IGVFDS6863PGGX

{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS6863PGGX/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS6863PGGX",
    "aliases": [
        "gary-hon:differentited_WTC11_CM_Pilot2_Mini_LPv4_LW427"
    ],
    "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 [IGVFDS5699EGGK](/auxiliary-sets/IGVFDS5699EGGK/) has a sequence file [IGVFFI1042XEFF](/sequence-files/IGVFFI1042XEFF/) 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/IGVFDS5699EGGK/"
            },
            {
                "category": "inconsistent sequencing kit",
                "detail": "Auxiliary set [IGVFDS5699EGGK](/auxiliary-sets/IGVFDS5699EGGK/) has a sequence file [IGVFFI7040RYGM](/sequence-files/IGVFFI7040RYGM/) 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/IGVFDS5699EGGK/"
            },
            {
                "category": "inconsistent sequencing kit",
                "detail": "Auxiliary set [IGVFDS5699EGGK](/auxiliary-sets/IGVFDS5699EGGK/) has a sequence file [IGVFFI2605PQQK](/sequence-files/IGVFFI2605PQQK/) 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/IGVFDS5699EGGK/"
            },
            {
                "category": "inconsistent sequencing kit",
                "detail": "Auxiliary set [IGVFDS5699EGGK](/auxiliary-sets/IGVFDS5699EGGK/) has a sequence file [IGVFFI0411GLKE](/sequence-files/IGVFFI0411GLKE/) 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/IGVFDS5699EGGK/"
            },
            {
                "category": "inconsistent sequencing kit",
                "detail": "Auxiliary set [IGVFDS0465GFSG](/auxiliary-sets/IGVFDS0465GFSG/) has a sequence file [IGVFFI5575KDRV](/sequence-files/IGVFFI5575KDRV/) 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/IGVFDS0465GFSG/"
            },
            {
                "category": "inconsistent sequencing kit",
                "detail": "Auxiliary set [IGVFDS0465GFSG](/auxiliary-sets/IGVFDS0465GFSG/) has a sequence file [IGVFFI4151SZSL](/sequence-files/IGVFFI4151SZSL/) 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/IGVFDS0465GFSG/"
            },
            {
                "category": "inconsistent sequencing kit",
                "detail": "Auxiliary set [IGVFDS0465GFSG](/auxiliary-sets/IGVFDS0465GFSG/) has a sequence file [IGVFFI5902FATE](/sequence-files/IGVFFI5902FATE/) 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/IGVFDS0465GFSG/"
            },
            {
                "category": "inconsistent sequencing kit",
                "detail": "Auxiliary set [IGVFDS0465GFSG](/auxiliary-sets/IGVFDS0465GFSG/) has a sequence file [IGVFFI2355JSHD](/sequence-files/IGVFFI2355JSHD/) 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/IGVFDS0465GFSG/"
            }
        ],
        "INTERNAL_ACTION": [
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS5699EGGK](/auxiliary-sets/IGVFDS5699EGGK/) has sequence file(s): [IGVFFI1042XEFF](/sequence-files/IGVFFI1042XEFF/), [IGVFFI7040RYGM](/sequence-files/IGVFFI7040RYGM/), [IGVFFI2605PQQK](/sequence-files/IGVFFI2605PQQK/), [IGVFFI0411GLKE](/sequence-files/IGVFFI0411GLKE/) 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/IGVFDS5699EGGK/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS6863PGGX](/measurement-sets/IGVFDS6863PGGX/) has sequence file(s): [IGVFFI6800PCCO](/sequence-files/IGVFFI6800PCCO/), [IGVFFI3407PSDS](/sequence-files/IGVFFI3407PSDS/), [IGVFFI5941BIXV](/sequence-files/IGVFFI5941BIXV/), [IGVFFI4912HSIZ](/sequence-files/IGVFFI4912HSIZ/) 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/IGVFDS6863PGGX/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS0465GFSG](/auxiliary-sets/IGVFDS0465GFSG/) has sequence file(s): [IGVFFI5575KDRV](/sequence-files/IGVFFI5575KDRV/), [IGVFFI4151SZSL](/sequence-files/IGVFFI4151SZSL/), [IGVFFI5902FATE](/sequence-files/IGVFFI5902FATE/), [IGVFFI2355JSHD](/sequence-files/IGVFFI2355JSHD/) 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/IGVFDS0465GFSG/"
            }
        ]
    },
    "auxiliary_sets": [
        {
            "@id": "/auxiliary-sets/IGVFDS0465GFSG/",
            "accession": "IGVFDS0465GFSG",
            "aliases": [
                "gary-hon:differentited_WTC11_CM_Pilot2_Mini_LPv4_sgRNA_LW427"
            ],
            "file_set_type": "gRNA sequencing",
            "status": "preview"
        },
        {
            "@id": "/auxiliary-sets/IGVFDS5699EGGK/",
            "accession": "IGVFDS5699EGGK",
            "aliases": [
                "gary-hon:differentited_WTC11_CM_Pilot2_Mini_LPv4_HTO_LW427"
            ],
            "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": "2024-08-16T20:31:52.045976+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/IGVFFI6800PCCO/",
            "accession": "IGVFFI6800PCCO",
            "aliases": [
                "gary-hon:LW427_4_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-12-20T21:06:01.883872+00:00",
            "file_format": "fastq",
            "file_size": 3101307243,
            "href": "/sequence-files/IGVFFI6800PCCO/@@download/IGVFFI6800PCCO.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/12/20/9fda2044-c2cf-4256-a362-07a179661360/IGVFFI6800PCCO.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///LW427_S3_L004_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3407PSDS/",
            "accession": "IGVFFI3407PSDS",
            "aliases": [
                "gary-hon:LW427_4_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-12-20T21:06:37.362586+00:00",
            "file_format": "fastq",
            "file_size": 3323150667,
            "href": "/sequence-files/IGVFFI3407PSDS/@@download/IGVFFI3407PSDS.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/12/20/951aa01a-2ecf-4729-9174-58c05b0fab26/IGVFFI3407PSDS.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///LW427_S3_L004_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI5941BIXV/",
            "accession": "IGVFFI5941BIXV",
            "aliases": [
                "gary-hon:LW427_4_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-12-20T21:07:13.658030+00:00",
            "file_format": "fastq",
            "file_size": 43228498843,
            "href": "/sequence-files/IGVFFI5941BIXV/@@download/IGVFFI5941BIXV.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/12/20/d389bfc3-4b38-45a4-99c9-56db5358cd7a/IGVFFI5941BIXV.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///LW427_S3_L004_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI4912HSIZ/",
            "accession": "IGVFFI4912HSIZ",
            "aliases": [
                "gary-hon:LW427_4_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-12-20T21:13:32.417520+00:00",
            "file_format": "fastq",
            "file_size": 43676184633,
            "href": "/sequence-files/IGVFFI4912HSIZ/@@download/IGVFFI4912HSIZ.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/12/20/2845c96d-ad56-4549-915a-dc2c7b1094dc/IGVFFI4912HSIZ.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///LW427_S3_L004_R2_001.fastq.gz",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS5498SDRJ/"
    ],
    "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/IGVFSM0565MLZG/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM0565MLZG",
            "aliases": [
                "nikhil-munshi:differentited_WTC11_CM_Pilot2_Mini_LPv4_LW427"
            ],
            "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_LW427), 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": "23",
    "status": "preview",
    "submitted_by": {
        "@id": "/users/b05645f1-2d56-4a5e-b272-4601e555a3fa/",
        "title": "Mpathi Nzima"
    },
    "submitted_files_timestamp": "2024-12-20T21:00:07.712594+00:00",
    "submitter_comment": "Transcriptiome for LW427",
    "summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "4dccbacb-fd28-4d3b-861e-913892cbd6d6"
}