IGVFDS5864UGFT

released
{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS5864UGFT/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS5864UGFT",
    "aliases": [
        "jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-THP1-PE2_Exp2_NegControl_AmpliconSequencing"
    ],
    "assay_term": {
        "@id": "/assay-terms/OBI_0003661/",
        "assay_slims": [
            "CRISPR screens"
        ],
        "status": "released",
        "term_name": "in vitro CRISPR screen using flow cytometry"
    },
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequencing kit",
                "detail": "Measurement set [IGVFDS5864UGFT](/measurement-sets/IGVFDS5864UGFT/) has sequence file(s) [IGVFFI2901MSWB](/sequence-files/IGVFFI2901MSWB/), [IGVFFI5738GCOE](/sequence-files/IGVFFI5738GCOE/), [IGVFFI5264KOJB](/sequence-files/IGVFFI5264KOJB/), [IGVFFI7478BMNB](/sequence-files/IGVFFI7478BMNB/), [IGVFFI6767GQPX](/sequence-files/IGVFFI6767GQPX/), [IGVFFI8285QUQB](/sequence-files/IGVFFI8285QUQB/), [IGVFFI4202ZWWK](/sequence-files/IGVFFI4202ZWWK/), [IGVFFI6396HFWS](/sequence-files/IGVFFI6396HFWS/), [IGVFFI3230WTRR](/sequence-files/IGVFFI3230WTRR/), [IGVFFI6235MNEI](/sequence-files/IGVFFI6235MNEI/), [IGVFFI7915NGDF](/sequence-files/IGVFFI7915NGDF/), [IGVFFI5305KTDF](/sequence-files/IGVFFI5305KTDF/), [IGVFFI2838LQVE](/sequence-files/IGVFFI2838LQVE/), [IGVFFI4285ZZFD](/sequence-files/IGVFFI4285ZZFD/), [IGVFFI0960MBFN](/sequence-files/IGVFFI0960MBFN/), [IGVFFI9811QIHQ](/sequence-files/IGVFFI9811QIHQ/) which lack specification of a `sequencing_kit`. Sequence files in a file set associated wtih bulk data should specify a sequencing kit.",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_inconsistent_sequencing_kit",
                "path": "/measurement-sets/IGVFDS5864UGFT/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS5864UGFT](/measurement-sets/IGVFDS5864UGFT/) has sequence file(s): [IGVFFI2901MSWB](/sequence-files/IGVFFI2901MSWB/), [IGVFFI5738GCOE](/sequence-files/IGVFFI5738GCOE/), [IGVFFI5264KOJB](/sequence-files/IGVFFI5264KOJB/), [IGVFFI7478BMNB](/sequence-files/IGVFFI7478BMNB/), [IGVFFI6767GQPX](/sequence-files/IGVFFI6767GQPX/), [IGVFFI8285QUQB](/sequence-files/IGVFFI8285QUQB/), [IGVFFI4202ZWWK](/sequence-files/IGVFFI4202ZWWK/), [IGVFFI6396HFWS](/sequence-files/IGVFFI6396HFWS/), [IGVFFI3230WTRR](/sequence-files/IGVFFI3230WTRR/), [IGVFFI6235MNEI](/sequence-files/IGVFFI6235MNEI/), [IGVFFI7915NGDF](/sequence-files/IGVFFI7915NGDF/), [IGVFFI5305KTDF](/sequence-files/IGVFFI5305KTDF/), [IGVFFI2838LQVE](/sequence-files/IGVFFI2838LQVE/), [IGVFFI4285ZZFD](/sequence-files/IGVFFI4285ZZFD/), [IGVFFI0960MBFN](/sequence-files/IGVFFI0960MBFN/), [IGVFFI9811QIHQ](/sequence-files/IGVFFI9811QIHQ/) which do not have any `seqspecs`. Sequence files in a file set associated with bulk data are expected to link to a sequence specification file.",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_missing_seqspec",
                "path": "/measurement-sets/IGVFDS5864UGFT/"
            }
        ],
        "WARNING": [
            {
                "category": "missing auxiliary set",
                "detail": "Measurement set [IGVFDS5864UGFT](/measurement-sets/IGVFDS5864UGFT/) has no cell sorting `auxiliary_sets`. CRISPR-based measurement sets that utilize flow cytometry are expected to link to a cell sorting auxiliary set.",
                "level": 40,
                "level_name": "WARNING",
                "name": "audit_missing_auxiliary_set",
                "path": "/measurement-sets/IGVFDS5864UGFT/"
            },
            {
                "category": "missing targeted genes",
                "detail": "Measurement set [IGVFDS5864UGFT](/measurement-sets/IGVFDS5864UGFT/) has no `targeted_genes`. ChIP-seq and CRISPR flow cytometry assays are expected to specify targeted gene(s).",
                "level": 40,
                "level_name": "WARNING",
                "name": "audit_targeted_genes",
                "path": "/measurement-sets/IGVFDS5864UGFT/"
            }
        ]
    },
    "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": [
        {
            "@id": "/measurement-sets/IGVFDS4745BLLN/",
            "accession": "IGVFDS4745BLLN",
            "aliases": [
                "jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep2-FACS_Input_AmpliconSequencing"
            ],
            "status": "released"
        },
        {
            "@id": "/measurement-sets/IGVFDS8290UELV/",
            "accession": "IGVFDS8290UELV",
            "aliases": [
                "jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep2-BinA_AmpliconSequencing"
            ],
            "status": "released"
        },
        {
            "@id": "/measurement-sets/IGVFDS6761PEJX/",
            "accession": "IGVFDS6761PEJX",
            "aliases": [
                "jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep3-BinB_AmpliconSequencing"
            ],
            "status": "released"
        },
        {
            "@id": "/measurement-sets/IGVFDS6622DPIT/",
            "accession": "IGVFDS6622DPIT",
            "aliases": [
                "jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep1-BinB_AmpliconSequencing"
            ],
            "status": "released"
        },
        {
            "@id": "/measurement-sets/IGVFDS6551IWAB/",
            "accession": "IGVFDS6551IWAB",
            "aliases": [
                "jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep3-BinA_AmpliconSequencing"
            ],
            "status": "released"
        },
        {
            "@id": "/measurement-sets/IGVFDS5733FUWG/",
            "accession": "IGVFDS5733FUWG",
            "aliases": [
                "jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep3-FACS_Input_AmpliconSequencing"
            ],
            "status": "released"
        },
        {
            "@id": "/measurement-sets/IGVFDS0336ABEV/",
            "accession": "IGVFDS0336ABEV",
            "aliases": [
                "jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep4-FACS_Input_AmpliconSequencing"
            ],
            "status": "released"
        },
        {
            "@id": "/measurement-sets/IGVFDS1783OBDQ/",
            "accession": "IGVFDS1783OBDQ",
            "aliases": [
                "jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep3-BinB_AmpliconSequencing"
            ],
            "status": "released"
        },
        {
            "@id": "/measurement-sets/IGVFDS4761MJPK/",
            "accession": "IGVFDS4761MJPK",
            "aliases": [
                "jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep1-BinD_AmpliconSequencing"
            ],
            "status": "released"
        },
        {
            "@id": "/measurement-sets/IGVFDS6267YRNH/",
            "accession": "IGVFDS6267YRNH",
            "aliases": [
                "jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep3-BinD_AmpliconSequencing"
            ],
            "status": "released"
        },
        {
            "@id": "/measurement-sets/IGVFDS5699JBLV/",
            "accession": "IGVFDS5699JBLV",
            "aliases": [
                "jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-BinC_AmpliconSequencing"
            ],
            "status": "released"
        },
        {
            "@id": "/measurement-sets/IGVFDS3532HUSQ/",
            "accession": "IGVFDS3532HUSQ",
            "aliases": [
                "jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-BinD_AmpliconSequencing"
            ],
            "status": "released"
        },
        {
            "@id": "/measurement-sets/IGVFDS9665GYVE/",
            "accession": "IGVFDS9665GYVE",
            "aliases": [
                "jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep4-BinC_AmpliconSequencing"
            ],
            "status": "released"
        },
        {
            "@id": "/measurement-sets/IGVFDS0629YEMD/",
            "accession": "IGVFDS0629YEMD",
            "aliases": [
                "jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-FACS_Input_AmpliconSequencing"
            ],
            "status": "released"
        },
        {
            "@id": "/measurement-sets/IGVFDS4715UUNW/",
            "accession": "IGVFDS4715UUNW",
            "aliases": [
                "jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-BinB_AmpliconSequencing"
            ],
            "status": "released"
        },
        {
            "@id": "/measurement-sets/IGVFDS1402WRSD/",
            "accession": "IGVFDS1402WRSD",
            "aliases": [
                "jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-BinA_AmpliconSequencing"
            ],
            "status": "released"
        },
        {
            "@id": "/measurement-sets/IGVFDS4750CFGI/",
            "accession": "IGVFDS4750CFGI",
            "aliases": [
                "jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep2-BinD_AmpliconSequencing"
            ],
            "status": "released"
        },
        {
            "@id": "/measurement-sets/IGVFDS3537WUVG/",
            "accession": "IGVFDS3537WUVG",
            "aliases": [
                "jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep3-FACS_Input_AmpliconSequencing"
            ],
            "status": "released"
        },
        {
            "@id": "/measurement-sets/IGVFDS9084GQXI/",
            "accession": "IGVFDS9084GQXI",
            "aliases": [
                "jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep2-BinD_AmpliconSequencing"
            ],
            "status": "released"
        },
        {
            "@id": "/measurement-sets/IGVFDS6566NSFE/",
            "accession": "IGVFDS6566NSFE",
            "aliases": [
                "jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep1-BinC_AmpliconSequencing"
            ],
            "status": "released"
        },
        {
            "@id": "/measurement-sets/IGVFDS1674OUCP/",
            "accession": "IGVFDS1674OUCP",
            "aliases": [
                "jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep2-BinB_AmpliconSequencing"
            ],
            "status": "released"
        },
        {
            "@id": "/measurement-sets/IGVFDS8517SHZG/",
            "accession": "IGVFDS8517SHZG",
            "aliases": [
                "jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep2-BinC_AmpliconSequencing"
            ],
            "status": "released"
        },
        {
            "@id": "/measurement-sets/IGVFDS8736JDCM/",
            "accession": "IGVFDS8736JDCM",
            "aliases": [
                "jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep3-BinC_AmpliconSequencing"
            ],
            "status": "released"
        },
        {
            "@id": "/measurement-sets/IGVFDS2978YQVA/",
            "accession": "IGVFDS2978YQVA",
            "aliases": [
                "jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input_AmpliconSequencing"
            ],
            "status": "released"
        },
        {
            "@id": "/measurement-sets/IGVFDS0403DJHI/",
            "accession": "IGVFDS0403DJHI",
            "aliases": [
                "jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-BinB_AmpliconSequencing"
            ],
            "status": "released"
        },
        {
            "@id": "/measurement-sets/IGVFDS8801DBGC/",
            "accession": "IGVFDS8801DBGC",
            "aliases": [
                "jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep2-BinB_AmpliconSequencing"
            ],
            "status": "released"
        },
        {
            "@id": "/measurement-sets/IGVFDS7403HHLV/",
            "accession": "IGVFDS7403HHLV",
            "aliases": [
                "jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep2-BinC_AmpliconSequencing"
            ],
            "status": "released"
        },
        {
            "@id": "/measurement-sets/IGVFDS3226EEYN/",
            "accession": "IGVFDS3226EEYN",
            "aliases": [
                "jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep3-BinD_AmpliconSequencing"
            ],
            "status": "released"
        },
        {
            "@id": "/measurement-sets/IGVFDS8854UNCC/",
            "accession": "IGVFDS8854UNCC",
            "aliases": [
                "jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep4-BinD_AmpliconSequencing"
            ],
            "status": "released"
        },
        {
            "@id": "/measurement-sets/IGVFDS6512WYQI/",
            "accession": "IGVFDS6512WYQI",
            "aliases": [
                "jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep1-BinA_AmpliconSequencing"
            ],
            "status": "released"
        },
        {
            "@id": "/measurement-sets/IGVFDS8631OYNB/",
            "accession": "IGVFDS8631OYNB",
            "aliases": [
                "jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep2-FACS_Input_AmpliconSequencing"
            ],
            "status": "released"
        },
        {
            "@id": "/measurement-sets/IGVFDS9894YFSM/",
            "accession": "IGVFDS9894YFSM",
            "aliases": [
                "jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep3-BinC_AmpliconSequencing"
            ],
            "status": "released"
        },
        {
            "@id": "/measurement-sets/IGVFDS4761PXVO/",
            "accession": "IGVFDS4761PXVO",
            "aliases": [
                "jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep4-BinA_AmpliconSequencing"
            ],
            "status": "released"
        },
        {
            "@id": "/measurement-sets/IGVFDS1646OXQU/",
            "accession": "IGVFDS1646OXQU",
            "aliases": [
                "jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep4-BinB_AmpliconSequencing"
            ],
            "status": "released"
        },
        {
            "@id": "/measurement-sets/IGVFDS6147NJBC/",
            "accession": "IGVFDS6147NJBC",
            "aliases": [
                "jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep1-FACS_Input_AmpliconSequencing"
            ],
            "status": "released"
        },
        {
            "@id": "/measurement-sets/IGVFDS7009ITAD/",
            "accession": "IGVFDS7009ITAD",
            "aliases": [
                "jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep2-BinA_AmpliconSequencing"
            ],
            "status": "released"
        },
        {
            "@id": "/measurement-sets/IGVFDS1327XCCU/",
            "accession": "IGVFDS1327XCCU",
            "aliases": [
                "jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep3-BinA_AmpliconSequencing"
            ],
            "status": "released"
        },
        {
            "@id": "/measurement-sets/IGVFDS0744DITV/",
            "accession": "IGVFDS0744DITV",
            "aliases": [
                "jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-BinA_AmpliconSequencing"
            ],
            "status": "released"
        },
        {
            "@id": "/measurement-sets/IGVFDS8356GTHO/",
            "accession": "IGVFDS8356GTHO",
            "aliases": [
                "jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-BinD_AmpliconSequencing"
            ],
            "status": "released"
        },
        {
            "@id": "/measurement-sets/IGVFDS7791SSYA/",
            "accession": "IGVFDS7791SSYA",
            "aliases": [
                "jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-BinC_AmpliconSequencing"
            ],
            "status": "released"
        }
    ],
    "control_type": "untransfected",
    "creation_timestamp": "2023-11-30T22:49:34.691226+00:00",
    "donors": [
        {
            "@id": "/human-donors/IGVFDO7359LVPI/",
            "accession": "IGVFDO7359LVPI",
            "aliases": [
                "igvf:donor_of_THP1"
            ],
            "sex": "male",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "externally_hosted": false,
    "file_set_type": "experimental data",
    "files": [
        {
            "@id": "/sequence-files/IGVFFI2901MSWB/",
            "accession": "IGVFFI2901MSWB",
            "aliases": [
                "jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-THP1-PE2_Exp2_NegControl-PCRrep3_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2023-12-05T21:32:16.518847+00:00",
            "file_format": "fastq",
            "file_size": 1235454,
            "href": "/sequence-files/IGVFFI2901MSWB/@@download/IGVFFI2901MSWB.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/05/3e3eda2d-54fe-4f72-9fb5-1aa34972a689/IGVFFI2901MSWB.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0008566/",
                "status": "released",
                "term_name": "Illumina NextSeq 550"
            },
            "status": "released",
            "submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrepNA-BinNeg-PCRrep3_S411_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI5738GCOE/",
            "accession": "IGVFFI5738GCOE",
            "aliases": [
                "jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-THP1-PE2_Exp2_NegControl-PCRrep3_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2023-12-05T21:32:25.293840+00:00",
            "file_format": "fastq",
            "file_size": 3895544,
            "href": "/sequence-files/IGVFFI5738GCOE/@@download/IGVFFI5738GCOE.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/05/ac2405e4-4084-473b-942a-3ddc5bc009ed/IGVFFI5738GCOE.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0008566/",
                "status": "released",
                "term_name": "Illumina NextSeq 550"
            },
            "status": "released",
            "submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrepNA-BinNeg-PCRrep3_S411_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI5264KOJB/",
            "accession": "IGVFFI5264KOJB",
            "aliases": [
                "jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-THP1-PE2_Exp2_NegControl-PCRrep3_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2023-12-05T21:32:07.835758+00:00",
            "file_format": "fastq",
            "file_size": 1230365,
            "href": "/sequence-files/IGVFFI5264KOJB/@@download/IGVFFI5264KOJB.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/05/0e1729b5-70b5-4c37-bf63-1dc8c8963786/IGVFFI5264KOJB.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0008566/",
                "status": "released",
                "term_name": "Illumina NextSeq 550"
            },
            "status": "released",
            "submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrepNA-BinNeg-PCRrep3_S411_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI7478BMNB/",
            "accession": "IGVFFI7478BMNB",
            "aliases": [
                "jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-THP1-PE2_Exp2_NegControl-PCRrep3_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2023-12-05T21:32:34.069237+00:00",
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