category": "missing sequence specification",
                "detail": "File set [IGVFDS2192NCTH](/measurement-sets/IGVFDS2192NCTH/) has sequence file(s): [IGVFFI5305PVWV](/sequence-files/IGVFFI5305PVWV/), [IGVFFI5476FOPQ](/sequence-files/IGVFFI5476FOPQ/), [IGVFFI3349WKOP](/sequence-files/IGVFFI3349WKOP/), [IGVFFI1165AJSO](/sequence-files/IGVFFI1165AJSO/), [IGVFFI6649IDBY](/sequence-files/IGVFFI6649IDBY/), [IGVFFI1854RBAF](/sequence-files/IGVFFI1854RBAF/), [IGVFFI8749BGVD](/sequence-files/IGVFFI8749BGVD/), [IGVFFI2200CONX](/sequence-files/IGVFFI2200CONX/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_missing_seqspec",
                "path": "/measurement-sets/IGVFDS2192NCTH/"
            },
            {
                "category": "missing auxiliary set",
                "detail": "Measurement set [IGVFDS2192NCTH](/measurement-sets/IGVFDS2192NCTH/) is a CRISPR-based assay but has no gRNA sequencing `auxiliary_sets`. Measurement sets from CRISPR-based assays are expected to link to a gRNA sequencing auxiliary set.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_CRISPR_screen_lacking_auxiliary_set",
                "path": "/measurement-sets/IGVFDS2192NCTH/"
            }
        ],
        "WARNING": [
            {
                "category": "missing sequencing kit",
                "detail": "File set [IGVFDS2192NCTH](/measurement-sets/IGVFDS2192NCTH/) has sequence file(s) [IGVFFI5305PVWV](/sequence-files/IGVFFI5305PVWV/), [IGVFFI5476FOPQ](/sequence-files/IGVFFI5476FOPQ/), [IGVFFI3349WKOP](/sequence-files/IGVFFI3349WKOP/), [IGVFFI1165AJSO](/sequence-files/IGVFFI1165AJSO/), [IGVFFI6649IDBY](/sequence-files/IGVFFI6649IDBY/), [IGVFFI1854RBAF](/sequence-files/IGVFFI1854RBAF/), [IGVFFI8749BGVD](/sequence-files/IGVFFI8749BGVD/), [IGVFFI2200CONX](/sequence-files/IGVFFI2200CONX/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
                "level": 40,
                "level_name": "WARNING",
                "name": "audit_inconsistent_sequencing_kit",
                "path": "/measurement-sets/IGVFDS2192NCTH/"
            }
        ]
    },
    "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_file_sets": [
        {
            "@id": "/measurement-sets/IGVFDS9477ARWI/",
            "accession": "IGVFDS9477ARWI",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-Jurkat-PE2_Exp1_NegControl_AmpliconSequencing",
                "jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-Jurkat-PE2_Exp1_NegControl_AmpliconSequencing"
            ]
        }
    ],
    "control_for": [],
    "creation_timestamp": "2023-11-30T22:48:06.065303+00:00",
    "donors": [
        {
            "@id": "/human-donors/IGVFDO1080XFGV/",
            "accession": "IGVFDO1080XFGV",
            "aliases": [
                "igvf:donor_of_Jurkat"
            ],
            "sex": "male",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "file_set_type": "experimental data",
    "files": [
        {
            "@id": "/sequence-files/IGVFFI5305PVWV/",
            "accession": "IGVFFI5305PVWV",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinD-PCRrep1_R1"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-05T19:33:18.204741+00:00",
            "file_format": "fastq",
            "file_size": 7326838,
            "href": "/sequence-files/IGVFFI5305PVWV/@@download/IGVFFI5305PVWV.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/05/891bd198-e987-431e-9e26-4a1ba02a3657/IGVFFI5305PVWV.fastq.gz",
            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S15-BioRep2-FFRep1-BinD-PCRrep1_S130_R1_001.fastq.gz"
        },
        {
            "@id": "/sequence-files/IGVFFI5476FOPQ/",
            "accession": "IGVFFI5476FOPQ",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinD-PCRrep1_R2"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-05T19:41:40.421062+00:00",
            "file_format": "fastq",
            "file_size": 13591326,
            "href": "/sequence-files/IGVFFI5476FOPQ/@@download/IGVFFI5476FOPQ.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/05/d234f289-66d5-4ef3-bc57-5da57cc2363c/IGVFFI5476FOPQ.fastq.gz",
            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S15-BioRep2-FFRep1-BinD-PCRrep1_S130_R2_001.fastq.gz"
        },
        {
            "@id": "/sequence-files/IGVFFI3349WKOP/",
            "accession": "IGVFFI3349WKOP",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinD-PCRrep1_I1"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-05T19:50:10.916878+00:00",
            "file_format": "fastq",
            "file_size": 3094968,
            "href": "/sequence-files/IGVFFI3349WKOP/@@download/IGVFFI3349WKOP.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/05/b2e812d3-8fd0-42fb-b021-caf59f2a94c1/IGVFFI3349WKOP.fastq.gz",
            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S15-BioRep2-FFRep1-BinD-PCRrep1_S130_I1_001.fastq.gz"
        },
        {
            "@id": "/sequence-files/IGVFFI1165AJSO/",
            "accession": "IGVFFI1165AJSO",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinD-PCRrep1_I2"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-05T19:58:18.462157+00:00",
            "file_format": "fastq",
            "file_size": 3060311,
            "href": "/sequence-files/IGVFFI1165AJSO/@@download/IGVFFI1165AJSO.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/05/fffcd64e-af02-4675-8953-7352459ee06a/IGVFFI1165AJSO.fastq.gz",
            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S15-BioRep2-FFRep1-BinD-PCRrep1_S130_I2_001.fastq.gz"
        },
        {
            "@id": "/sequence-files/IGVFFI6649IDBY/",
            "accession": "IGVFFI6649IDBY",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinD-PCRrep2_R1"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-05T20:06:30.353713+00:00",
            "file_format": "fastq",
            "file_size": 7666433,
            "href": "/sequence-files/IGVFFI6649IDBY/@@download/IGVFFI6649IDBY.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/05/fd5b4894-a7fb-4d6c-bb52-d1d60bcab392/IGVFFI6649IDBY.fastq.gz",
            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S15-BioRep2-FFRep1-BinD-PCRrep2_S187_R1_001.fastq.gz"
        },
        {
            "@id": "/sequence-files/IGVFFI1854RBAF/",
            "accession": "IGVFFI1854RBAF",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinD-PCRrep2_R2"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-05T20:14:50.900707+00:00",
            "file_format": "fastq",
            "file_size": 14206284,
            "href": "/sequence-files/IGVFFI1854RBAF/@@download/IGVFFI1854RBAF.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/05/2b17aaec-063c-4139-aea6-61644ff26122/IGVFFI1854RBAF.fastq.gz",
            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S15-BioRep2-FFRep1-BinD-PCRrep2_S187_R2_001.fastq.gz"
        },
        {
            "@id": "/sequence-files/IGVFFI8749BGVD/",
            "accession": "IGVFFI8749BGVD",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinD-PCRrep2_I1"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-05T20:23:15.943875+00:00",
            "file_format": "fastq",
            "file_size": 3216940,
            "href": "/sequence-files/IGVFFI8749BGVD/@@download/IGVFFI8749BGVD.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/05/838ae421-5868-4fad-ac32-18fba713b076/IGVFFI8749BGVD.fastq.gz",
            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S15-BioRep2-FFRep1-BinD-PCRrep2_S187_I1_001.fastq.gz"
        },
        {
            "@id": "/sequence-files/IGVFFI2200CONX/",
            "accession": "IGVFFI2200CONX",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinD-PCRrep2_I2"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-05T20:31:36.353598+00:00",
            "file_format": "fastq",
            "file_size": 3251108,
            "href": "/sequence-files/IGVFFI2200CONX/@@download/IGVFFI2200CONX.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/05/010a78f6-fc3b-4f36-8681-580e578645d8/IGVFFI2200CONX.fastq.gz",
            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S15-BioRep2-FFRep1-BinD-PCRrep2_S187_I2_001.fastq.gz"
        }
    ],
    "input_file_set_for": [
        "/analysis-sets/IGVFDS1863TJOE/"
    ],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "preferred_assay_title": "Variant FlowFISH",
    "protocols": [
        "https://www.protocols.io/view/flowfish-with-primeflow-36wgq3q4olk5/v1"
    ],
    "readout": {
        "@id": "/assay-terms/OBI_0000626/",
        "term_name": "DNA sequencing assay"
    },
    "release_timestamp": "2023-12-20T23:03:48.633132+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM4221WRQS/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM4221WRQS",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinD"
            ],
            "construct_library_sets": [
                {
                    "@id": "/construct-library-sets/IGVFDS6377KNCH/",
                    "accession": "IGVFDS6377KNCH",
                    "summary": "Guide (sgRNA) library targeting sequence variants in a genomic locus"
                }
            ],
            "modifications": [
                {
                    "@id": "/modifications/e8d549e6-cef0-482a-9deb-76d3b7ecaac3/",
                    "modality": "prime editing"
                }
            ],
            "sample_terms": [
                {
                    "@id": "/sample-terms/EFO_0002796/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
                        "Item"
                    ],
                    "aliases": [
                        "igvf:Jurkat"
                    ],
                    "status": "released",
                    "summary": "f0ddc19a-ac2c-46b0-a96e-bfc3cca37151",
                    "term_name": "Jurkat"
                }
            ],
            "status": "released",
            "summary": "Jurkat cell line, male, Homo sapiens (sorting details: FACS bin for 55-65% expression of PPIF) treated with 100 ng/mL phorbol 13-acetate 12-myristate for 4 hours, 5 μg/mL T-cell surface glycoprotein CD3 gamma chain for 4 hours, modified with a guide library",
            "taxa": "Homo sapiens",
            "treatments": [
                {
                    "@id": "/treatments/df02c0d4-f796-4f77-bfbc-388cdbfcc615/",
                    "purpose": "stimulation",
                    "summary": "Treatment of 5 μg/mL T-cell surface glycoprotein CD3 gamma chain for 4 hours",
                    "treatment_type": "protein"
                },
                {
                    "@id": "/treatments/42b3c61d-38de-4bd2-bb39-33c125a417cb/",
                    "purpose": "stimulation",
                    "summary": "Treatment of 100 ng/mL phorbol 13-acetate 12-myristate for 4 hours",
                    "treatment_type": "chemical"
                }
            ]
        }
    ],
    "schema_version": "15",
    "status": "released",
    "submitted_by": {
        "@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
        "title": "Michael Montgomery"
    },
    "submitted_files_timestamp": "2023-12-05T19:33:18.204741+00:00",
    "summary": "cas mediated mutagenesis (Variant FlowFISH) integrating a guide (sgRNA) library targeting sequence variants in a genomic locus followed by DNA sequencing assay",
    "uuid": "99727558-a187-4e25-948d-5aaedde23246"
}