IGVFDS6787YPNQ

{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS6787YPNQ/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS6787YPNQ",
    "aliases": [
        "gary-hon:CM_Pilot_2_Lenti_sgRNA_LW267"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS6787YPNQ](/auxiliary-sets/IGVFDS6787YPNQ/) has sequence file(s) [IGVFFI7677YUQR](/sequence-files/IGVFFI7677YUQR/), [IGVFFI9760OIHQ](/sequence-files/IGVFFI9760OIHQ/), [IGVFFI3213XORW](/sequence-files/IGVFFI3213XORW/), [IGVFFI7835NCQX](/sequence-files/IGVFFI7835NCQX/) 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/IGVFDS6787YPNQ/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS6787YPNQ](/auxiliary-sets/IGVFDS6787YPNQ/) has sequence file(s): [IGVFFI7677YUQR](/sequence-files/IGVFFI7677YUQR/), [IGVFFI9760OIHQ](/sequence-files/IGVFFI9760OIHQ/), [IGVFFI3213XORW](/sequence-files/IGVFFI3213XORW/), [IGVFFI7835NCQX](/sequence-files/IGVFFI7835NCQX/) 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/IGVFDS6787YPNQ/"
            }
        ]
    },
    "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": "2024-02-15T23:36:02.669622+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/IGVFFI7677YUQR/",
            "accession": "IGVFFI7677YUQR",
            "aliases": [
                "gary-hon:LW267B_1_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-20T20:40:09.598456+00:00",
            "file_format": "fastq",
            "file_size": 240464425,
            "href": "/sequence-files/IGVFFI7677YUQR/@@download/IGVFFI7677YUQR.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/02/20/e4bea2d1-9cb0-4d67-bbeb-b73d03968575/IGVFFI7677YUQR.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0010963/",
            "status": "preview",
            "submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-07-07-McDermott-NextSeq.10X.run1.sgRNA_HTO/2023-07-07/outs/fastq_path/AACV7CFM5/LW267B_S7_L001_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9760OIHQ/",
            "accession": "IGVFFI9760OIHQ",
            "aliases": [
                "gary-hon:LW267B_1_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-20T20:40:15.616256+00:00",
            "file_format": "fastq",
            "file_size": 263698472,
            "href": "/sequence-files/IGVFFI9760OIHQ/@@download/IGVFFI9760OIHQ.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/02/20/1cf5b9d6-ea6b-4fd0-a375-fd1c45a99279/IGVFFI9760OIHQ.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0010963/",
            "status": "preview",
            "submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-07-07-McDermott-NextSeq.10X.run1.sgRNA_HTO/2023-07-07/outs/fastq_path/AACV7CFM5/LW267B_S7_L001_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3213XORW/",
            "accession": "IGVFFI3213XORW",
            "aliases": [
                "gary-hon:LW267B_1_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-20T20:40:21.812244+00:00",
            "file_format": "fastq",
            "file_size": 811343256,
            "href": "/sequence-files/IGVFFI3213XORW/@@download/IGVFFI3213XORW.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/02/20/95b7ff07-97b2-40fc-a6ed-99e78aca0b43/IGVFFI3213XORW.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0010963/",
            "status": "preview",
            "submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-07-07-McDermott-NextSeq.10X.run1.sgRNA_HTO/2023-07-07/outs/fastq_path/AACV7CFM5/LW267B_S7_L001_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI7835NCQX/",
            "accession": "IGVFFI7835NCQX",
            "aliases": [
                "gary-hon:LW267B_1_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-20T20:40:32.873379+00:00",
            "file_format": "fastq",
            "file_size": 1330463815,
            "href": "/sequence-files/IGVFFI7835NCQX/@@download/IGVFFI7835NCQX.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/02/20/23ab9ac5-c1fc-4eaa-826d-c237a51c5b55/IGVFFI7835NCQX.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0010963/",
            "status": "preview",
            "submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-07-07-McDermott-NextSeq.10X.run1.sgRNA_HTO/2023-07-07/outs/fastq_path/AACV7CFM5/LW267B_S7_L001_R2_001.fastq.gz",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS4003HZAB/"
    ],
    "lab": {
        "@id": "/labs/gary-hon/",
        "title": "Gary Hon, UT"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS4088YJYC/",
            "accession": "IGVFDS4088YJYC",
            "aliases": [
                "gary-hon:CM_Pilot_2_Lenti_RNA_LW267"
            ],
            "preferred_assay_title": "Perturb-seq",
            "status": "preview"
        }
    ],
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM5628VVVG/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM5628VVVG",
            "aliases": [
                "nikhil-munshi:differentited_WTC11_CM_Pilot1_Lenti_LW267"
            ],
            "classifications": [
                "differentiated cell specimen"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS9629YZLO/"
            ],
            "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_LW267), 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": "2024-02-20T20:40:09.598456+00:00",
    "summary": "gRNA sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "25bce165-5ca8-4db2-8b48-d4ea25f813dc"
}