IGVFDS0997MTQA

{
    "@context": "/terms/",
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    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS0997MTQA",
    "aliases": [
        "gary-hon:TF_Perturb_Seq_Pilot_Lenti_CM_sgRNA_LW279"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS0997MTQA](/auxiliary-sets/IGVFDS0997MTQA/) has sequence file(s) [IGVFFI5758JYDL](/sequence-files/IGVFFI5758JYDL/), [IGVFFI0808FCCO](/sequence-files/IGVFFI0808FCCO/), [IGVFFI7852BFOU](/sequence-files/IGVFFI7852BFOU/), [IGVFFI3938OJKT](/sequence-files/IGVFFI3938OJKT/), [IGVFFI9797JSJB](/sequence-files/IGVFFI9797JSJB/), [IGVFFI2834JYDA](/sequence-files/IGVFFI2834JYDA/), [IGVFFI7620POLB](/sequence-files/IGVFFI7620POLB/), [IGVFFI4290KTZN](/sequence-files/IGVFFI4290KTZN/) 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/IGVFDS0997MTQA/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS0997MTQA](/auxiliary-sets/IGVFDS0997MTQA/) has sequence file(s): [IGVFFI5758JYDL](/sequence-files/IGVFFI5758JYDL/), [IGVFFI0808FCCO](/sequence-files/IGVFFI0808FCCO/), [IGVFFI7852BFOU](/sequence-files/IGVFFI7852BFOU/), [IGVFFI3938OJKT](/sequence-files/IGVFFI3938OJKT/), [IGVFFI9797JSJB](/sequence-files/IGVFFI9797JSJB/), [IGVFFI2834JYDA](/sequence-files/IGVFFI2834JYDA/), [IGVFFI7620POLB](/sequence-files/IGVFFI7620POLB/), [IGVFFI4290KTZN](/sequence-files/IGVFFI4290KTZN/) 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/IGVFDS0997MTQA/"
            }
        ]
    },
    "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": "2024-02-21T21:01:50.759246+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",
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            "accession": "IGVFFI5758JYDL",
            "aliases": [
                "gary-hon:LW279B-3_1_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:11:11.419344+00:00",
            "file_format": "fastq",
            "file_size": 216775264,
            "href": "/sequence-files/IGVFFI5758JYDL/@@download/IGVFFI5758JYDL.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/01/f0bc43b0-d0f6-4ccb-a594-b38956147bba/IGVFFI5758JYDL.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/LW279B-3_S25_L001_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI0808FCCO/",
            "accession": "IGVFFI0808FCCO",
            "aliases": [
                "gary-hon:LW279B-3_2_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:11:46.602381+00:00",
            "file_format": "fastq",
            "file_size": 575050009,
            "href": "/sequence-files/IGVFFI0808FCCO/@@download/IGVFFI0808FCCO.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/01/035d7b43-aa37-4550-ae92-e597d7b6e9e2/IGVFFI0808FCCO.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/LW279B-3_S25_L002_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI7852BFOU/",
            "accession": "IGVFFI7852BFOU",
            "aliases": [
                "gary-hon:LW279B-3_2_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:11:55.358224+00:00",
            "file_format": "fastq",
            "file_size": 613159377,
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            "s3_uri": "s3://igvf-files/2024/03/01/ba88acdb-b8e4-443e-8820-08b8de6e124f/IGVFFI7852BFOU.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/LW279B-3_S25_L002_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3938OJKT/",
            "accession": "IGVFFI3938OJKT",
            "aliases": [
                "gary-hon:LW279B-3_1_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:11:06.130701+00:00",
            "file_format": "fastq",
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            "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/LW279B-3_S25_L001_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9797JSJB/",
            "accession": "IGVFFI9797JSJB",
            "aliases": [
                "gary-hon:LW279B-3_1_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:11:17.189681+00:00",
            "file_format": "fastq",
            "file_size": 621448352,
            "href": "/sequence-files/IGVFFI9797JSJB/@@download/IGVFFI9797JSJB.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/01/e06fe53a-ea56-4419-b8ec-f7ae0ec78bb3/IGVFFI9797JSJB.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0010963/",
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            "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/LW279B-3_S25_L001_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI2834JYDA/",
            "accession": "IGVFFI2834JYDA",
            "aliases": [
                "gary-hon:LW279B-3_1_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:11:26.198007+00:00",
            "file_format": "fastq",
            "file_size": 670029663,
            "href": "/sequence-files/IGVFFI2834JYDA/@@download/IGVFFI2834JYDA.fastq.gz",
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            "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/LW279B-3_S25_L001_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI7620POLB/",
            "accession": "IGVFFI7620POLB",
            "aliases": [
                "gary-hon:LW279B-3_2_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:11:35.856062+00:00",
            "file_format": "fastq",
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            "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/LW279B-3_S25_L002_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI4290KTZN/",
            "accession": "IGVFFI4290KTZN",
            "aliases": [
                "gary-hon:LW279B-3_2_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:11:41.177285+00:00",
            "file_format": "fastq",
            "file_size": 194748424,
            "href": "/sequence-files/IGVFFI4290KTZN/@@download/IGVFFI4290KTZN.fastq.gz",
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            "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/LW279B-3_S25_L002_I2_001.fastq.gz",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS4389OUWU/"
    ],
    "lab": {
        "@id": "/labs/gary-hon/",
        "title": "Gary Hon, UT"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS7733OTCA/",
            "accession": "IGVFDS7733OTCA",
            "aliases": [
                "gary-hon:TF_Perturb_Seq_Pilot_Lenti_CM_LW279"
            ],
            "preferred_assay_title": "Perturb-seq",
            "status": "preview"
        }
    ],
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM0559UNMK/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM0559UNMK",
            "aliases": [
                "nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_CMs_Lenti_LW279"
            ],
            "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 cardiac muscle cell for 12 days (cellular sub pool: subpool_LW279), male, Homo sapiens modified with CRISPRi Sp-dCas9, transduced (lentivirus) with a guide library",
            "targeted_sample_term": {
                "@id": "/sample-terms/CL_0000746/",
                "status": "released",
                "term_name": "cardiac muscle cell"
            },
            "taxa": "Homo sapiens"
        }
    ],
    "schema_version": "12",
    "status": "preview",
    "submitted_by": {
        "@id": "/users/b05645f1-2d56-4a5e-b272-4601e555a3fa/",
        "title": "Mpathi Nzima"
    },
    "submitted_files_timestamp": "2024-03-01T17:11:06.130701+00:00",
    "summary": "gRNA sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "af2acaa2-b27d-4126-b2b2-653e1197cdf1"
}