IGVFDS3030YDAT

released
{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS3030YDAT/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS3030YDAT",
    "aliases": [
        "jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep2-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 [IGVFSM4844JJJX](/in-vitro-systems/IGVFSM4844JJJX/) 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/IGVFSM4844JJJX/"
            }
        ],
        "NOT_COMPLIANT": [
            {
                "category": "missing sequence specification",
                "detail": "File set [IGVFDS3030YDAT](/measurement-sets/IGVFDS3030YDAT/) has sequence file(s): [IGVFFI4629OYMM](/sequence-files/IGVFFI4629OYMM/), [IGVFFI4153PMOZ](/sequence-files/IGVFFI4153PMOZ/), [IGVFFI0498WYXK](/sequence-files/IGVFFI0498WYXK/), [IGVFFI0842IMRO](/sequence-files/IGVFFI0842IMRO/), [IGVFFI9472VVFS](/sequence-files/IGVFFI9472VVFS/), [IGVFFI1055BRCU](/sequence-files/IGVFFI1055BRCU/), [IGVFFI3549GFKG](/sequence-files/IGVFFI3549GFKG/), [IGVFFI3359XMWY](/sequence-files/IGVFFI3359XMWY/) 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/IGVFDS3030YDAT/"
            },
            {
                "category": "missing auxiliary set",
                "detail": "Measurement set [IGVFDS3030YDAT](/measurement-sets/IGVFDS3030YDAT/) 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/IGVFDS3030YDAT/"
            }
        ],
        "WARNING": [
            {
                "category": "missing sequencing kit",
                "detail": "File set [IGVFDS3030YDAT](/measurement-sets/IGVFDS3030YDAT/) has sequence file(s) [IGVFFI4629OYMM](/sequence-files/IGVFFI4629OYMM/), [IGVFFI4153PMOZ](/sequence-files/IGVFFI4153PMOZ/), [IGVFFI0498WYXK](/sequence-files/IGVFFI0498WYXK/), [IGVFFI0842IMRO](/sequence-files/IGVFFI0842IMRO/), [IGVFFI9472VVFS](/sequence-files/IGVFFI9472VVFS/), [IGVFFI1055BRCU](/sequence-files/IGVFFI1055BRCU/), [IGVFFI3549GFKG](/sequence-files/IGVFFI3549GFKG/), [IGVFFI3359XMWY](/sequence-files/IGVFFI3359XMWY/) 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/IGVFDS3030YDAT/"
            }
        ]
    },
    "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": "2023-11-30T22:48:29.172183+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/IGVFFI4629OYMM/",
            "accession": "IGVFFI4629OYMM",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinD-PCRrep1_R1"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-05T19:36:24.517218+00:00",
            "file_format": "fastq",
            "file_size": 7425974,
            "href": "/sequence-files/IGVFFI4629OYMM/@@download/IGVFFI4629OYMM.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/05/1b12f7e7-96f8-47a8-ab7e-806bea61b002/IGVFFI4629OYMM.fastq.gz",
            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S18-BioRep3-FFRep2-BinD-PCRrep1_S151_R1_001.fastq.gz"
        },
        {
            "@id": "/sequence-files/IGVFFI4153PMOZ/",
            "accession": "IGVFFI4153PMOZ",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinD-PCRrep1_R2"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-05T19:44:52.457918+00:00",
            "file_format": "fastq",
            "file_size": 13920546,
            "href": "/sequence-files/IGVFFI4153PMOZ/@@download/IGVFFI4153PMOZ.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/05/028d35e1-6e49-492b-9d7e-0af8280386dc/IGVFFI4153PMOZ.fastq.gz",
            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S18-BioRep3-FFRep2-BinD-PCRrep1_S151_R2_001.fastq.gz"
        },
        {
            "@id": "/sequence-files/IGVFFI0498WYXK/",
            "accession": "IGVFFI0498WYXK",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinD-PCRrep1_I1"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-05T19:53:14.077499+00:00",
            "file_format": "fastq",
            "file_size": 3300288,
            "href": "/sequence-files/IGVFFI0498WYXK/@@download/IGVFFI0498WYXK.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/05/c03707f6-87cd-4680-b807-e6669a0b68fb/IGVFFI0498WYXK.fastq.gz",
            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S18-BioRep3-FFRep2-BinD-PCRrep1_S151_I1_001.fastq.gz"
        },
        {
            "@id": "/sequence-files/IGVFFI0842IMRO/",
            "accession": "IGVFFI0842IMRO",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinD-PCRrep1_I2"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-05T20:01:21.388775+00:00",
            "file_format": "fastq",
            "file_size": 3116004,
            "href": "/sequence-files/IGVFFI0842IMRO/@@download/IGVFFI0842IMRO.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/05/07d344d2-5a1c-4837-8567-2fb091c46b3f/IGVFFI0842IMRO.fastq.gz",
            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S18-BioRep3-FFRep2-BinD-PCRrep1_S151_I2_001.fastq.gz"
        },
        {
            "@id": "/sequence-files/IGVFFI9472VVFS/",
            "accession": "IGVFFI9472VVFS",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinD-PCRrep2_R1"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-05T20:09:35.592580+00:00",
            "file_format": "fastq",
            "file_size": 7829063,
            "href": "/sequence-files/IGVFFI9472VVFS/@@download/IGVFFI9472VVFS.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/05/49634226-7161-4c3f-a547-f36a31ba4446/IGVFFI9472VVFS.fastq.gz",
            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S18-BioRep3-FFRep2-BinD-PCRrep2_S208_R1_001.fastq.gz"
        },
        {
            "@id": "/sequence-files/IGVFFI1055BRCU/",
            "accession": "IGVFFI1055BRCU",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinD-PCRrep2_R2"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-05T20:18:03.747922+00:00",
            "file_format": "fastq",
            "file_size": 14571209,
            "href": "/sequence-files/IGVFFI1055BRCU/@@download/IGVFFI1055BRCU.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/05/ff5aa3f3-b6b3-49d1-9067-0d2ddcc64388/IGVFFI1055BRCU.fastq.gz",
            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S18-BioRep3-FFRep2-BinD-PCRrep2_S208_R2_001.fastq.gz"
        },
        {
            "@id": "/sequence-files/IGVFFI3549GFKG/",
            "accession": "IGVFFI3549GFKG",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinD-PCRrep2_I1"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-05T20:26:27.381234+00:00",
            "file_format": "fastq",
            "file_size": 3415292,
            "href": "/sequence-files/IGVFFI3549GFKG/@@download/IGVFFI3549GFKG.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/05/c46bd23b-b0a9-48b9-bfcc-dfe357945964/IGVFFI3549GFKG.fastq.gz",
            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S18-BioRep3-FFRep2-BinD-PCRrep2_S208_I1_001.fastq.gz"
        },
        {
            "@id": "/sequence-files/IGVFFI3359XMWY/",
            "accession": "IGVFFI3359XMWY",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinD-PCRrep2_I2"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-05T20:34:40.477818+00:00",
            "file_format": "fastq",
            "file_size": 3265095,
            "href": "/sequence-files/IGVFFI3359XMWY/@@download/IGVFFI3359XMWY.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/05/bb8824e2-524d-44ab-9812-89fa5d43894a/IGVFFI3359XMWY.fastq.gz",
            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S18-BioRep3-FFRep2-BinD-PCRrep2_S208_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": "2023-12-20T23:04:25.476875+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM4844JJJX/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM4844JJJX",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep2-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": "2023-12-05T19:36:24.517218+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": "c668d941-4a5b-491e-b035-772b3be524d6"
}