IGVFDS0262BREE

{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS0262BREE/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS0262BREE",
    "aliases": [
        "gary-hon:CM_Pilot_2_Lenti_RNA_LW261"
    ],
    "assay_term": {
        "@id": "/assay-terms/OBI_0003660/",
        "status": "released",
        "term_name": "in vitro CRISPR screen using single-cell RNA-seq"
    },
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS7783CMAZ](/auxiliary-sets/IGVFDS7783CMAZ/) has sequence file(s) [IGVFFI4960KIPY](/sequence-files/IGVFFI4960KIPY/), [IGVFFI0465HHKI](/sequence-files/IGVFFI0465HHKI/), [IGVFFI2358HDWU](/sequence-files/IGVFFI2358HDWU/), [IGVFFI0811GSLQ](/sequence-files/IGVFFI0811GSLQ/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_inconsistent_sequencing_kit",
                "path": "/auxiliary-sets/IGVFDS7783CMAZ/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS7783CMAZ](/auxiliary-sets/IGVFDS7783CMAZ/) has sequence file(s): [IGVFFI4960KIPY](/sequence-files/IGVFFI4960KIPY/), [IGVFFI0465HHKI](/sequence-files/IGVFFI0465HHKI/), [IGVFFI2358HDWU](/sequence-files/IGVFFI2358HDWU/), [IGVFFI0811GSLQ](/sequence-files/IGVFFI0811GSLQ/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_missing_seqspec",
                "path": "/auxiliary-sets/IGVFDS7783CMAZ/"
            },
            {
                "category": "missing sequencing kit",
                "detail": "Measurement set [IGVFDS0262BREE](/measurement-sets/IGVFDS0262BREE/) has sequence file(s) [IGVFFI6482UUDY](/sequence-files/IGVFFI6482UUDY/), [IGVFFI5673JAWE](/sequence-files/IGVFFI5673JAWE/), [IGVFFI5023CDRX](/sequence-files/IGVFFI5023CDRX/), [IGVFFI0458UOKL](/sequence-files/IGVFFI0458UOKL/), [IGVFFI3649RJAY](/sequence-files/IGVFFI3649RJAY/), [IGVFFI4342WYGO](/sequence-files/IGVFFI4342WYGO/), [IGVFFI0141AYNM](/sequence-files/IGVFFI0141AYNM/), [IGVFFI8875BMHJ](/sequence-files/IGVFFI8875BMHJ/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_inconsistent_sequencing_kit",
                "path": "/measurement-sets/IGVFDS0262BREE/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS0262BREE](/measurement-sets/IGVFDS0262BREE/) has sequence file(s): [IGVFFI6482UUDY](/sequence-files/IGVFFI6482UUDY/), [IGVFFI5673JAWE](/sequence-files/IGVFFI5673JAWE/), [IGVFFI5023CDRX](/sequence-files/IGVFFI5023CDRX/), [IGVFFI0458UOKL](/sequence-files/IGVFFI0458UOKL/), [IGVFFI3649RJAY](/sequence-files/IGVFFI3649RJAY/), [IGVFFI4342WYGO](/sequence-files/IGVFFI4342WYGO/), [IGVFFI0141AYNM](/sequence-files/IGVFFI0141AYNM/), [IGVFFI8875BMHJ](/sequence-files/IGVFFI8875BMHJ/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_missing_seqspec",
                "path": "/measurement-sets/IGVFDS0262BREE/"
            },
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS1373ALPP](/auxiliary-sets/IGVFDS1373ALPP/) has sequence file(s) [IGVFFI8947XMLR](/sequence-files/IGVFFI8947XMLR/), [IGVFFI4740QPJS](/sequence-files/IGVFFI4740QPJS/), [IGVFFI4786EANZ](/sequence-files/IGVFFI4786EANZ/), [IGVFFI7495WDFC](/sequence-files/IGVFFI7495WDFC/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_inconsistent_sequencing_kit",
                "path": "/auxiliary-sets/IGVFDS1373ALPP/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS1373ALPP](/auxiliary-sets/IGVFDS1373ALPP/) has sequence file(s): [IGVFFI8947XMLR](/sequence-files/IGVFFI8947XMLR/), [IGVFFI4740QPJS](/sequence-files/IGVFFI4740QPJS/), [IGVFFI4786EANZ](/sequence-files/IGVFFI4786EANZ/), [IGVFFI7495WDFC](/sequence-files/IGVFFI7495WDFC/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_missing_seqspec",
                "path": "/auxiliary-sets/IGVFDS1373ALPP/"
            }
        ]
    },
    "auxiliary_sets": [
        {
            "@id": "/auxiliary-sets/IGVFDS7783CMAZ/",
            "accession": "IGVFDS7783CMAZ",
            "aliases": [
                "gary-hon:CM_Pilot_2_Lenti_HTO_LW261"
            ],
            "file_set_type": "cell hashing barcode sequencing",
            "status": "preview"
        },
        {
            "@id": "/auxiliary-sets/IGVFDS1373ALPP/",
            "accession": "IGVFDS1373ALPP",
            "aliases": [
                "gary-hon:CM_Pilot_2_Lenti_sgRNA_LW261"
            ],
            "file_set_type": "gRNA sequencing",
            "status": "preview"
        }
    ],
    "award": {
        "@id": "/awards/HG011996/",
        "component": "functional characterization",
        "contact_pi": {
            "@id": "/users/95d84f03-8ce0-489c-a755-f33ced139c5d/",
            "title": "Gary Hon"
        },
        "title": "Multiscale functional characterization of genomic variation in human developmental disorders"
    },
    "control_for": [],
    "creation_timestamp": "2024-02-15T23:43:20.830909+00:00",
    "donors": [
        {
            "@id": "/human-donors/IGVFDO1756PPKO/",
            "accession": "IGVFDO1756PPKO",
            "aliases": [
                "igvf:donor_of_WTC11"
            ],
            "sex": "male",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "externally_hosted": false,
    "file_set_type": "experimental data",
    "files": [
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            "@id": "/sequence-files/IGVFFI6482UUDY/",
            "accession": "IGVFFI6482UUDY",
            "aliases": [
                "gary-hon:LW261_1_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-20T17:47:55.945063+00:00",
            "file_format": "fastq",
            "file_size": 546643462,
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            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0010963/",
                "status": "released",
                "term_name": "Illumina NextSeq 2000"
            },
            "status": "preview",
            "submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-07-13-McDermott-NextSeq.10X.run3.transcriptome/2023-07-13/outs/fastq_path/AAC5GH5HV/LW261_S1_L001_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI5673JAWE/",
            "accession": "IGVFFI5673JAWE",
            "aliases": [
                "gary-hon:LW261_1_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-20T17:48:05.447006+00:00",
            "file_format": "fastq",
            "file_size": 528039440,
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            "sequencing_platform": {
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                "status": "released",
                "term_name": "Illumina NextSeq 2000"
            },
            "status": "preview",
            "submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-07-13-McDermott-NextSeq.10X.run3.transcriptome/2023-07-13/outs/fastq_path/AAC5GH5HV/LW261_S1_L001_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI5023CDRX/",
            "accession": "IGVFFI5023CDRX",
            "aliases": [
                "gary-hon:LW261_1_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-20T17:48:14.047408+00:00",
            "file_format": "fastq",
            "file_size": 1828680501,
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            "s3_uri": "s3://igvf-files/2024/02/20/4d81362e-72bf-495e-aa4b-62c1474bc2cc/IGVFFI5023CDRX.fastq.gz",
            "sequencing_platform": {
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                "status": "released",
                "term_name": "Illumina NextSeq 2000"
            },
            "status": "preview",
            "submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-07-13-McDermott-NextSeq.10X.run3.transcriptome/2023-07-13/outs/fastq_path/AAC5GH5HV/LW261_S1_L001_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI0458UOKL/",
            "accession": "IGVFFI0458UOKL",
            "aliases": [
                "gary-hon:LW261_1_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-20T17:48:37.877899+00:00",
            "file_format": "fastq",
            "file_size": 4508972059,
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            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0010963/",
                "status": "released",
                "term_name": "Illumina NextSeq 2000"
            },
            "status": "preview",
            "submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-07-13-McDermott-NextSeq.10X.run3.transcriptome/2023-07-13/outs/fastq_path/AAC5GH5HV/LW261_S1_L001_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3649RJAY/",
            "accession": "IGVFFI3649RJAY",
            "aliases": [
                "gary-hon:LW261_2_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-20T17:49:21.041177+00:00",
            "file_format": "fastq",
            "file_size": 569178908,
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            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0010963/",
                "status": "released",
                "term_name": "Illumina NextSeq 2000"
            },
            "status": "preview",
            "submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-07-13-McDermott-NextSeq.10X.run3.transcriptome/2023-07-13/outs/fastq_path/AAC5GH5HV/LW261_S1_L002_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI4342WYGO/",
            "accession": "IGVFFI4342WYGO",
            "aliases": [
                "gary-hon:LW261_2_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-20T17:49:30.280034+00:00",
            "file_format": "fastq",
            "file_size": 508572205,
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            "sequencing_platform": {
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                "status": "released",
                "term_name": "Illumina NextSeq 2000"
            },
            "status": "preview",
            "submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-07-13-McDermott-NextSeq.10X.run3.transcriptome/2023-07-13/outs/fastq_path/AAC5GH5HV/LW261_S1_L002_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI0141AYNM/",
            "accession": "IGVFFI0141AYNM",
            "aliases": [
                "gary-hon:LW261_2_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-20T17:49:38.735519+00:00",
            "file_format": "fastq",
            "file_size": 1665556348,
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            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0010963/",
                "status": "released",
                "term_name": "Illumina NextSeq 2000"
            },
            "status": "preview",
            "submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-07-13-McDermott-NextSeq.10X.run3.transcriptome/2023-07-13/outs/fastq_path/AAC5GH5HV/LW261_S1_L002_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8875BMHJ/",
            "accession": "IGVFFI8875BMHJ",
            "aliases": [
                "gary-hon:LW261_2_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-20T17:49:57.218504+00:00",
            "file_format": "fastq",
            "file_size": 4166124945,
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            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0010963/",
                "status": "released",
                "term_name": "Illumina NextSeq 2000"
            },
            "status": "preview",
            "submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-07-13-McDermott-NextSeq.10X.run3.transcriptome/2023-07-13/outs/fastq_path/AAC5GH5HV/LW261_S1_L002_R2_001.fastq.gz",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS4003HZAB/"
    ],
    "lab": {
        "@id": "/labs/gary-hon/",
        "title": "Gary Hon, UT"
    },
    "preferred_assay_title": "Perturb-seq",
    "protocols": [
        "https://www.protocols.io/view/experimental-procedures-for-tf-perturb-seq-ut-sout-denf3dbn"
    ],
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM1972EKCJ/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM1972EKCJ",
            "aliases": [
                "nikhil-munshi:differentited_WTC11_CM_Pilot1_Lenti_LW261"
            ],
            "classifications": [
                "differentiated cell specimen"
            ],
            "construct_library_sets": [
                {
                    "@id": "/construct-library-sets/IGVFDS9629YZLO/",
                    "accession": "IGVFDS9629YZLO",
                    "file_set_type": "guide library",
                    "status": "preview",
                    "summary": "guide (sgRNA) library targeting accessible genome regions in many genomic loci"
                }
            ],
            "modifications": [
                {
                    "@id": "/crispr-modifications/0a63b754-eca4-44aa-bbc2-fccdc6c44fb5/",
                    "modality": "interference",
                    "status": "preview"
                }
            ],
            "sample_terms": [
                {
                    "@id": "/sample-terms/EFO_0009747/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
                        "Item"
                    ],
                    "aliases": [
                        "igvf:WTC11"
                    ],
                    "status": "released",
                    "summary": "GM25256 (WTC-11)",
                    "term_name": "GM25256 (WTC-11)"
                }
            ],
            "status": "preview",
            "summary": "GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW261), male, Homo sapiens modified with CRISPRi Sp-dCas9, transduced (lentivirus) with a guide library",
            "targeted_sample_term": {
                "@id": "/sample-terms/CL_0000746/",
                "status": "released",
                "term_name": "cardiac muscle cell"
            },
            "taxa": "Homo sapiens"
        }
    ],
    "schema_version": "23",
    "status": "preview",
    "submitted_by": {
        "@id": "/users/b05645f1-2d56-4a5e-b272-4601e555a3fa/",
        "title": "Mpathi Nzima"
    },
    "submitted_files_timestamp": "2024-02-20T17:47:55.945063+00:00",
    "submitter_comment": "Transcriptiome for LW261'",
    "summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "05642a32-4377-4b02-9bc8-5ac17067a4bd"
}