IGVFDS1937JPZI

{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS1937JPZI/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS1937JPZI",
    "aliases": [
        "gary-hon:TF_Perturb_Seq_Pilot_Lenti_iPSC_sgRNA_LW287"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS1937JPZI](/auxiliary-sets/IGVFDS1937JPZI/) has sequence file(s) [IGVFFI8385HABJ](/sequence-files/IGVFFI8385HABJ/), [IGVFFI3275ZEBW](/sequence-files/IGVFFI3275ZEBW/), [IGVFFI1518BMVF](/sequence-files/IGVFFI1518BMVF/), [IGVFFI7286ZUUS](/sequence-files/IGVFFI7286ZUUS/) 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/IGVFDS1937JPZI/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS1937JPZI](/auxiliary-sets/IGVFDS1937JPZI/) has sequence file(s): [IGVFFI8385HABJ](/sequence-files/IGVFFI8385HABJ/), [IGVFFI3275ZEBW](/sequence-files/IGVFFI3275ZEBW/), [IGVFFI1518BMVF](/sequence-files/IGVFFI1518BMVF/), [IGVFFI7286ZUUS](/sequence-files/IGVFFI7286ZUUS/) 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/IGVFDS1937JPZI/"
            }
        ]
    },
    "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": "2024-02-21T21:22:39.581301+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/IGVFFI8385HABJ/",
            "accession": "IGVFFI8385HABJ",
            "aliases": [
                "gary-hon:LW287B_1_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-04T20:04:12.498570+00:00",
            "file_format": "fastq",
            "file_size": 375700900,
            "href": "/sequence-files/IGVFFI8385HABJ/@@download/IGVFFI8385HABJ.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/04/f00dd93c-e367-4114-b933-fad67de66f67/IGVFFI8385HABJ.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0010963/",
            "status": "preview",
            "submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-11-03-McDermott-NextSeq.10X.run2.10X/2023-11-03/outs/fastq_path/AAF3JCVM5//LW287B_S2_L001_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3275ZEBW/",
            "accession": "IGVFFI3275ZEBW",
            "aliases": [
                "gary-hon:LW287B_1_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-04T20:04:34.151158+00:00",
            "file_format": "fastq",
            "file_size": 1296422121,
            "href": "/sequence-files/IGVFFI3275ZEBW/@@download/IGVFFI3275ZEBW.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/04/f2cdf4bd-feb7-41e9-8e61-541ad7d989ac/IGVFFI3275ZEBW.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0010963/",
            "status": "preview",
            "submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-11-03-McDermott-NextSeq.10X.run2.10X/2023-11-03/outs/fastq_path/AAF3JCVM5//LW287B_S2_L001_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI1518BMVF/",
            "accession": "IGVFFI1518BMVF",
            "aliases": [
                "gary-hon:LW287B_1_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-04T20:04:19.656655+00:00",
            "file_format": "fastq",
            "file_size": 1229341418,
            "href": "/sequence-files/IGVFFI1518BMVF/@@download/IGVFFI1518BMVF.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/04/7170fbb6-dff0-4b57-8a43-7e727386d9a3/IGVFFI1518BMVF.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0010963/",
            "status": "preview",
            "submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-11-03-McDermott-NextSeq.10X.run2.10X/2023-11-03/outs/fastq_path/AAF3JCVM5//LW287B_S2_L001_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI7286ZUUS/",
            "accession": "IGVFFI7286ZUUS",
            "aliases": [
                "gary-hon:LW287B_1_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-04T20:04:05.436529+00:00",
            "file_format": "fastq",
            "file_size": 369135930,
            "href": "/sequence-files/IGVFFI7286ZUUS/@@download/IGVFFI7286ZUUS.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/04/1d415f05-b619-470c-bca5-6e6f3a5d2011/IGVFFI7286ZUUS.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0010963/",
            "status": "preview",
            "submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-11-03-McDermott-NextSeq.10X.run2.10X/2023-11-03/outs/fastq_path/AAF3JCVM5//LW287B_S2_L001_I1_001.fastq.gz",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS7340YDHF/"
    ],
    "lab": {
        "@id": "/labs/gary-hon/",
        "title": "Gary Hon, UT"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS2692VBHQ/",
            "accession": "IGVFDS2692VBHQ",
            "aliases": [
                "gary-hon:TF_Perturb_Seq_Pilot_Lenti_iPSC_LW287"
            ],
            "preferred_assay_title": "Perturb-seq",
            "status": "preview"
        }
    ],
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM1153INDY/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM1153INDY",
            "aliases": [
                "nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_iPSC_Lenti_LW287"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS2302LCEO/"
            ],
            "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) cell line (cellular sub pool: subpool_LW287), male, Homo sapiens modified with CRISPRi Sp-dCas9, transduced (lentivirus) with a guide library",
            "taxa": "Homo sapiens"
        }
    ],
    "schema_version": "12",
    "status": "preview",
    "submitted_by": {
        "@id": "/users/b05645f1-2d56-4a5e-b272-4601e555a3fa/",
        "title": "Mpathi Nzima"
    },
    "submitted_files_timestamp": "2024-03-04T20:04:05.436529+00:00",
    "summary": "gRNA sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "1de99972-e596-423e-84ad-0d3cf37bf659"
}