IGVFDS5339UNRP

{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS5339UNRP/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS5339UNRP",
    "aliases": [
        "gary-hon:TF_Perturb_Seq_Pilot_Lenti_NPC_sgRNA_LW284"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS5339UNRP](/auxiliary-sets/IGVFDS5339UNRP/) has sequence file(s) [IGVFFI2235WFJR](/sequence-files/IGVFFI2235WFJR/), [IGVFFI3240FCBJ](/sequence-files/IGVFFI3240FCBJ/), [IGVFFI5213ZPGN](/sequence-files/IGVFFI5213ZPGN/), [IGVFFI7051FHND](/sequence-files/IGVFFI7051FHND/), [IGVFFI8462WRNK](/sequence-files/IGVFFI8462WRNK/), [IGVFFI1428MDRF](/sequence-files/IGVFFI1428MDRF/), [IGVFFI8576TNCS](/sequence-files/IGVFFI8576TNCS/), [IGVFFI9815IGUY](/sequence-files/IGVFFI9815IGUY/) 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/IGVFDS5339UNRP/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS5339UNRP](/auxiliary-sets/IGVFDS5339UNRP/) has sequence file(s): [IGVFFI2235WFJR](/sequence-files/IGVFFI2235WFJR/), [IGVFFI3240FCBJ](/sequence-files/IGVFFI3240FCBJ/), [IGVFFI5213ZPGN](/sequence-files/IGVFFI5213ZPGN/), [IGVFFI7051FHND](/sequence-files/IGVFFI7051FHND/), [IGVFFI8462WRNK](/sequence-files/IGVFFI8462WRNK/), [IGVFFI1428MDRF](/sequence-files/IGVFFI1428MDRF/), [IGVFFI8576TNCS](/sequence-files/IGVFFI8576TNCS/), [IGVFFI9815IGUY](/sequence-files/IGVFFI9815IGUY/) 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/IGVFDS5339UNRP/"
            }
        ]
    },
    "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": "2024-02-29T16:49:45.692648+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/IGVFFI2235WFJR/",
            "accession": "IGVFFI2235WFJR",
            "aliases": [
                "gary-hon:LW284B-3_1_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:24:18.297553+00:00",
            "file_format": "fastq",
            "file_size": 196686811,
            "href": "/sequence-files/IGVFFI2235WFJR/@@download/IGVFFI2235WFJR.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/01/6bffc524-e26c-472a-b847-dc644ad8e642/IGVFFI2235WFJR.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/LW284B-3_S30_L001_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3240FCBJ/",
            "accession": "IGVFFI3240FCBJ",
            "aliases": [
                "gary-hon:LW284B-3_1_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:24:23.943777+00:00",
            "file_format": "fastq",
            "file_size": 511568132,
            "href": "/sequence-files/IGVFFI3240FCBJ/@@download/IGVFFI3240FCBJ.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/01/194064f9-308c-49cd-8ba5-b49ead4e7542/IGVFFI3240FCBJ.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/LW284B-3_S30_L001_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI5213ZPGN/",
            "accession": "IGVFFI5213ZPGN",
            "aliases": [
                "gary-hon:LW284B-3_1_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:24:32.498309+00:00",
            "file_format": "fastq",
            "file_size": 530503031,
            "href": "/sequence-files/IGVFFI5213ZPGN/@@download/IGVFFI5213ZPGN.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/01/58bd3bf4-b1b4-4544-baa4-cb2d8a7642e4/IGVFFI5213ZPGN.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/LW284B-3_S30_L001_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI7051FHND/",
            "accession": "IGVFFI7051FHND",
            "aliases": [
                "gary-hon:LW284B-3_2_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:25:03.088307+00:00",
            "file_format": "fastq",
            "file_size": 495543128,
            "href": "/sequence-files/IGVFFI7051FHND/@@download/IGVFFI7051FHND.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/01/4f2ec9ce-a6fc-413a-9d43-8b4324ebb20f/IGVFFI7051FHND.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/LW284B-3_S30_L002_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8462WRNK/",
            "accession": "IGVFFI8462WRNK",
            "aliases": [
                "gary-hon:LW284B-3_2_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:24:41.044282+00:00",
            "file_format": "fastq",
            "file_size": 162053922,
            "href": "/sequence-files/IGVFFI8462WRNK/@@download/IGVFFI8462WRNK.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/01/ab8c0269-7397-4696-a4d9-3a25e75af909/IGVFFI8462WRNK.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/LW284B-3_S30_L002_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI1428MDRF/",
            "accession": "IGVFFI1428MDRF",
            "aliases": [
                "gary-hon:LW284B-3_2_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:24:46.375732+00:00",
            "file_format": "fastq",
            "file_size": 184165125,
            "href": "/sequence-files/IGVFFI1428MDRF/@@download/IGVFFI1428MDRF.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/01/447132ed-e319-4612-888c-65c7eb460800/IGVFFI1428MDRF.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/LW284B-3_S30_L002_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8576TNCS/",
            "accession": "IGVFFI8576TNCS",
            "aliases": [
                "gary-hon:LW284B-3_2_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:24:55.035785+00:00",
            "file_format": "fastq",
            "file_size": 485071070,
            "href": "/sequence-files/IGVFFI8576TNCS/@@download/IGVFFI8576TNCS.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/01/89a51af2-ed1e-49c4-b258-ce5bfa8b6d72/IGVFFI8576TNCS.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/LW284B-3_S30_L002_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9815IGUY/",
            "accession": "IGVFFI9815IGUY",
            "aliases": [
                "gary-hon:LW284B-3_1_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:24:12.594077+00:00",
            "file_format": "fastq",
            "file_size": 173529973,
            "href": "/sequence-files/IGVFFI9815IGUY/@@download/IGVFFI9815IGUY.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/01/b246c6e3-fd5c-4e6a-8ca4-fe70fa212749/IGVFFI9815IGUY.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/LW284B-3_S30_L001_I1_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/IGVFDS0657YBVN/",
            "accession": "IGVFDS0657YBVN",
            "aliases": [
                "gary-hon:TF_Perturb_Seq_Pilot_Lenti_NPC_LW284"
            ],
            "preferred_assay_title": "Perturb-seq",
            "status": "preview"
        }
    ],
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM2597WGYB/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM2597WGYB",
            "aliases": [
                "nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_NPC_Lenti_LW284"
            ],
            "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_LW284), 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": "2024-03-01T17:24:12.594077+00:00",
    "summary": "gRNA sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "e36698e3-fe43-40f7-8d16-111e73bef39b"
}