IGVFDS4940ELQK

{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS4940ELQK/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS4940ELQK",
    "aliases": [
        "gary-hon:CM_Pilot_2_Mini_Lenti_LW272"
    ],
    "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": "Auxiliary set [IGVFDS8839RSIR](/auxiliary-sets/IGVFDS8839RSIR/) has sequence file(s) [IGVFFI3688WTIX](/sequence-files/IGVFFI3688WTIX/), [IGVFFI0982WORL](/sequence-files/IGVFFI0982WORL/), [IGVFFI9175HBPO](/sequence-files/IGVFFI9175HBPO/), [IGVFFI8689DYXM](/sequence-files/IGVFFI8689DYXM/) 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/IGVFDS8839RSIR/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS8839RSIR](/auxiliary-sets/IGVFDS8839RSIR/) has sequence file(s): [IGVFFI3688WTIX](/sequence-files/IGVFFI3688WTIX/), [IGVFFI0982WORL](/sequence-files/IGVFFI0982WORL/), [IGVFFI9175HBPO](/sequence-files/IGVFFI9175HBPO/), [IGVFFI8689DYXM](/sequence-files/IGVFFI8689DYXM/) 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/IGVFDS8839RSIR/"
            },
            {
                "category": "missing sequencing kit",
                "detail": "Measurement set [IGVFDS4940ELQK](/measurement-sets/IGVFDS4940ELQK/) has sequence file(s) [IGVFFI9431GCYS](/sequence-files/IGVFFI9431GCYS/), [IGVFFI9849UOCQ](/sequence-files/IGVFFI9849UOCQ/), [IGVFFI3780QGTX](/sequence-files/IGVFFI3780QGTX/), [IGVFFI5596FJTD](/sequence-files/IGVFFI5596FJTD/) 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/IGVFDS4940ELQK/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS4940ELQK](/measurement-sets/IGVFDS4940ELQK/) has sequence file(s): [IGVFFI9431GCYS](/sequence-files/IGVFFI9431GCYS/), [IGVFFI9849UOCQ](/sequence-files/IGVFFI9849UOCQ/), [IGVFFI3780QGTX](/sequence-files/IGVFFI3780QGTX/), [IGVFFI5596FJTD](/sequence-files/IGVFFI5596FJTD/) 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/IGVFDS4940ELQK/"
            },
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS8726ORVQ](/auxiliary-sets/IGVFDS8726ORVQ/) has sequence file(s) [IGVFFI9255ZWLL](/sequence-files/IGVFFI9255ZWLL/), [IGVFFI9316DTIE](/sequence-files/IGVFFI9316DTIE/), [IGVFFI0045RQHO](/sequence-files/IGVFFI0045RQHO/), [IGVFFI8537ABID](/sequence-files/IGVFFI8537ABID/) 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/IGVFDS8726ORVQ/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS8726ORVQ](/auxiliary-sets/IGVFDS8726ORVQ/) has sequence file(s): [IGVFFI9255ZWLL](/sequence-files/IGVFFI9255ZWLL/), [IGVFFI9316DTIE](/sequence-files/IGVFFI9316DTIE/), [IGVFFI0045RQHO](/sequence-files/IGVFFI0045RQHO/), [IGVFFI8537ABID](/sequence-files/IGVFFI8537ABID/) 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/IGVFDS8726ORVQ/"
            }
        ]
    },
    "auxiliary_sets": [
        {
            "@id": "/auxiliary-sets/IGVFDS8726ORVQ/",
            "accession": "IGVFDS8726ORVQ",
            "aliases": [
                "gary-hon:CM_Pilot_2_Mini_sgRNA_Lenti_LW272"
            ],
            "file_set_type": "gRNA sequencing",
            "status": "preview"
        },
        {
            "@id": "/auxiliary-sets/IGVFDS8839RSIR/",
            "accession": "IGVFDS8839RSIR",
            "aliases": [
                "gary-hon:CM_Pilot_2_Mini_HTO_Lenti_LW272"
            ],
            "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": "2024-04-25T21:58:44.556894+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/IGVFFI9431GCYS/",
            "accession": "IGVFFI9431GCYS",
            "aliases": [
                "gary-hon:LW272_8_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-04-25T22:32:05.459034+00:00",
            "file_format": "fastq",
            "file_size": 10744168192,
            "href": "/sequence-files/IGVFFI9431GCYS/@@download/IGVFFI9431GCYS.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/04/25/676a7e46-c861-471c-8af4-1cb124e61f66/IGVFFI9431GCYS.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//LW272_S4_L008_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9849UOCQ/",
            "accession": "IGVFFI9849UOCQ",
            "aliases": [
                "gary-hon:LW272_8_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-04-25T22:31:41.435010+00:00",
            "file_format": "fastq",
            "file_size": 889063652,
            "href": "/sequence-files/IGVFFI9849UOCQ/@@download/IGVFFI9849UOCQ.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/04/25/d3a9aa1b-8b4e-4580-b64f-1aa3a691883c/IGVFFI9849UOCQ.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//LW272_S4_L008_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3780QGTX/",
            "accession": "IGVFFI3780QGTX",
            "aliases": [
                "gary-hon:LW272_8_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-04-25T22:33:40.548950+00:00",
            "file_format": "fastq",
            "file_size": 10712159102,
            "href": "/sequence-files/IGVFFI3780QGTX/@@download/IGVFFI3780QGTX.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/04/25/d2e152f9-470f-4da0-b8a0-09e04a91c94f/IGVFFI3780QGTX.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//LW272_S4_L008_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI5596FJTD/",
            "accession": "IGVFFI5596FJTD",
            "aliases": [
                "gary-hon:LW272_8_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-04-25T22:31:53.164601+00:00",
            "file_format": "fastq",
            "file_size": 962108499,
            "href": "/sequence-files/IGVFFI5596FJTD/@@download/IGVFFI5596FJTD.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/04/25/a6528dbe-ed27-4546-8ab5-86fa4e3c51d1/IGVFFI5596FJTD.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//LW272_S4_L008_I2_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/IGVFSM1608DJBB/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM1608DJBB",
            "aliases": [
                "gary-hon:differentiated_H9_shen_construct_sgRNA_Lenti_LW272"
            ],
            "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_LW272), 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": "2024-04-25T22:31:41.435010+00:00",
    "submitter_comment": "Transcriptiome for LW272",
    "summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "b3693b1f-c89a-4184-8c00-652813a7fdf4"
}