IGVFDS7944GWTS

{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS7944GWTS/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS7944GWTS",
    "aliases": [
        "gary-hon:CM_Pilot_2_Lenti_sgRNA_LW266"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "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/"
            }
        ]
    },
    "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": "2024-02-15T23:36:00.617052+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/IGVFFI9006RKCZ/",
            "accession": "IGVFFI9006RKCZ",
            "aliases": [
                "gary-hon:LW266B_1_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-20T20:39:05.213782+00:00",
            "file_format": "fastq",
            "file_size": 293920622,
            "href": "/sequence-files/IGVFFI9006RKCZ/@@download/IGVFFI9006RKCZ.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/02/20/bf9f8d13-2fd0-4dda-b950-60c04fc23029/IGVFFI9006RKCZ.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/LW266B_S6_L001_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI0638VNPV/",
            "accession": "IGVFFI0638VNPV",
            "aliases": [
                "gary-hon:LW266B_1_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-20T20:39:12.000596+00:00",
            "file_format": "fastq",
            "file_size": 828798636,
            "href": "/sequence-files/IGVFFI0638VNPV/@@download/IGVFFI0638VNPV.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/02/20/b7392542-df68-4aae-a830-6c0cbb1fe739/IGVFFI0638VNPV.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/LW266B_S6_L001_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3275XOUB/",
            "accession": "IGVFFI3275XOUB",
            "aliases": [
                "gary-hon:LW266B_1_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-20T20:38:58.971691+00:00",
            "file_format": "fastq",
            "file_size": 242698174,
            "href": "/sequence-files/IGVFFI3275XOUB/@@download/IGVFFI3275XOUB.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/02/20/2c6009f5-9ca9-47c8-845f-abbc836f4df0/IGVFFI3275XOUB.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/LW266B_S6_L001_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI2007EPSH/",
            "accession": "IGVFFI2007EPSH",
            "aliases": [
                "gary-hon:LW266B_1_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-20T20:39:23.637568+00:00",
            "file_format": "fastq",
            "file_size": 1373273120,
            "href": "/sequence-files/IGVFFI2007EPSH/@@download/IGVFFI2007EPSH.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/02/20/9123d3c8-f6c5-46a1-91f0-3f20e6d50591/IGVFFI2007EPSH.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/LW266B_S6_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/IGVFDS5931MYJN/",
            "accession": "IGVFDS5931MYJN",
            "aliases": [
                "gary-hon:CM_Pilot_2_Lenti_RNA_LW266"
            ],
            "preferred_assay_title": "Perturb-seq",
            "status": "preview"
        }
    ],
    "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": [
                "/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_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": "12",
    "status": "preview",
    "submitted_by": {
        "@id": "/users/b05645f1-2d56-4a5e-b272-4601e555a3fa/",
        "title": "Mpathi Nzima"
    },
    "submitted_files_timestamp": "2024-02-20T20:38:58.971691+00:00",
    "summary": "gRNA sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "e3b952a4-aa67-48cb-aaa2-d62839596c82"
}