IGVFDS0465GFSG

{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS0465GFSG/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS0465GFSG",
    "aliases": [
        "gary-hon:differentited_WTC11_CM_Pilot2_Mini_LPv4_sgRNA_LW427"
    ],
    "audit": {
        "ERROR": [
            {
                "category": "inconsistent sequencing kit",
                "detail": "Auxiliary set [IGVFDS0465GFSG](/auxiliary-sets/IGVFDS0465GFSG/) has a sequence file [IGVFFI5575KDRV](/sequence-files/IGVFFI5575KDRV/) sequenced on a `sequencing_platform` [EFO_0008637](/platform-terms/EFO_0008637/) that is inconsistent with its `sequencing_kit` NovaSeq X Series 25B Reagent Kit. Sequence files should specify a sequencing kit which is consistent with their sequencing platform. Sequence files in the same sequencing run should also specify the same sequencing kit.",
                "level": 60,
                "level_name": "ERROR",
                "name": "audit_inconsistent_sequencing_kit",
                "path": "/auxiliary-sets/IGVFDS0465GFSG/"
            },
            {
                "category": "inconsistent sequencing kit",
                "detail": "Auxiliary set [IGVFDS0465GFSG](/auxiliary-sets/IGVFDS0465GFSG/) has a sequence file [IGVFFI4151SZSL](/sequence-files/IGVFFI4151SZSL/) sequenced on a `sequencing_platform` [EFO_0008637](/platform-terms/EFO_0008637/) that is inconsistent with its `sequencing_kit` NovaSeq X Series 25B Reagent Kit. Sequence files should specify a sequencing kit which is consistent with their sequencing platform. Sequence files in the same sequencing run should also specify the same sequencing kit.",
                "level": 60,
                "level_name": "ERROR",
                "name": "audit_inconsistent_sequencing_kit",
                "path": "/auxiliary-sets/IGVFDS0465GFSG/"
            },
            {
                "category": "inconsistent sequencing kit",
                "detail": "Auxiliary set [IGVFDS0465GFSG](/auxiliary-sets/IGVFDS0465GFSG/) has a sequence file [IGVFFI5902FATE](/sequence-files/IGVFFI5902FATE/) sequenced on a `sequencing_platform` [EFO_0008637](/platform-terms/EFO_0008637/) that is inconsistent with its `sequencing_kit` NovaSeq X Series 25B Reagent Kit. Sequence files should specify a sequencing kit which is consistent with their sequencing platform. Sequence files in the same sequencing run should also specify the same sequencing kit.",
                "level": 60,
                "level_name": "ERROR",
                "name": "audit_inconsistent_sequencing_kit",
                "path": "/auxiliary-sets/IGVFDS0465GFSG/"
            },
            {
                "category": "inconsistent sequencing kit",
                "detail": "Auxiliary set [IGVFDS0465GFSG](/auxiliary-sets/IGVFDS0465GFSG/) has a sequence file [IGVFFI2355JSHD](/sequence-files/IGVFFI2355JSHD/) sequenced on a `sequencing_platform` [EFO_0008637](/platform-terms/EFO_0008637/) that is inconsistent with its `sequencing_kit` NovaSeq X Series 25B Reagent Kit. Sequence files should specify a sequencing kit which is consistent with their sequencing platform. Sequence files in the same sequencing run should also specify the same sequencing kit.",
                "level": 60,
                "level_name": "ERROR",
                "name": "audit_inconsistent_sequencing_kit",
                "path": "/auxiliary-sets/IGVFDS0465GFSG/"
            }
        ],
        "INTERNAL_ACTION": [
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS0465GFSG](/auxiliary-sets/IGVFDS0465GFSG/) has sequence file(s): [IGVFFI5575KDRV](/sequence-files/IGVFFI5575KDRV/), [IGVFFI4151SZSL](/sequence-files/IGVFFI4151SZSL/), [IGVFFI5902FATE](/sequence-files/IGVFFI5902FATE/), [IGVFFI2355JSHD](/sequence-files/IGVFFI2355JSHD/) 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/IGVFDS0465GFSG/"
            }
        ]
    },
    "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": "2024-08-16T20:05:06.035088+00:00",
    "donors": [
        {
            "@id": "/human-donors/IGVFDO1756PPKO/",
            "accession": "IGVFDO1756PPKO",
            "aliases": [
                "igvf:donor_of_WTC11"
            ],
            "sex": "male",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "file_set_type": "gRNA sequencing",
    "files": [
        {
            "@id": "/sequence-files/IGVFFI5575KDRV/",
            "accession": "IGVFFI5575KDRV",
            "aliases": [
                "gary-hon:LW427B_6_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-12-20T21:02:18.770823+00:00",
            "file_format": "fastq",
            "file_size": 1153934722,
            "href": "/sequence-files/IGVFFI5575KDRV/@@download/IGVFFI5575KDRV.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/12/20/7c0f9092-e25c-426b-a43f-8e9cfd15d80a/IGVFFI5575KDRV.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008637/",
            "status": "preview",
            "submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2024/2024-05-01-Novogene-NovaSeq.Hon19_20/sgRNA//LW427B_S13_L006_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI4151SZSL/",
            "accession": "IGVFFI4151SZSL",
            "aliases": [
                "gary-hon:LW427B_6_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-12-20T21:02:35.753140+00:00",
            "file_format": "fastq",
            "file_size": 1042708874,
            "href": "/sequence-files/IGVFFI4151SZSL/@@download/IGVFFI4151SZSL.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/12/20/ace12be1-7d7c-4365-bf6c-bbca9e9c7506/IGVFFI4151SZSL.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008637/",
            "status": "preview",
            "submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2024/2024-05-01-Novogene-NovaSeq.Hon19_20/sgRNA//LW427B_S13_L006_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI5902FATE/",
            "accession": "IGVFFI5902FATE",
            "aliases": [
                "gary-hon:LW427B_6_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-12-20T21:02:52.541865+00:00",
            "file_format": "fastq",
            "file_size": 9984764694,
            "href": "/sequence-files/IGVFFI5902FATE/@@download/IGVFFI5902FATE.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/12/20/52f9740c-e73a-4b8b-88e0-ebecd6a6acce/IGVFFI5902FATE.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008637/",
            "status": "preview",
            "submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2024/2024-05-01-Novogene-NovaSeq.Hon19_20/sgRNA//LW427B_S13_L006_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI2355JSHD/",
            "accession": "IGVFFI2355JSHD",
            "aliases": [
                "gary-hon:LW427B_6_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-12-20T21:04:25.304138+00:00",
            "file_format": "fastq",
            "file_size": 10161728609,
            "href": "/sequence-files/IGVFFI2355JSHD/@@download/IGVFFI2355JSHD.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/12/20/b08f2036-1ff5-4385-82d2-7a07ff0bd413/IGVFFI2355JSHD.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008637/",
            "status": "preview",
            "submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2024/2024-05-01-Novogene-NovaSeq.Hon19_20/sgRNA//LW427B_S13_L006_R2_001.fastq.gz",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS5498SDRJ/"
    ],
    "lab": {
        "@id": "/labs/gary-hon/",
        "title": "Gary Hon, UT"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS6863PGGX/",
            "accession": "IGVFDS6863PGGX",
            "aliases": [
                "gary-hon:differentited_WTC11_CM_Pilot2_Mini_LPv4_LW427"
            ],
            "preferred_assay_title": "Perturb-seq",
            "status": "preview"
        }
    ],
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM0565MLZG/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM0565MLZG",
            "aliases": [
                "nikhil-munshi:differentited_WTC11_CM_Pilot2_Mini_LPv4_LW427"
            ],
            "classifications": [
                "differentiated cell specimen"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS0346MQBH/"
            ],
            "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_LW427), 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": "12",
    "status": "preview",
    "submitted_by": {
        "@id": "/users/b05645f1-2d56-4a5e-b272-4601e555a3fa/",
        "title": "Mpathi Nzima"
    },
    "submitted_files_timestamp": "2024-12-20T21:02:18.770823+00:00",
    "summary": "gRNA sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "3fd9c48c-b1ba-4ff0-a8a0-c3893c571736"
}