IGVFDS3465KEWH

{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS3465KEWH/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS3465KEWH",
    "aliases": [
        "gary-hon:TF_Perturb_Seq_Pilot_Lenti_iPSC_HTO_LW286"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS3465KEWH](/auxiliary-sets/IGVFDS3465KEWH/) has sequence file(s) [IGVFFI3046CEDS](/sequence-files/IGVFFI3046CEDS/), [IGVFFI2095GWCE](/sequence-files/IGVFFI2095GWCE/), [IGVFFI4014VOTR](/sequence-files/IGVFFI4014VOTR/), [IGVFFI6603ZNLC](/sequence-files/IGVFFI6603ZNLC/) 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/IGVFDS3465KEWH/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS3465KEWH](/auxiliary-sets/IGVFDS3465KEWH/) has sequence file(s): [IGVFFI3046CEDS](/sequence-files/IGVFFI3046CEDS/), [IGVFFI2095GWCE](/sequence-files/IGVFFI2095GWCE/), [IGVFFI4014VOTR](/sequence-files/IGVFFI4014VOTR/), [IGVFFI6603ZNLC](/sequence-files/IGVFFI6603ZNLC/) 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/IGVFDS3465KEWH/"
            }
        ]
    },
    "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": "2024-02-21T21:22:37.791237+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/IGVFFI3046CEDS/",
            "accession": "IGVFFI3046CEDS",
            "aliases": [
                "gary-hon:LW286C_1_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-04T20:03:59.339508+00:00",
            "file_format": "fastq",
            "file_size": 258677637,
            "href": "/sequence-files/IGVFFI3046CEDS/@@download/IGVFFI3046CEDS.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/04/3dc76a1f-534c-47c8-beb5-cdd004f6aecf/IGVFFI3046CEDS.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//LW286C_S5_L001_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI2095GWCE/",
            "accession": "IGVFFI2095GWCE",
            "aliases": [
                "gary-hon:LW286C_1_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-04T20:03:46.139107+00:00",
            "file_format": "fastq",
            "file_size": 43260257,
            "href": "/sequence-files/IGVFFI2095GWCE/@@download/IGVFFI2095GWCE.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/04/5233b62c-9305-413d-8773-da4ef8a15eeb/IGVFFI2095GWCE.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//LW286C_S5_L001_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI4014VOTR/",
            "accession": "IGVFFI4014VOTR",
            "aliases": [
                "gary-hon:LW286C_1_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-04T20:03:50.221142+00:00",
            "file_format": "fastq",
            "file_size": 51112022,
            "href": "/sequence-files/IGVFFI4014VOTR/@@download/IGVFFI4014VOTR.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/04/57790cdc-80bf-498d-bfd6-c9e28e4379b1/IGVFFI4014VOTR.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//LW286C_S5_L001_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI6603ZNLC/",
            "accession": "IGVFFI6603ZNLC",
            "aliases": [
                "gary-hon:LW286C_1_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-04T20:03:54.413800+00:00",
            "file_format": "fastq",
            "file_size": 130696069,
            "href": "/sequence-files/IGVFFI6603ZNLC/@@download/IGVFFI6603ZNLC.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/04/75129726-2a03-4ec8-8ccf-705b8a8aae1d/IGVFFI6603ZNLC.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//LW286C_S5_L001_R1_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/IGVFDS5429CXNB/",
            "accession": "IGVFDS5429CXNB",
            "aliases": [
                "gary-hon:TF_Perturb_Seq_Pilot_Lenti_iPSC_LW286"
            ],
            "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/IGVFSM2726ORRN/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM2726ORRN",
            "aliases": [
                "nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_iPSC_Lenti_LW286"
            ],
            "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_LW286), 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": "2024-03-04T20:03:46.139107+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": "ba93f970-aa8e-4e39-9d38-89526d6e31b2"
}