IGVFDS1004SBHR

{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS1004SBHR/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS1004SBHR",
    "aliases": [
        "gary-hon:CM_Pilot_2_Mini_sgRNA_Lenti_LW271"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS1004SBHR](/auxiliary-sets/IGVFDS1004SBHR/) has sequence file(s) [IGVFFI9760OTIA](/sequence-files/IGVFFI9760OTIA/), [IGVFFI4252XXXZ](/sequence-files/IGVFFI4252XXXZ/), [IGVFFI4807QOWK](/sequence-files/IGVFFI4807QOWK/), [IGVFFI8064PBYP](/sequence-files/IGVFFI8064PBYP/) 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/IGVFDS1004SBHR/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS1004SBHR](/auxiliary-sets/IGVFDS1004SBHR/) has sequence file(s): [IGVFFI9760OTIA](/sequence-files/IGVFFI9760OTIA/), [IGVFFI4252XXXZ](/sequence-files/IGVFFI4252XXXZ/), [IGVFFI4807QOWK](/sequence-files/IGVFFI4807QOWK/), [IGVFFI8064PBYP](/sequence-files/IGVFFI8064PBYP/) 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/IGVFDS1004SBHR/"
            }
        ]
    },
    "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": "2024-04-25T21:44:10.138290+00:00",
    "donors": [
        {
            "@id": "/human-donors/IGVFDO2718IDDQ/",
            "accession": "IGVFDO2718IDDQ",
            "aliases": [
                "igvf:donor_of_H9"
            ],
            "sex": "female",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "file_set_type": "gRNA sequencing",
    "files": [
        {
            "@id": "/sequence-files/IGVFFI9760OTIA/",
            "accession": "IGVFFI9760OTIA",
            "aliases": [
                "gary-hon:LW271B_1_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-04-25T22:53:09.358901+00:00",
            "file_format": "fastq",
            "file_size": 130400213,
            "href": "/sequence-files/IGVFFI9760OTIA/@@download/IGVFFI9760OTIA.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/04/25/6c9c89f2-dacb-412e-b197-780ca6598c8b/IGVFFI9760OTIA.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0010963/",
            "status": "preview",
            "submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-12-22-McDermott-NextSeq.10X/2023-12-22/outs/fastq_path/AAF5CKNM5//LW271B_S9_L001_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI4252XXXZ/",
            "accession": "IGVFFI4252XXXZ",
            "aliases": [
                "gary-hon:LW271B_1_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-04-25T22:53:20.663521+00:00",
            "file_format": "fastq",
            "file_size": 457820219,
            "href": "/sequence-files/IGVFFI4252XXXZ/@@download/IGVFFI4252XXXZ.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/04/25/37c1ca08-3d78-44cc-9d79-7dabf77d4263/IGVFFI4252XXXZ.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0010963/",
            "status": "preview",
            "submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-12-22-McDermott-NextSeq.10X/2023-12-22/outs/fastq_path/AAF5CKNM5//LW271B_S9_L001_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI4807QOWK/",
            "accession": "IGVFFI4807QOWK",
            "aliases": [
                "gary-hon:LW271B_1_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-04-25T22:53:28.646510+00:00",
            "file_format": "fastq",
            "file_size": 522671045,
            "href": "/sequence-files/IGVFFI4807QOWK/@@download/IGVFFI4807QOWK.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/04/25/0508fa51-7826-46f3-a61a-9e1855c61db8/IGVFFI4807QOWK.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0010963/",
            "status": "preview",
            "submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-12-22-McDermott-NextSeq.10X/2023-12-22/outs/fastq_path/AAF5CKNM5//LW271B_S9_L001_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8064PBYP/",
            "accession": "IGVFFI8064PBYP",
            "aliases": [
                "gary-hon:LW271B_1_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-04-25T22:53:14.648490+00:00",
            "file_format": "fastq",
            "file_size": 139747723,
            "href": "/sequence-files/IGVFFI8064PBYP/@@download/IGVFFI8064PBYP.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/04/25/a93abb83-ffbd-4a36-b8a3-ab2ef7f38b81/IGVFFI8064PBYP.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0010963/",
            "status": "preview",
            "submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-12-22-McDermott-NextSeq.10X/2023-12-22/outs/fastq_path/AAF5CKNM5//LW271B_S9_L001_I2_001.fastq.gz",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS2873EPIU/"
    ],
    "lab": {
        "@id": "/labs/gary-hon/",
        "title": "Gary Hon, UT"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS8449CDOE/",
            "accession": "IGVFDS8449CDOE",
            "aliases": [
                "gary-hon:CM_Pilot_2_Mini_Lenti_LW271"
            ],
            "preferred_assay_title": "Perturb-seq",
            "status": "preview"
        }
    ],
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM5657YKPN/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM5657YKPN",
            "aliases": [
                "gary-hon:differentiated_H9_shen_construct_sgRNA_Lenti_LW271"
            ],
            "classifications": [
                "differentiated cell specimen"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS9629YZLO/"
            ],
            "modifications": [
                {
                    "@id": "/crispr-modifications/0a63b754-eca4-44aa-bbc2-fccdc6c44fb5/",
                    "modality": "interference",
                    "status": "preview"
                }
            ],
            "sample_terms": [
                {
                    "@id": "/sample-terms/EFO_0003045/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
                        "Item"
                    ],
                    "aliases": [
                        "igvf:H9"
                    ],
                    "status": "released",
                    "summary": "H9",
                    "term_name": "H9"
                }
            ],
            "status": "preview",
            "summary": "H9 differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW271), female, 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": "2024-04-25T22:53:09.358901+00:00",
    "summary": "gRNA sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "2c01f458-6853-4425-8b9c-7e18950f3d8d"
}