IGVFDS2612LSTD

{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS2612LSTD/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS2612LSTD",
    "aliases": [
        "gary-hon:TF_Perturb_Seq_Pilot_Lenti_NPC_sgRNA_LW281"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS2612LSTD](/auxiliary-sets/IGVFDS2612LSTD/) has sequence file(s) [IGVFFI6611BGPK](/sequence-files/IGVFFI6611BGPK/), [IGVFFI4582VNCZ](/sequence-files/IGVFFI4582VNCZ/), [IGVFFI1807ZQQP](/sequence-files/IGVFFI1807ZQQP/), [IGVFFI6515ZKTF](/sequence-files/IGVFFI6515ZKTF/), [IGVFFI4919JJPZ](/sequence-files/IGVFFI4919JJPZ/), [IGVFFI8349NVKT](/sequence-files/IGVFFI8349NVKT/), [IGVFFI5164GGZB](/sequence-files/IGVFFI5164GGZB/), [IGVFFI4061QSKL](/sequence-files/IGVFFI4061QSKL/) 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/IGVFDS2612LSTD/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS2612LSTD](/auxiliary-sets/IGVFDS2612LSTD/) has sequence file(s): [IGVFFI6611BGPK](/sequence-files/IGVFFI6611BGPK/), [IGVFFI4582VNCZ](/sequence-files/IGVFFI4582VNCZ/), [IGVFFI1807ZQQP](/sequence-files/IGVFFI1807ZQQP/), [IGVFFI6515ZKTF](/sequence-files/IGVFFI6515ZKTF/), [IGVFFI4919JJPZ](/sequence-files/IGVFFI4919JJPZ/), [IGVFFI8349NVKT](/sequence-files/IGVFFI8349NVKT/), [IGVFFI5164GGZB](/sequence-files/IGVFFI5164GGZB/), [IGVFFI4061QSKL](/sequence-files/IGVFFI4061QSKL/) 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/IGVFDS2612LSTD/"
            }
        ]
    },
    "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": "2024-02-29T16:49:37.703831+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/IGVFFI6611BGPK/",
            "accession": "IGVFFI6611BGPK",
            "aliases": [
                "gary-hon:LW281B-3_2_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:17:06.238498+00:00",
            "file_format": "fastq",
            "file_size": 586933448,
            "href": "/sequence-files/IGVFFI6611BGPK/@@download/IGVFFI6611BGPK.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/01/15e25596-3605-4c54-944f-cf7f1004e20e/IGVFFI6611BGPK.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/LW281B-3_S27_L002_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI4582VNCZ/",
            "accession": "IGVFFI4582VNCZ",
            "aliases": [
                "gary-hon:LW281B-3_2_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:16:46.744625+00:00",
            "file_format": "fastq",
            "file_size": 193538045,
            "href": "/sequence-files/IGVFFI4582VNCZ/@@download/IGVFFI4582VNCZ.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/01/c9e219ce-63ad-4bb9-b892-a3e82555837f/IGVFFI4582VNCZ.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/LW281B-3_S27_L002_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI1807ZQQP/",
            "accession": "IGVFFI1807ZQQP",
            "aliases": [
                "gary-hon:LW281B-3_1_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:16:28.589903+00:00",
            "file_format": "fastq",
            "file_size": 582616929,
            "href": "/sequence-files/IGVFFI1807ZQQP/@@download/IGVFFI1807ZQQP.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/01/0e688549-7b9f-424a-8018-852825133dbc/IGVFFI1807ZQQP.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/LW281B-3_S27_L001_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI6515ZKTF/",
            "accession": "IGVFFI6515ZKTF",
            "aliases": [
                "gary-hon:LW281B-3_1_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:16:23.329751+00:00",
            "file_format": "fastq",
            "file_size": 181647966,
            "href": "/sequence-files/IGVFFI6515ZKTF/@@download/IGVFFI6515ZKTF.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/01/d2924814-a516-40d2-8adb-3669f34c7192/IGVFFI6515ZKTF.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/LW281B-3_S27_L001_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI4919JJPZ/",
            "accession": "IGVFFI4919JJPZ",
            "aliases": [
                "gary-hon:LW281B-3_1_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:16:37.919712+00:00",
            "file_format": "fastq",
            "file_size": 614190993,
            "href": "/sequence-files/IGVFFI4919JJPZ/@@download/IGVFFI4919JJPZ.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/01/f9baa631-ca13-4779-8e87-48fdad0b1c37/IGVFFI4919JJPZ.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/LW281B-3_S27_L001_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8349NVKT/",
            "accession": "IGVFFI8349NVKT",
            "aliases": [
                "gary-hon:LW281B-3_1_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:16:17.730047+00:00",
            "file_format": "fastq",
            "file_size": 204112954,
            "href": "/sequence-files/IGVFFI8349NVKT/@@download/IGVFFI8349NVKT.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/01/d9578b2c-beaa-4c70-a433-67bc7e3fe8f3/IGVFFI8349NVKT.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/LW281B-3_S27_L001_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI5164GGZB/",
            "accession": "IGVFFI5164GGZB",
            "aliases": [
                "gary-hon:LW281B-3_2_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:16:57.478554+00:00",
            "file_format": "fastq",
            "file_size": 563712755,
            "href": "/sequence-files/IGVFFI5164GGZB/@@download/IGVFFI5164GGZB.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/01/3211f4fa-fb32-4ba2-805c-e2487485fe02/IGVFFI5164GGZB.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/LW281B-3_S27_L002_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI4061QSKL/",
            "accession": "IGVFFI4061QSKL",
            "aliases": [
                "gary-hon:LW281B-3_2_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:16:52.249456+00:00",
            "file_format": "fastq",
            "file_size": 173951364,
            "href": "/sequence-files/IGVFFI4061QSKL/@@download/IGVFFI4061QSKL.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/01/4d9995c0-5185-440a-8b89-ff90e271e739/IGVFFI4061QSKL.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/LW281B-3_S27_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/IGVFDS2143BSOH/",
            "accession": "IGVFDS2143BSOH",
            "aliases": [
                "gary-hon:TF_Perturb_Seq_Pilot_Lenti_NPC_LW281"
            ],
            "preferred_assay_title": "Perturb-seq",
            "status": "preview"
        }
    ],
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM0956HKRJ/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM0956HKRJ",
            "aliases": [
                "nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_NPC_Lenti_LW281"
            ],
            "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_LW281), 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": "2024-03-01T17:16:17.730047+00:00",
    "summary": "gRNA sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "39a74093-2660-47a2-9d6b-49eb043722bb"
}