IGVFDS8449CDOE

{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS8449CDOE/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS8449CDOE",
    "aliases": [
        "gary-hon:CM_Pilot_2_Mini_Lenti_LW271"
    ],
    "assay_term": {
        "@id": "/assay-terms/OBI_0003660/",
        "status": "released",
        "term_name": "in vitro CRISPR screen using single-cell RNA-seq"
    },
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequencing kit",
                "detail": "Measurement set [IGVFDS8449CDOE](/measurement-sets/IGVFDS8449CDOE/) has sequence file(s) [IGVFFI5001MIUK](/sequence-files/IGVFFI5001MIUK/), [IGVFFI5546ZOPL](/sequence-files/IGVFFI5546ZOPL/), [IGVFFI1688NGJH](/sequence-files/IGVFFI1688NGJH/), [IGVFFI0481HFTE](/sequence-files/IGVFFI0481HFTE/) 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": "/measurement-sets/IGVFDS8449CDOE/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS8449CDOE](/measurement-sets/IGVFDS8449CDOE/) has sequence file(s): [IGVFFI5001MIUK](/sequence-files/IGVFFI5001MIUK/), [IGVFFI5546ZOPL](/sequence-files/IGVFFI5546ZOPL/), [IGVFFI1688NGJH](/sequence-files/IGVFFI1688NGJH/), [IGVFFI0481HFTE](/sequence-files/IGVFFI0481HFTE/) 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": "/measurement-sets/IGVFDS8449CDOE/"
            },
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS2739QDQI](/auxiliary-sets/IGVFDS2739QDQI/) has sequence file(s) [IGVFFI3740ZALO](/sequence-files/IGVFFI3740ZALO/), [IGVFFI8094TZOG](/sequence-files/IGVFFI8094TZOG/), [IGVFFI2030EWBH](/sequence-files/IGVFFI2030EWBH/), [IGVFFI3294VBIM](/sequence-files/IGVFFI3294VBIM/) 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/IGVFDS2739QDQI/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS2739QDQI](/auxiliary-sets/IGVFDS2739QDQI/) has sequence file(s): [IGVFFI3740ZALO](/sequence-files/IGVFFI3740ZALO/), [IGVFFI8094TZOG](/sequence-files/IGVFFI8094TZOG/), [IGVFFI2030EWBH](/sequence-files/IGVFFI2030EWBH/), [IGVFFI3294VBIM](/sequence-files/IGVFFI3294VBIM/) 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/IGVFDS2739QDQI/"
            },
            {
                "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/"
            }
        ]
    },
    "auxiliary_sets": [
        {
            "@id": "/auxiliary-sets/IGVFDS1004SBHR/",
            "accession": "IGVFDS1004SBHR",
            "aliases": [
                "gary-hon:CM_Pilot_2_Mini_sgRNA_Lenti_LW271"
            ],
            "file_set_type": "gRNA sequencing",
            "status": "preview"
        },
        {
            "@id": "/auxiliary-sets/IGVFDS2739QDQI/",
            "accession": "IGVFDS2739QDQI",
            "aliases": [
                "gary-hon:CM_Pilot_2_Mini_HTO_Lenti_LW271"
            ],
            "file_set_type": "cell hashing barcode sequencing",
            "status": "preview"
        }
    ],
    "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": "2024-04-25T21:58:43.638412+00:00",
    "donors": [
        {
            "@id": "/human-donors/IGVFDO2718IDDQ/",
            "accession": "IGVFDO2718IDDQ",
            "aliases": [
                "igvf:donor_of_H9"
            ],
            "sex": "female",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "externally_hosted": false,
    "file_set_type": "experimental data",
    "files": [
        {
            "@id": "/sequence-files/IGVFFI5001MIUK/",
            "accession": "IGVFFI5001MIUK",
            "aliases": [
                "gary-hon:LW271_8_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-04-25T22:28:12.931754+00:00",
            "file_format": "fastq",
            "file_size": 874407323,
            "href": "/sequence-files/IGVFFI5001MIUK/@@download/IGVFFI5001MIUK.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/04/25/dca356b5-0124-471a-bc9d-af375bfe9da1/IGVFFI5001MIUK.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0010963/",
                "status": "released",
                "term_name": "Illumina NextSeq 2000"
            },
            "status": "preview",
            "submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-25-McDermott-NovaSeq.lane8.10X/10X//LW271_S3_L008_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI5546ZOPL/",
            "accession": "IGVFFI5546ZOPL",
            "aliases": [
                "gary-hon:LW271_8_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-04-25T22:27:58.287854+00:00",
            "file_format": "fastq",
            "file_size": 865861914,
            "href": "/sequence-files/IGVFFI5546ZOPL/@@download/IGVFFI5546ZOPL.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/04/25/0ec4cd32-bff4-4160-9baf-579a50d47fda/IGVFFI5546ZOPL.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0010963/",
                "status": "released",
                "term_name": "Illumina NextSeq 2000"
            },
            "status": "preview",
            "submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-25-McDermott-NovaSeq.lane8.10X/10X//LW271_S3_L008_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI1688NGJH/",
            "accession": "IGVFFI1688NGJH",
            "aliases": [
                "gary-hon:LW271_8_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-04-25T22:28:25.349257+00:00",
            "file_format": "fastq",
            "file_size": 10991337743,
            "href": "/sequence-files/IGVFFI1688NGJH/@@download/IGVFFI1688NGJH.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/04/25/d2fc3984-f893-4064-867f-f419a4917ccf/IGVFFI1688NGJH.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0010963/",
                "status": "released",
                "term_name": "Illumina NextSeq 2000"
            },
            "status": "preview",
            "submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-25-McDermott-NovaSeq.lane8.10X/10X//LW271_S3_L008_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI0481HFTE/",
            "accession": "IGVFFI0481HFTE",
            "aliases": [
                "gary-hon:LW271_8_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-04-25T22:30:03.314205+00:00",
            "file_format": "fastq",
            "file_size": 10995988393,
            "href": "/sequence-files/IGVFFI0481HFTE/@@download/IGVFFI0481HFTE.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/04/25/22c043da-0084-4ecf-980f-2d3a65f3751e/IGVFFI0481HFTE.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0010963/",
                "status": "released",
                "term_name": "Illumina NextSeq 2000"
            },
            "status": "preview",
            "submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-25-McDermott-NovaSeq.lane8.10X/10X//LW271_S3_L008_R2_001.fastq.gz",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS2873EPIU/"
    ],
    "lab": {
        "@id": "/labs/gary-hon/",
        "title": "Gary Hon, UT"
    },
    "preferred_assay_title": "Perturb-seq",
    "protocols": [
        "https://www.protocols.io/view/experimental-procedures-for-tf-perturb-seq-ut-sout-denf3dbn"
    ],
    "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": [
                {
                    "@id": "/construct-library-sets/IGVFDS9629YZLO/",
                    "accession": "IGVFDS9629YZLO",
                    "file_set_type": "guide library",
                    "status": "preview",
                    "summary": "guide (sgRNA) library targeting accessible genome regions in many genomic loci"
                }
            ],
            "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": "23",
    "status": "preview",
    "submitted_by": {
        "@id": "/users/b05645f1-2d56-4a5e-b272-4601e555a3fa/",
        "title": "Mpathi Nzima"
    },
    "submitted_files_timestamp": "2024-04-25T22:27:58.287854+00:00",
    "submitter_comment": "Transcriptiome for LW271",
    "summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "604b254c-9e53-4ede-a459-9908fb7822e9"
}