IGVFDS6884MESW

released
{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS6884MESW/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS6884MESW",
    "aliases": [
        "jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinC_AmpliconSequencing"
    ],
    "assay_term": {
        "@id": "/assay-terms/OBI_0003133/",
        "term_name": "cas mediated mutagenesis"
    },
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "mismatched status",
                "detail": "Released in vitro system [IGVFSM7935BTPN](/in-vitro-systems/IGVFSM7935BTPN/) 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/IGVFSM7935BTPN/"
            }
        ],
        "NOT_COMPLIANT": [
            {
                "category": "missing sequence specification",
                "detail": "File set [IGVFDS6884MESW](/measurement-sets/IGVFDS6884MESW/) has sequence file(s): [IGVFFI8006YZRM](/sequence-files/IGVFFI8006YZRM/), [IGVFFI5655NKLE](/sequence-files/IGVFFI5655NKLE/), [IGVFFI2316STRE](/sequence-files/IGVFFI2316STRE/), [IGVFFI3326JQOC](/sequence-files/IGVFFI3326JQOC/), [IGVFFI1219VFUN](/sequence-files/IGVFFI1219VFUN/), [IGVFFI8365HPGR](/sequence-files/IGVFFI8365HPGR/), [IGVFFI0717LTHJ](/sequence-files/IGVFFI0717LTHJ/), [IGVFFI5749XIDR](/sequence-files/IGVFFI5749XIDR/) 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/IGVFDS6884MESW/"
            },
            {
                "category": "missing auxiliary set",
                "detail": "Measurement set [IGVFDS6884MESW](/measurement-sets/IGVFDS6884MESW/) 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/IGVFDS6884MESW/"
            }
        ],
        "WARNING": [
            {
                "category": "missing sequencing kit",
                "detail": "File set [IGVFDS6884MESW](/measurement-sets/IGVFDS6884MESW/) has sequence file(s) [IGVFFI8006YZRM](/sequence-files/IGVFFI8006YZRM/), [IGVFFI5655NKLE](/sequence-files/IGVFFI5655NKLE/), [IGVFFI2316STRE](/sequence-files/IGVFFI2316STRE/), [IGVFFI3326JQOC](/sequence-files/IGVFFI3326JQOC/), [IGVFFI1219VFUN](/sequence-files/IGVFFI1219VFUN/), [IGVFFI8365HPGR](/sequence-files/IGVFFI8365HPGR/), [IGVFFI0717LTHJ](/sequence-files/IGVFFI0717LTHJ/), [IGVFFI5749XIDR](/sequence-files/IGVFFI5749XIDR/) 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/IGVFDS6884MESW/"
            }
        ]
    },
    "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": "2023-11-30T22:48:20.144980+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/IGVFFI8006YZRM/",
            "accession": "IGVFFI8006YZRM",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinC-PCRrep1_R1"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-05T19:35:13.422866+00:00",
            "file_format": "fastq",
            "file_size": 7542054,
            "href": "/sequence-files/IGVFFI8006YZRM/@@download/IGVFFI8006YZRM.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/05/340f6159-454e-4ef4-856d-c3a9fe783f40/IGVFFI8006YZRM.fastq.gz",
            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S17-BioRep3-FFRep1-BinC-PCRrep1_S143_R1_001.fastq.gz"
        },
        {
            "@id": "/sequence-files/IGVFFI5655NKLE/",
            "accession": "IGVFFI5655NKLE",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinC-PCRrep1_R2"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-05T19:43:39.248777+00:00",
            "file_format": "fastq",
            "file_size": 13969061,
            "href": "/sequence-files/IGVFFI5655NKLE/@@download/IGVFFI5655NKLE.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/05/f6109d67-0c85-46d8-8dec-cd9332de92d8/IGVFFI5655NKLE.fastq.gz",
            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S17-BioRep3-FFRep1-BinC-PCRrep1_S143_R2_001.fastq.gz"
        },
        {
            "@id": "/sequence-files/IGVFFI2316STRE/",
            "accession": "IGVFFI2316STRE",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinC-PCRrep1_I1"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-05T19:52:04.471219+00:00",
            "file_format": "fastq",
            "file_size": 3242107,
            "href": "/sequence-files/IGVFFI2316STRE/@@download/IGVFFI2316STRE.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/05/ba7e896a-3185-457f-88b8-a3ac549144d0/IGVFFI2316STRE.fastq.gz",
            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S17-BioRep3-FFRep1-BinC-PCRrep1_S143_I1_001.fastq.gz"
        },
        {
            "@id": "/sequence-files/IGVFFI3326JQOC/",
            "accession": "IGVFFI3326JQOC",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinC-PCRrep1_I2"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-05T20:00:11.640252+00:00",
            "file_format": "fastq",
            "file_size": 3158646,
            "href": "/sequence-files/IGVFFI3326JQOC/@@download/IGVFFI3326JQOC.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/05/29547d3c-2194-4a58-b783-143486433da3/IGVFFI3326JQOC.fastq.gz",
            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S17-BioRep3-FFRep1-BinC-PCRrep1_S143_I2_001.fastq.gz"
        },
        {
            "@id": "/sequence-files/IGVFFI1219VFUN/",
            "accession": "IGVFFI1219VFUN",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinC-PCRrep2_R1"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-05T20:08:24.744430+00:00",
            "file_format": "fastq",
            "file_size": 7354088,
            "href": "/sequence-files/IGVFFI1219VFUN/@@download/IGVFFI1219VFUN.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/05/616e90f7-dea8-4762-82eb-cef86baef465/IGVFFI1219VFUN.fastq.gz",
            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S17-BioRep3-FFRep1-BinC-PCRrep2_S200_R1_001.fastq.gz"
        },
        {
            "@id": "/sequence-files/IGVFFI8365HPGR/",
            "accession": "IGVFFI8365HPGR",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinC-PCRrep2_R2"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-05T20:16:50.613869+00:00",
            "file_format": "fastq",
            "file_size": 13570142,
            "href": "/sequence-files/IGVFFI8365HPGR/@@download/IGVFFI8365HPGR.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/05/87c0c115-fbff-42b7-a051-aafe50bd493b/IGVFFI8365HPGR.fastq.gz",
            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S17-BioRep3-FFRep1-BinC-PCRrep2_S200_R2_001.fastq.gz"
        },
        {
            "@id": "/sequence-files/IGVFFI0717LTHJ/",
            "accession": "IGVFFI0717LTHJ",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinC-PCRrep2_I2"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-05T20:33:30.655770+00:00",
            "file_format": "fastq",
            "file_size": 3080263,
            "href": "/sequence-files/IGVFFI0717LTHJ/@@download/IGVFFI0717LTHJ.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/05/0422e4e2-e136-456b-8184-8ab9bdd51599/IGVFFI0717LTHJ.fastq.gz",
            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S17-BioRep3-FFRep1-BinC-PCRrep2_S200_I2_001.fastq.gz"
        },
        {
            "@id": "/sequence-files/IGVFFI5749XIDR/",
            "accession": "IGVFFI5749XIDR",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinC-PCRrep2_I1"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-05T20:25:17.464997+00:00",
            "file_format": "fastq",
            "file_size": 3159483,
            "href": "/sequence-files/IGVFFI5749XIDR/@@download/IGVFFI5749XIDR.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/05/4e5a68c1-1c2b-4556-ad00-53b41f9464ea/IGVFFI5749XIDR.fastq.gz",
            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S17-BioRep3-FFRep1-BinC-PCRrep2_S200_I1_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": "2023-12-20T23:05:13.034937+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM7935BTPN/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM7935BTPN",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinC"
            ],
            "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 35-45% 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": "2023-12-05T19:35:13.422866+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": "f7f1f2fc-675d-4e2b-818c-b1716303967b"
}