IGVFDS0961NLGM

{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS0961NLGM/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS0961NLGM",
    "aliases": [
        "gary-hon:differentited_WTC11_CM_Pilot2_Mini_PB9_LW438"
    ],
    "assay_term": {
        "@id": "/assay-terms/OBI_0003660/",
        "status": "released",
        "term_name": "in vitro CRISPR screen using single-cell RNA-seq"
    },
    "audit": {
        "ERROR": [
            {
                "category": "inconsistent sequencing kit",
                "detail": "Auxiliary set [IGVFDS3701EFIG](/auxiliary-sets/IGVFDS3701EFIG/) has a sequence file [IGVFFI2410SQSR](/sequence-files/IGVFFI2410SQSR/) sequenced on a `sequencing_platform` [EFO_0008637](/platform-terms/EFO_0008637/) that is inconsistent with its `sequencing_kit` NovaSeq X Series 25B Reagent Kit. Sequence files should specify a sequencing kit which is consistent with their sequencing platform. Sequence files in the same sequencing run should also specify the same sequencing kit.",
                "level": 60,
                "level_name": "ERROR",
                "name": "audit_inconsistent_sequencing_kit",
                "path": "/auxiliary-sets/IGVFDS3701EFIG/"
            },
            {
                "category": "inconsistent sequencing kit",
                "detail": "Auxiliary set [IGVFDS3701EFIG](/auxiliary-sets/IGVFDS3701EFIG/) has a sequence file [IGVFFI9959PZPC](/sequence-files/IGVFFI9959PZPC/) sequenced on a `sequencing_platform` [EFO_0008637](/platform-terms/EFO_0008637/) that is inconsistent with its `sequencing_kit` NovaSeq X Series 25B Reagent Kit. Sequence files should specify a sequencing kit which is consistent with their sequencing platform. Sequence files in the same sequencing run should also specify the same sequencing kit.",
                "level": 60,
                "level_name": "ERROR",
                "name": "audit_inconsistent_sequencing_kit",
                "path": "/auxiliary-sets/IGVFDS3701EFIG/"
            },
            {
                "category": "inconsistent sequencing kit",
                "detail": "Auxiliary set [IGVFDS3701EFIG](/auxiliary-sets/IGVFDS3701EFIG/) has a sequence file [IGVFFI9583JOVR](/sequence-files/IGVFFI9583JOVR/) sequenced on a `sequencing_platform` [EFO_0008637](/platform-terms/EFO_0008637/) that is inconsistent with its `sequencing_kit` NovaSeq X Series 25B Reagent Kit. Sequence files should specify a sequencing kit which is consistent with their sequencing platform. Sequence files in the same sequencing run should also specify the same sequencing kit.",
                "level": 60,
                "level_name": "ERROR",
                "name": "audit_inconsistent_sequencing_kit",
                "path": "/auxiliary-sets/IGVFDS3701EFIG/"
            },
            {
                "category": "inconsistent sequencing kit",
                "detail": "Auxiliary set [IGVFDS3701EFIG](/auxiliary-sets/IGVFDS3701EFIG/) has a sequence file [IGVFFI0287KKJM](/sequence-files/IGVFFI0287KKJM/) sequenced on a `sequencing_platform` [EFO_0008637](/platform-terms/EFO_0008637/) that is inconsistent with its `sequencing_kit` NovaSeq X Series 25B Reagent Kit. Sequence files should specify a sequencing kit which is consistent with their sequencing platform. Sequence files in the same sequencing run should also specify the same sequencing kit.",
                "level": 60,
                "level_name": "ERROR",
                "name": "audit_inconsistent_sequencing_kit",
                "path": "/auxiliary-sets/IGVFDS3701EFIG/"
            }
        ],
        "INTERNAL_ACTION": [
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS3701EFIG](/auxiliary-sets/IGVFDS3701EFIG/) has sequence file(s): [IGVFFI2410SQSR](/sequence-files/IGVFFI2410SQSR/), [IGVFFI9959PZPC](/sequence-files/IGVFFI9959PZPC/), [IGVFFI9583JOVR](/sequence-files/IGVFFI9583JOVR/), [IGVFFI0287KKJM](/sequence-files/IGVFFI0287KKJM/) 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/IGVFDS3701EFIG/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS0961NLGM](/measurement-sets/IGVFDS0961NLGM/) has sequence file(s): [IGVFFI3598BJXU](/sequence-files/IGVFFI3598BJXU/), [IGVFFI9922VQUJ](/sequence-files/IGVFFI9922VQUJ/), [IGVFFI2499SPMY](/sequence-files/IGVFFI2499SPMY/), [IGVFFI9761CWFK](/sequence-files/IGVFFI9761CWFK/) 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/IGVFDS0961NLGM/"
            }
        ],
        "WARNING": [
            {
                "category": "missing files",
                "detail": "Auxiliary set [IGVFDS0373CFJS](/auxiliary-sets/IGVFDS0373CFJS/) has no `files`. File sets are expected to have files.",
                "level": 40,
                "level_name": "WARNING",
                "name": "audit_no_files",
                "path": "/auxiliary-sets/IGVFDS0373CFJS/"
            }
        ]
    },
    "auxiliary_sets": [
        {
            "@id": "/auxiliary-sets/IGVFDS0373CFJS/",
            "accession": "IGVFDS0373CFJS",
            "aliases": [
                "gary-hon:differentited_WTC11_CM_Pilot2_Mini_PB9_sgRNA_LW438"
            ],
            "file_set_type": "gRNA sequencing",
            "status": "preview"
        },
        {
            "@id": "/auxiliary-sets/IGVFDS3701EFIG/",
            "accession": "IGVFDS3701EFIG",
            "aliases": [
                "gary-hon:differentited_WTC11_CM_Pilot2_Mini_PB9_HTO_LW438"
            ],
            "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": "2024-08-16T20:32:15.197046+00:00",
    "donors": [
        {
            "@id": "/human-donors/IGVFDO1756PPKO/",
            "accession": "IGVFDO1756PPKO",
            "aliases": [
                "igvf:donor_of_WTC11"
            ],
            "sex": "male",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "externally_hosted": false,
    "file_set_type": "experimental data",
    "files": [
        {
            "@id": "/sequence-files/IGVFFI3598BJXU/",
            "accession": "IGVFFI3598BJXU",
            "aliases": [
                "gary-hon:LW438_5_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-13T21:41:36.117828+00:00",
            "file_format": "fastq",
            "file_size": 35934686996,
            "href": "/sequence-files/IGVFFI3598BJXU/@@download/IGVFFI3598BJXU.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/11/13/ce5e39d3-632b-4312-8402-8d94ed9748bb/IGVFFI3598BJXU.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0022841/",
                "status": "released",
                "term_name": "Illumina NovaSeq X Plus"
            },
            "status": "preview",
            "submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2024/2024-05-01-Novogene-NovaSeq.Hon17_18/scRNA//LW438_S7_L005_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9922VQUJ/",
            "accession": "IGVFFI9922VQUJ",
            "aliases": [
                "gary-hon:LW438_5_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-13T21:40:22.440720+00:00",
            "file_format": "fastq",
            "file_size": 2764946291,
            "href": "/sequence-files/IGVFFI9922VQUJ/@@download/IGVFFI9922VQUJ.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/11/13/07b4f9c2-6018-434a-b62b-ff8e3e551c77/IGVFFI9922VQUJ.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0022841/",
                "status": "released",
                "term_name": "Illumina NovaSeq X Plus"
            },
            "status": "preview",
            "submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2024/2024-05-01-Novogene-NovaSeq.Hon17_18/scRNA//LW438_S7_L005_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI2499SPMY/",
            "accession": "IGVFFI2499SPMY",
            "aliases": [
                "gary-hon:LW438_5_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-13T21:47:00.201464+00:00",
            "file_format": "fastq",
            "file_size": 36173394436,
            "href": "/sequence-files/IGVFFI2499SPMY/@@download/IGVFFI2499SPMY.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/11/13/4cb3c0a4-dcd3-415d-bf76-06ab28c92596/IGVFFI2499SPMY.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0022841/",
                "status": "released",
                "term_name": "Illumina NovaSeq X Plus"
            },
            "status": "preview",
            "submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2024/2024-05-01-Novogene-NovaSeq.Hon17_18/scRNA//LW438_S7_L005_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9761CWFK/",
            "accession": "IGVFFI9761CWFK",
            "aliases": [
                "gary-hon:LW438_5_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-13T21:40:58.247330+00:00",
            "file_format": "fastq",
            "file_size": 2837004682,
            "href": "/sequence-files/IGVFFI9761CWFK/@@download/IGVFFI9761CWFK.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/11/13/69c18e64-3661-43e0-a0ad-81e45407e3ee/IGVFFI9761CWFK.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0022841/",
                "status": "released",
                "term_name": "Illumina NovaSeq X Plus"
            },
            "status": "preview",
            "submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2024/2024-05-01-Novogene-NovaSeq.Hon17_18/scRNA//LW438_S7_L005_I2_001.fastq.gz",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS4252LFRU/"
    ],
    "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/IGVFSM2176YXFG/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM2176YXFG",
            "aliases": [
                "nikhil-munshi:differentited_WTC11_CM_Pilot2_Mini_PB9_LW438"
            ],
            "classifications": [
                "differentiated cell specimen"
            ],
            "construct_library_sets": [
                {
                    "@id": "/construct-library-sets/IGVFDS0346MQBH/",
                    "accession": "IGVFDS0346MQBH",
                    "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_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_LW438), male, Homo sapiens modified with CRISPRi Sp-dCas9, transfected 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": "2024-11-13T20:00:33.887059+00:00",
    "submitter_comment": "Transcriptiome for LW438",
    "summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "6308637e-5295-49f5-8071-bf0d8db8ea4c"
}