IGVFDS4926IAGY

{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS4926IAGY/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS4926IAGY",
    "aliases": [
        "gary-hon:CM_Pilot_2_Lenti_HTO_LW264"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS4926IAGY](/auxiliary-sets/IGVFDS4926IAGY/) has sequence file(s) [IGVFFI5091VQUO](/sequence-files/IGVFFI5091VQUO/), [IGVFFI9705OPKD](/sequence-files/IGVFFI9705OPKD/), [IGVFFI9390TIHO](/sequence-files/IGVFFI9390TIHO/), [IGVFFI3694DSSY](/sequence-files/IGVFFI3694DSSY/) 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/IGVFDS4926IAGY/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS4926IAGY](/auxiliary-sets/IGVFDS4926IAGY/) has sequence file(s): [IGVFFI5091VQUO](/sequence-files/IGVFFI5091VQUO/), [IGVFFI9705OPKD](/sequence-files/IGVFFI9705OPKD/), [IGVFFI9390TIHO](/sequence-files/IGVFFI9390TIHO/), [IGVFFI3694DSSY](/sequence-files/IGVFFI3694DSSY/) 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/IGVFDS4926IAGY/"
            }
        ]
    },
    "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": "2024-02-15T23:35:55.560836+00:00",
    "donors": [
        {
            "@id": "/human-donors/IGVFDO1756PPKO/",
            "accession": "IGVFDO1756PPKO",
            "aliases": [
                "igvf:donor_of_WTC11"
            ],
            "sex": "male",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "file_set_type": "cell hashing barcode sequencing",
    "files": [
        {
            "@id": "/sequence-files/IGVFFI5091VQUO/",
            "accession": "IGVFFI5091VQUO",
            "aliases": [
                "gary-hon:LW264C_1_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-20T20:37:24.141793+00:00",
            "file_format": "fastq",
            "file_size": 133554747,
            "href": "/sequence-files/IGVFFI5091VQUO/@@download/IGVFFI5091VQUO.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/02/20/e18cb2ea-82d5-410a-874a-5076ccb4b1fd/IGVFFI5091VQUO.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/LW264C_S12_L001_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9705OPKD/",
            "accession": "IGVFFI9705OPKD",
            "aliases": [
                "gary-hon:LW264C_1_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-20T20:37:42.334137+00:00",
            "file_format": "fastq",
            "file_size": 913843143,
            "href": "/sequence-files/IGVFFI9705OPKD/@@download/IGVFFI9705OPKD.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/02/20/b6357471-d023-4e20-b0cf-c79d336789bb/IGVFFI9705OPKD.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/LW264C_S12_L001_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9390TIHO/",
            "accession": "IGVFFI9390TIHO",
            "aliases": [
                "gary-hon:LW264C_1_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-20T20:37:34.889669+00:00",
            "file_format": "fastq",
            "file_size": 349501917,
            "href": "/sequence-files/IGVFFI9390TIHO/@@download/IGVFFI9390TIHO.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/02/20/e1d9dbb2-2837-404b-b9f4-9bf0f09e87e2/IGVFFI9390TIHO.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/LW264C_S12_L001_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3694DSSY/",
            "accession": "IGVFFI3694DSSY",
            "aliases": [
                "gary-hon:LW264C_1_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-20T20:37:29.635001+00:00",
            "file_format": "fastq",
            "file_size": 139874124,
            "href": "/sequence-files/IGVFFI3694DSSY/@@download/IGVFFI3694DSSY.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/02/20/99e7dab3-96d1-4544-af91-4d968ae45d47/IGVFFI3694DSSY.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/LW264C_S12_L001_I2_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/IGVFDS6054GEKL/",
            "accession": "IGVFDS6054GEKL",
            "aliases": [
                "gary-hon:CM_Pilot_2_Lenti_RNA_LW264"
            ],
            "preferred_assay_title": "Perturb-seq",
            "status": "preview"
        }
    ],
    "notes": "File_set_type enum cell hashing has been renamed to be cell hashing barcode sequencing.",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM0981UTUA/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM0981UTUA",
            "aliases": [
                "nikhil-munshi:differentited_WTC11_CM_Pilot1_Lenti_LW264"
            ],
            "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_LW264), 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": "2024-02-20T20:37:24.141793+00:00",
    "summary": "cell hashing barcode sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "ae9912d2-7108-499e-9b31-02806794315c"
}