IGVFDS3567LQMB

{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS3567LQMB/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS3567LQMB",
    "aliases": [
        "gary-hon:TF_Perturb_Seq_Pilot_Lenti_NPC_HTO_LW282"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS3567LQMB](/auxiliary-sets/IGVFDS3567LQMB/) has sequence file(s) [IGVFFI1692PBQW](/sequence-files/IGVFFI1692PBQW/), [IGVFFI5482BVUW](/sequence-files/IGVFFI5482BVUW/), [IGVFFI9298IPBX](/sequence-files/IGVFFI9298IPBX/), [IGVFFI0409KOWK](/sequence-files/IGVFFI0409KOWK/), [IGVFFI3785WYDT](/sequence-files/IGVFFI3785WYDT/), [IGVFFI5436EVPV](/sequence-files/IGVFFI5436EVPV/), [IGVFFI2912RLLI](/sequence-files/IGVFFI2912RLLI/), [IGVFFI4099YBZW](/sequence-files/IGVFFI4099YBZW/) 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/IGVFDS3567LQMB/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS3567LQMB](/auxiliary-sets/IGVFDS3567LQMB/) has sequence file(s): [IGVFFI1692PBQW](/sequence-files/IGVFFI1692PBQW/), [IGVFFI5482BVUW](/sequence-files/IGVFFI5482BVUW/), [IGVFFI9298IPBX](/sequence-files/IGVFFI9298IPBX/), [IGVFFI0409KOWK](/sequence-files/IGVFFI0409KOWK/), [IGVFFI3785WYDT](/sequence-files/IGVFFI3785WYDT/), [IGVFFI5436EVPV](/sequence-files/IGVFFI5436EVPV/), [IGVFFI2912RLLI](/sequence-files/IGVFFI2912RLLI/), [IGVFFI4099YBZW](/sequence-files/IGVFFI4099YBZW/) 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/IGVFDS3567LQMB/"
            }
        ]
    },
    "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": "2024-02-29T16:49:42.163081+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/IGVFFI1692PBQW/",
            "accession": "IGVFFI1692PBQW",
            "aliases": [
                "gary-hon:LW282C_2_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:20:24.853473+00:00",
            "file_format": "fastq",
            "file_size": 393349835,
            "href": "/sequence-files/IGVFFI1692PBQW/@@download/IGVFFI1692PBQW.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/01/34371965-fc0f-460f-9ac2-28d751756a27/IGVFFI1692PBQW.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0010963/",
            "status": "preview",
            "submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW282C_S6_L002_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI5482BVUW/",
            "accession": "IGVFFI5482BVUW",
            "aliases": [
                "gary-hon:LW282C_1_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:19:48.002089+00:00",
            "file_format": "fastq",
            "file_size": 90462073,
            "href": "/sequence-files/IGVFFI5482BVUW/@@download/IGVFFI5482BVUW.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/01/ff7eefbf-9b3e-4484-baba-8591dd7d2e37/IGVFFI5482BVUW.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0010963/",
            "status": "preview",
            "submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW282C_S6_L001_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9298IPBX/",
            "accession": "IGVFFI9298IPBX",
            "aliases": [
                "gary-hon:LW282C_1_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:19:57.274288+00:00",
            "file_format": "fastq",
            "file_size": 206346812,
            "href": "/sequence-files/IGVFFI9298IPBX/@@download/IGVFFI9298IPBX.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/01/2dc1bcfd-dbff-4206-af56-bdfa9fbd7e28/IGVFFI9298IPBX.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0010963/",
            "status": "preview",
            "submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW282C_S6_L001_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI0409KOWK/",
            "accession": "IGVFFI0409KOWK",
            "aliases": [
                "gary-hon:LW282C_1_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:20:02.908423+00:00",
            "file_format": "fastq",
            "file_size": 423929610,
            "href": "/sequence-files/IGVFFI0409KOWK/@@download/IGVFFI0409KOWK.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/01/b11daee1-d1bc-4ce0-913e-476bf0c5deff/IGVFFI0409KOWK.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0010963/",
            "status": "preview",
            "submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW282C_S6_L001_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3785WYDT/",
            "accession": "IGVFFI3785WYDT",
            "aliases": [
                "gary-hon:LW282C_2_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:20:10.246303+00:00",
            "file_format": "fastq",
            "file_size": 84289667,
            "href": "/sequence-files/IGVFFI3785WYDT/@@download/IGVFFI3785WYDT.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/01/aab3fbc0-d849-4238-ae8b-46ccec1aa85f/IGVFFI3785WYDT.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0010963/",
            "status": "preview",
            "submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW282C_S6_L002_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI5436EVPV/",
            "accession": "IGVFFI5436EVPV",
            "aliases": [
                "gary-hon:LW282C_2_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:20:14.781715+00:00",
            "file_format": "fastq",
            "file_size": 85770859,
            "href": "/sequence-files/IGVFFI5436EVPV/@@download/IGVFFI5436EVPV.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/01/ab0c232c-5a85-485b-b87b-f034a4e8211a/IGVFFI5436EVPV.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0010963/",
            "status": "preview",
            "submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW282C_S6_L002_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI2912RLLI/",
            "accession": "IGVFFI2912RLLI",
            "aliases": [
                "gary-hon:LW282C_1_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:19:52.656142+00:00",
            "file_format": "fastq",
            "file_size": 91193292,
            "href": "/sequence-files/IGVFFI2912RLLI/@@download/IGVFFI2912RLLI.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/01/fdfe24d8-3b66-4a26-8d3b-ee01d493e126/IGVFFI2912RLLI.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0010963/",
            "status": "preview",
            "submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW282C_S6_L001_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI4099YBZW/",
            "accession": "IGVFFI4099YBZW",
            "aliases": [
                "gary-hon:LW282C_2_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:20:19.178355+00:00",
            "file_format": "fastq",
            "file_size": 192242176,
            "href": "/sequence-files/IGVFFI4099YBZW/@@download/IGVFFI4099YBZW.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/01/a451df1d-70bd-4b71-ada8-25ecc3fe8b5e/IGVFFI4099YBZW.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0010963/",
            "status": "preview",
            "submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW282C_S6_L002_R1_001.fastq.gz",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS1588TVKF/"
    ],
    "lab": {
        "@id": "/labs/gary-hon/",
        "title": "Gary Hon, UT"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS8810ABUD/",
            "accession": "IGVFDS8810ABUD",
            "aliases": [
                "gary-hon:TF_Perturb_Seq_Pilot_Lenti_NPC_LW282"
            ],
            "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/IGVFSM1288TQKF/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM1288TQKF",
            "aliases": [
                "nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_NPC_Lenti_LW282"
            ],
            "classifications": [
                "differentiated cell specimen"
            ],
            "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) differentiated cell specimen induced to neural stem cell for 20 days (cellular sub pool: subpool_LW282), male, Homo sapiens modified with CRISPRi Sp-dCas9, transduced (lentivirus) with a guide library",
            "targeted_sample_term": {
                "@id": "/sample-terms/CL_0000047/",
                "status": "preview",
                "term_name": "neural stem cell"
            },
            "taxa": "Homo sapiens"
        }
    ],
    "schema_version": "12",
    "status": "preview",
    "submitted_by": {
        "@id": "/users/b05645f1-2d56-4a5e-b272-4601e555a3fa/",
        "title": "Mpathi Nzima"
    },
    "submitted_files_timestamp": "2024-03-01T17:19:48.002089+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": "61960601-2019-48b6-98b6-5e516b4285b4"
}