IGVFDS5931MYJN

{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS5931MYJN/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS5931MYJN",
    "aliases": [
        "gary-hon:CM_Pilot_2_Lenti_RNA_LW266"
    ],
    "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": "Measurement set [IGVFDS5931MYJN](/measurement-sets/IGVFDS5931MYJN/) has sequence file(s) [IGVFFI3699NCKX](/sequence-files/IGVFFI3699NCKX/), [IGVFFI3642MWTS](/sequence-files/IGVFFI3642MWTS/), [IGVFFI8404FJNJ](/sequence-files/IGVFFI8404FJNJ/), [IGVFFI7291HRWW](/sequence-files/IGVFFI7291HRWW/), [IGVFFI8529FWOJ](/sequence-files/IGVFFI8529FWOJ/), [IGVFFI3491XAHR](/sequence-files/IGVFFI3491XAHR/), [IGVFFI4944IHCL](/sequence-files/IGVFFI4944IHCL/), [IGVFFI4338NFLG](/sequence-files/IGVFFI4338NFLG/) 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/IGVFDS5931MYJN/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS5931MYJN](/measurement-sets/IGVFDS5931MYJN/) has sequence file(s): [IGVFFI3699NCKX](/sequence-files/IGVFFI3699NCKX/), [IGVFFI3642MWTS](/sequence-files/IGVFFI3642MWTS/), [IGVFFI8404FJNJ](/sequence-files/IGVFFI8404FJNJ/), [IGVFFI7291HRWW](/sequence-files/IGVFFI7291HRWW/), [IGVFFI8529FWOJ](/sequence-files/IGVFFI8529FWOJ/), [IGVFFI3491XAHR](/sequence-files/IGVFFI3491XAHR/), [IGVFFI4944IHCL](/sequence-files/IGVFFI4944IHCL/), [IGVFFI4338NFLG](/sequence-files/IGVFFI4338NFLG/) 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/IGVFDS5931MYJN/"
            },
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS8001EMIV](/auxiliary-sets/IGVFDS8001EMIV/) has sequence file(s) [IGVFFI2828PDNY](/sequence-files/IGVFFI2828PDNY/), [IGVFFI9244QRVR](/sequence-files/IGVFFI9244QRVR/), [IGVFFI5054QLBL](/sequence-files/IGVFFI5054QLBL/), [IGVFFI2658YFUQ](/sequence-files/IGVFFI2658YFUQ/) 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/IGVFDS8001EMIV/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS8001EMIV](/auxiliary-sets/IGVFDS8001EMIV/) has sequence file(s): [IGVFFI2828PDNY](/sequence-files/IGVFFI2828PDNY/), [IGVFFI9244QRVR](/sequence-files/IGVFFI9244QRVR/), [IGVFFI5054QLBL](/sequence-files/IGVFFI5054QLBL/), [IGVFFI2658YFUQ](/sequence-files/IGVFFI2658YFUQ/) 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/IGVFDS8001EMIV/"
            },
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS7944GWTS](/auxiliary-sets/IGVFDS7944GWTS/) has sequence file(s) [IGVFFI9006RKCZ](/sequence-files/IGVFFI9006RKCZ/), [IGVFFI0638VNPV](/sequence-files/IGVFFI0638VNPV/), [IGVFFI3275XOUB](/sequence-files/IGVFFI3275XOUB/), [IGVFFI2007EPSH](/sequence-files/IGVFFI2007EPSH/) 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/IGVFDS7944GWTS/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS7944GWTS](/auxiliary-sets/IGVFDS7944GWTS/) has sequence file(s): [IGVFFI9006RKCZ](/sequence-files/IGVFFI9006RKCZ/), [IGVFFI0638VNPV](/sequence-files/IGVFFI0638VNPV/), [IGVFFI3275XOUB](/sequence-files/IGVFFI3275XOUB/), [IGVFFI2007EPSH](/sequence-files/IGVFFI2007EPSH/) 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/IGVFDS7944GWTS/"
            }
        ]
    },
    "auxiliary_sets": [
        {
            "@id": "/auxiliary-sets/IGVFDS8001EMIV/",
            "accession": "IGVFDS8001EMIV",
            "aliases": [
                "gary-hon:CM_Pilot_2_Lenti_HTO_LW266"
            ],
            "file_set_type": "cell hashing barcode sequencing",
            "status": "preview"
        },
        {
            "@id": "/auxiliary-sets/IGVFDS7944GWTS/",
            "accession": "IGVFDS7944GWTS",
            "aliases": [
                "gary-hon:CM_Pilot_2_Lenti_sgRNA_LW266"
            ],
            "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": "2024-02-15T23:43:26.118162+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/IGVFFI3699NCKX/",
            "accession": "IGVFFI3699NCKX",
            "aliases": [
                "gary-hon:LW266_1_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-20T18:00:41.583734+00:00",
            "file_format": "fastq",
            "file_size": 1673459670,
            "href": "/sequence-files/IGVFFI3699NCKX/@@download/IGVFFI3699NCKX.fastq.gz",
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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/LW266_S6_L001_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3642MWTS/",
            "accession": "IGVFFI3642MWTS",
            "aliases": [
                "gary-hon:LW266_2_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-20T18:01:39.485752+00:00",
            "file_format": "fastq",
            "file_size": 473711837,
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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/LW266_S6_L002_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8404FJNJ/",
            "accession": "IGVFFI8404FJNJ",
            "aliases": [
                "gary-hon:LW266_2_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-20T18:01:56.688256+00:00",
            "file_format": "fastq",
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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/LW266_S6_L002_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI7291HRWW/",
            "accession": "IGVFFI7291HRWW",
            "aliases": [
                "gary-hon:LW266_2_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-20T18:02:13.666446+00:00",
            "file_format": "fastq",
            "file_size": 3870919877,
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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/LW266_S6_L002_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8529FWOJ/",
            "accession": "IGVFFI8529FWOJ",
            "aliases": [
                "gary-hon:LW266_1_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-20T18:00:32.561494+00:00",
            "file_format": "fastq",
            "file_size": 562451583,
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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/LW266_S6_L001_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3491XAHR/",
            "accession": "IGVFFI3491XAHR",
            "aliases": [
                "gary-hon:LW266_2_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-20T18:01:47.863514+00:00",
            "file_format": "fastq",
            "file_size": 500697055,
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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/LW266_S6_L002_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI4944IHCL/",
            "accession": "IGVFFI4944IHCL",
            "aliases": [
                "gary-hon:LW266_1_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-20T18:00:19.062269+00:00",
            "file_format": "fastq",
            "file_size": 523504998,
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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/LW266_S6_L001_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI4338NFLG/",
            "accession": "IGVFFI4338NFLG",
            "aliases": [
                "gary-hon:LW266_1_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-20T18:01:00.254106+00:00",
            "file_format": "fastq",
            "file_size": 4140010459,
            "href": "/sequence-files/IGVFFI4338NFLG/@@download/IGVFFI4338NFLG.fastq.gz",
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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/LW266_S6_L001_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/IGVFSM4930FDUF/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM4930FDUF",
            "aliases": [
                "nikhil-munshi:differentited_WTC11_CM_Pilot1_Lenti_LW266"
            ],
            "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_LW266), 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": "2024-02-20T18:00:19.062269+00:00",
    "submitter_comment": "Transcriptiome for LW266'",
    "summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "5da69cc0-f9db-46a7-a096-2ca8601c9401"
}