IGVFDS4262EBDF

{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS4262EBDF/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS4262EBDF",
    "aliases": [
        "gary-hon:TF_Perturb_Seq_Pilot_Lenti_NPC_sgRNA_LW283"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS4262EBDF](/auxiliary-sets/IGVFDS4262EBDF/) has sequence file(s) [IGVFFI1665CADL](/sequence-files/IGVFFI1665CADL/), [IGVFFI3519VNMQ](/sequence-files/IGVFFI3519VNMQ/), [IGVFFI2060GRST](/sequence-files/IGVFFI2060GRST/), [IGVFFI8010OOFR](/sequence-files/IGVFFI8010OOFR/), [IGVFFI9758LRXH](/sequence-files/IGVFFI9758LRXH/), [IGVFFI6625XXQD](/sequence-files/IGVFFI6625XXQD/), [IGVFFI1976NIRG](/sequence-files/IGVFFI1976NIRG/), [IGVFFI1491BIMR](/sequence-files/IGVFFI1491BIMR/) 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/IGVFDS4262EBDF/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS4262EBDF](/auxiliary-sets/IGVFDS4262EBDF/) has sequence file(s): [IGVFFI1665CADL](/sequence-files/IGVFFI1665CADL/), [IGVFFI3519VNMQ](/sequence-files/IGVFFI3519VNMQ/), [IGVFFI2060GRST](/sequence-files/IGVFFI2060GRST/), [IGVFFI8010OOFR](/sequence-files/IGVFFI8010OOFR/), [IGVFFI9758LRXH](/sequence-files/IGVFFI9758LRXH/), [IGVFFI6625XXQD](/sequence-files/IGVFFI6625XXQD/), [IGVFFI1976NIRG](/sequence-files/IGVFFI1976NIRG/), [IGVFFI1491BIMR](/sequence-files/IGVFFI1491BIMR/) 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/IGVFDS4262EBDF/"
            }
        ]
    },
    "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": "2024-02-29T16:49:43.565223+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/IGVFFI1665CADL/",
            "accession": "IGVFFI1665CADL",
            "aliases": [
                "gary-hon:LW283B-3_1_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:21:44.098772+00:00",
            "file_format": "fastq",
            "file_size": 208578277,
            "href": "/sequence-files/IGVFFI1665CADL/@@download/IGVFFI1665CADL.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/01/2d5ed479-154e-4dda-8e1c-02a1e8c11e5c/IGVFFI1665CADL.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/LW283B-3_S29_L001_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3519VNMQ/",
            "accession": "IGVFFI3519VNMQ",
            "aliases": [
                "gary-hon:LW283B-3_2_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:22:20.429635+00:00",
            "file_format": "fastq",
            "file_size": 561064454,
            "href": "/sequence-files/IGVFFI3519VNMQ/@@download/IGVFFI3519VNMQ.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/01/8fb1284e-81cc-44fe-98d9-8859b9049bbb/IGVFFI3519VNMQ.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/LW283B-3_S29_L002_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI2060GRST/",
            "accession": "IGVFFI2060GRST",
            "aliases": [
                "gary-hon:LW283B-3_1_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:21:38.396125+00:00",
            "file_format": "fastq",
            "file_size": 210628860,
            "href": "/sequence-files/IGVFFI2060GRST/@@download/IGVFFI2060GRST.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/01/d1379e90-1f4d-449e-8042-2c32b42de5a6/IGVFFI2060GRST.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/LW283B-3_S29_L001_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8010OOFR/",
            "accession": "IGVFFI8010OOFR",
            "aliases": [
                "gary-hon:LW283B-3_1_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:22:00.275103+00:00",
            "file_format": "fastq",
            "file_size": 634195130,
            "href": "/sequence-files/IGVFFI8010OOFR/@@download/IGVFFI8010OOFR.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/01/ecc1137b-b176-4c30-a472-a008497b23f7/IGVFFI8010OOFR.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/LW283B-3_S29_L001_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9758LRXH/",
            "accession": "IGVFFI9758LRXH",
            "aliases": [
                "gary-hon:LW283B-3_2_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:22:09.366212+00:00",
            "file_format": "fastq",
            "file_size": 190782618,
            "href": "/sequence-files/IGVFFI9758LRXH/@@download/IGVFFI9758LRXH.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/01/1cb03e63-9104-44e9-bd38-81b3cfb9b0d6/IGVFFI9758LRXH.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/LW283B-3_S29_L002_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI6625XXQD/",
            "accession": "IGVFFI6625XXQD",
            "aliases": [
                "gary-hon:LW283B-3_2_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:22:29.106457+00:00",
            "file_format": "fastq",
            "file_size": 575844907,
            "href": "/sequence-files/IGVFFI6625XXQD/@@download/IGVFFI6625XXQD.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/01/8e683f19-cfd0-4ec2-a6bb-ddd94bcf18d1/IGVFFI6625XXQD.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/LW283B-3_S29_L002_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI1976NIRG/",
            "accession": "IGVFFI1976NIRG",
            "aliases": [
                "gary-hon:LW283B-3_1_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:21:49.771418+00:00",
            "file_format": "fastq",
            "file_size": 609498759,
            "href": "/sequence-files/IGVFFI1976NIRG/@@download/IGVFFI1976NIRG.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/01/a070c17b-73b4-4928-9a96-020046b22578/IGVFFI1976NIRG.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/LW283B-3_S29_L001_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI1491BIMR/",
            "accession": "IGVFFI1491BIMR",
            "aliases": [
                "gary-hon:LW283B-3_2_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:22:14.962675+00:00",
            "file_format": "fastq",
            "file_size": 195020187,
            "href": "/sequence-files/IGVFFI1491BIMR/@@download/IGVFFI1491BIMR.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/01/64f34e4b-cb4a-4429-935c-58d6a6a98f98/IGVFFI1491BIMR.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/LW283B-3_S29_L002_I2_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/IGVFDS4028IRAH/",
            "accession": "IGVFDS4028IRAH",
            "aliases": [
                "gary-hon:TF_Perturb_Seq_Pilot_Lenti_NPC_LW283"
            ],
            "preferred_assay_title": "Perturb-seq",
            "status": "preview"
        }
    ],
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM8464JMJS/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM8464JMJS",
            "aliases": [
                "nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_NPC_Lenti_LW283"
            ],
            "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_LW283), 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": "2024-03-01T17:21:38.396125+00:00",
    "summary": "gRNA sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "f3917bb6-5094-49bc-ab07-cb8f10778ec0"
}