IGVFDS6647HVMC

released
{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS6647HVMC/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS6647HVMC",
    "aliases": [
        "jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinB_AmpliconSequencing"
    ],
    "assay_term": {
        "@id": "/assay-terms/OBI_0003133/",
        "term_name": "cas mediated mutagenesis"
    },
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "mismatched status",
                "detail": "Released in vitro system [IGVFSM8601WYGY](/in-vitro-systems/IGVFSM8601WYGY/) 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/IGVFSM8601WYGY/"
            }
        ],
        "NOT_COMPLIANT": [
            {
                "category": "missing sequence specification",
                "detail": "File set [IGVFDS6647HVMC](/measurement-sets/IGVFDS6647HVMC/) has sequence file(s): [IGVFFI1297OKBA](/sequence-files/IGVFFI1297OKBA/), [IGVFFI3724EHBW](/sequence-files/IGVFFI3724EHBW/), [IGVFFI3823QCOY](/sequence-files/IGVFFI3823QCOY/), [IGVFFI7167LWVZ](/sequence-files/IGVFFI7167LWVZ/), [IGVFFI7777XMXM](/sequence-files/IGVFFI7777XMXM/), [IGVFFI5602OVOR](/sequence-files/IGVFFI5602OVOR/), [IGVFFI2917GROT](/sequence-files/IGVFFI2917GROT/), [IGVFFI9638BNPL](/sequence-files/IGVFFI9638BNPL/) 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/IGVFDS6647HVMC/"
            },
            {
                "category": "missing auxiliary set",
                "detail": "Measurement set [IGVFDS6647HVMC](/measurement-sets/IGVFDS6647HVMC/) 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/IGVFDS6647HVMC/"
            }
        ],
        "WARNING": [
            {
                "category": "missing sequencing kit",
                "detail": "File set [IGVFDS6647HVMC](/measurement-sets/IGVFDS6647HVMC/) has sequence file(s) [IGVFFI1297OKBA](/sequence-files/IGVFFI1297OKBA/), [IGVFFI3724EHBW](/sequence-files/IGVFFI3724EHBW/), [IGVFFI3823QCOY](/sequence-files/IGVFFI3823QCOY/), [IGVFFI7167LWVZ](/sequence-files/IGVFFI7167LWVZ/), [IGVFFI7777XMXM](/sequence-files/IGVFFI7777XMXM/), [IGVFFI5602OVOR](/sequence-files/IGVFFI5602OVOR/), [IGVFFI2917GROT](/sequence-files/IGVFFI2917GROT/), [IGVFFI9638BNPL](/sequence-files/IGVFFI9638BNPL/) 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/IGVFDS6647HVMC/"
            }
        ]
    },
    "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": "2023-11-30T22:47:32.147601+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/IGVFFI1297OKBA/",
            "accession": "IGVFFI1297OKBA",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinB-PCRrep1_R1"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-05T18:44:07.994544+00:00",
            "file_format": "fastq",
            "file_size": 7231750,
            "href": "/sequence-files/IGVFFI1297OKBA/@@download/IGVFFI1297OKBA.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/05/c7113a6b-f352-4a89-a455-1b4794f7f90c/IGVFFI1297OKBA.fastq.gz",
            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S7-BioRep3-FFRep1-BinB-PCRrep1_S30_R1_001.fastq.gz"
        },
        {
            "@id": "/sequence-files/IGVFFI3724EHBW/",
            "accession": "IGVFFI3724EHBW",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinB-PCRrep2_R1"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-05T18:50:26.809417+00:00",
            "file_format": "fastq",
            "file_size": 7922851,
            "href": "/sequence-files/IGVFFI3724EHBW/@@download/IGVFFI3724EHBW.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/05/c78517e0-377d-4884-b391-37e1b0d3ca56/IGVFFI3724EHBW.fastq.gz",
            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S7-BioRep3-FFRep1-BinB-PCRrep2_S86_R1_001.fastq.gz"
        },
        {
            "@id": "/sequence-files/IGVFFI3823QCOY/",
            "accession": "IGVFFI3823QCOY",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinB-PCRrep2_R2"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-05T19:03:32.091399+00:00",
            "file_format": "fastq",
            "file_size": 14421299,
            "href": "/sequence-files/IGVFFI3823QCOY/@@download/IGVFFI3823QCOY.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/05/cc3cfe4e-37e9-46fd-96a5-6667518c8774/IGVFFI3823QCOY.fastq.gz",
            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S7-BioRep3-FFRep1-BinB-PCRrep2_S86_R2_001.fastq.gz"
        },
        {
            "@id": "/sequence-files/IGVFFI7167LWVZ/",
            "accession": "IGVFFI7167LWVZ",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinB-PCRrep1_R2"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-05T18:56:54.968677+00:00",
            "file_format": "fastq",
            "file_size": 13119631,
            "href": "/sequence-files/IGVFFI7167LWVZ/@@download/IGVFFI7167LWVZ.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/05/9bdcff2e-b0d7-41b5-a0e9-a9567361cb5e/IGVFFI7167LWVZ.fastq.gz",
            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S7-BioRep3-FFRep1-BinB-PCRrep1_S30_R2_001.fastq.gz"
        },
        {
            "@id": "/sequence-files/IGVFFI7777XMXM/",
            "accession": "IGVFFI7777XMXM",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinB-PCRrep1_I1"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-05T19:09:51.244876+00:00",
            "file_format": "fastq",
            "file_size": 3023678,
            "href": "/sequence-files/IGVFFI7777XMXM/@@download/IGVFFI7777XMXM.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/05/32f8b441-ee6c-4739-a77b-4a77e431427b/IGVFFI7777XMXM.fastq.gz",
            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S7-BioRep3-FFRep1-BinB-PCRrep1_S30_I1_001.fastq.gz"
        },
        {
            "@id": "/sequence-files/IGVFFI5602OVOR/",
            "accession": "IGVFFI5602OVOR",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinB-PCRrep2_I1"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-05T19:16:06.766451+00:00",
            "file_format": "fastq",
            "file_size": 3488285,
            "href": "/sequence-files/IGVFFI5602OVOR/@@download/IGVFFI5602OVOR.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/05/8bf99a2f-3943-4aa9-b46c-dd3354283f98/IGVFFI5602OVOR.fastq.gz",
            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S7-BioRep3-FFRep1-BinB-PCRrep2_S86_I1_001.fastq.gz"
        },
        {
            "@id": "/sequence-files/IGVFFI2917GROT/",
            "accession": "IGVFFI2917GROT",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinB-PCRrep1_I2"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-05T19:22:23.667058+00:00",
            "file_format": "fastq",
            "file_size": 2939965,
            "href": "/sequence-files/IGVFFI2917GROT/@@download/IGVFFI2917GROT.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/05/a20926a0-f84b-4b07-b558-256013c5c24e/IGVFFI2917GROT.fastq.gz",
            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S7-BioRep3-FFRep1-BinB-PCRrep1_S30_I2_001.fastq.gz"
        },
        {
            "@id": "/sequence-files/IGVFFI9638BNPL/",
            "accession": "IGVFFI9638BNPL",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinB-PCRrep2_I2"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-05T19:28:42.250780+00:00",
            "file_format": "fastq",
            "file_size": 3235597,
            "href": "/sequence-files/IGVFFI9638BNPL/@@download/IGVFFI9638BNPL.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/05/28ff8b79-ff2b-451e-af70-f6f9894b8236/IGVFFI9638BNPL.fastq.gz",
            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S7-BioRep3-FFRep1-BinB-PCRrep2_S86_I2_001.fastq.gz"
        }
    ],
    "input_file_set_for": [
        "/analysis-sets/IGVFDS9162RHFP/"
    ],
    "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": "2023-12-20T23:04:37.145369+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM8601WYGY/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM8601WYGY",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinB"
            ],
            "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 11-20% expression of PPIF) modified with a guide library",
            "taxa": "Homo sapiens"
        }
    ],
    "schema_version": "15",
    "status": "released",
    "submitted_by": {
        "@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
        "title": "Michael Montgomery"
    },
    "submitted_files_timestamp": "2023-12-05T18:44:07.994544+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": "feb7d08a-1287-4cac-b362-f81fd5ba1f81"
}