IGVFDS8110KLML

{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS8110KLML/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS8110KLML",
    "aliases": [
        "gary-hon:differentited_H9_CM_Pilot2_Mini_Inducible_LW424"
    ],
    "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 [IGVFDS7849GKLL](/auxiliary-sets/IGVFDS7849GKLL/) has a sequence file [IGVFFI8952AWPF](/sequence-files/IGVFFI8952AWPF/) 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/IGVFDS7849GKLL/"
            },
            {
                "category": "inconsistent sequencing kit",
                "detail": "Auxiliary set [IGVFDS7849GKLL](/auxiliary-sets/IGVFDS7849GKLL/) has a sequence file [IGVFFI0550YHLA](/sequence-files/IGVFFI0550YHLA/) 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/IGVFDS7849GKLL/"
            },
            {
                "category": "inconsistent sequencing kit",
                "detail": "Auxiliary set [IGVFDS7849GKLL](/auxiliary-sets/IGVFDS7849GKLL/) has a sequence file [IGVFFI4407QPXA](/sequence-files/IGVFFI4407QPXA/) 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/IGVFDS7849GKLL/"
            },
            {
                "category": "inconsistent sequencing kit",
                "detail": "Auxiliary set [IGVFDS7849GKLL](/auxiliary-sets/IGVFDS7849GKLL/) has a sequence file [IGVFFI2250RJUE](/sequence-files/IGVFFI2250RJUE/) 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/IGVFDS7849GKLL/"
            },
            {
                "category": "inconsistent sequencing kit",
                "detail": "Auxiliary set [IGVFDS3659SZDC](/auxiliary-sets/IGVFDS3659SZDC/) has a sequence file [IGVFFI3444OMRD](/sequence-files/IGVFFI3444OMRD/) 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/IGVFDS3659SZDC/"
            },
            {
                "category": "inconsistent sequencing kit",
                "detail": "Auxiliary set [IGVFDS3659SZDC](/auxiliary-sets/IGVFDS3659SZDC/) has a sequence file [IGVFFI3811FKOC](/sequence-files/IGVFFI3811FKOC/) 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/IGVFDS3659SZDC/"
            },
            {
                "category": "inconsistent sequencing kit",
                "detail": "Auxiliary set [IGVFDS3659SZDC](/auxiliary-sets/IGVFDS3659SZDC/) has a sequence file [IGVFFI2809JKMT](/sequence-files/IGVFFI2809JKMT/) 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/IGVFDS3659SZDC/"
            },
            {
                "category": "inconsistent sequencing kit",
                "detail": "Auxiliary set [IGVFDS3659SZDC](/auxiliary-sets/IGVFDS3659SZDC/) has a sequence file [IGVFFI2105PSHE](/sequence-files/IGVFFI2105PSHE/) 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/IGVFDS3659SZDC/"
            }
        ],
        "INTERNAL_ACTION": [
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS7849GKLL](/auxiliary-sets/IGVFDS7849GKLL/) has sequence file(s): [IGVFFI8952AWPF](/sequence-files/IGVFFI8952AWPF/), [IGVFFI0550YHLA](/sequence-files/IGVFFI0550YHLA/), [IGVFFI4407QPXA](/sequence-files/IGVFFI4407QPXA/), [IGVFFI2250RJUE](/sequence-files/IGVFFI2250RJUE/) 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/IGVFDS7849GKLL/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS3659SZDC](/auxiliary-sets/IGVFDS3659SZDC/) has sequence file(s): [IGVFFI3444OMRD](/sequence-files/IGVFFI3444OMRD/), [IGVFFI3811FKOC](/sequence-files/IGVFFI3811FKOC/), [IGVFFI2809JKMT](/sequence-files/IGVFFI2809JKMT/), [IGVFFI2105PSHE](/sequence-files/IGVFFI2105PSHE/) 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/IGVFDS3659SZDC/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS8110KLML](/measurement-sets/IGVFDS8110KLML/) has sequence file(s): [IGVFFI1835ZYQJ](/sequence-files/IGVFFI1835ZYQJ/), [IGVFFI1876MOKD](/sequence-files/IGVFFI1876MOKD/), [IGVFFI0952BGMF](/sequence-files/IGVFFI0952BGMF/), [IGVFFI6632FFZB](/sequence-files/IGVFFI6632FFZB/) 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/IGVFDS8110KLML/"
            }
        ]
    },
    "auxiliary_sets": [
        {
            "@id": "/auxiliary-sets/IGVFDS3659SZDC/",
            "accession": "IGVFDS3659SZDC",
            "aliases": [
                "gary-hon:differentited_H9_CM_Pilot2_Mini_Inducible_sgRNA_LW424"
            ],
            "file_set_type": "gRNA sequencing",
            "status": "preview"
        },
        {
            "@id": "/auxiliary-sets/IGVFDS7849GKLL/",
            "accession": "IGVFDS7849GKLL",
            "aliases": [
                "gary-hon:differentited_H9_CM_Pilot2_Mini_Inducible_HTO_LW424"
            ],
            "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": "2024-08-16T20:31:50.263781+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/IGVFFI1835ZYQJ/",
            "accession": "IGVFFI1835ZYQJ",
            "aliases": [
                "gary-hon:LW424_4_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-13T21:28:13.180876+00:00",
            "file_format": "fastq",
            "file_size": 2303338467,
            "href": "/sequence-files/IGVFFI1835ZYQJ/@@download/IGVFFI1835ZYQJ.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/11/13/bff0dbbc-6e6c-4c23-9669-72c4767f48a1/IGVFFI1835ZYQJ.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//LW424_S2_L004_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI1876MOKD/",
            "accession": "IGVFFI1876MOKD",
            "aliases": [
                "gary-hon:LW424_4_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-13T21:29:16.444058+00:00",
            "file_format": "fastq",
            "file_size": 27307857935,
            "href": "/sequence-files/IGVFFI1876MOKD/@@download/IGVFFI1876MOKD.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/11/13/2d0c1887-ede6-48f8-b682-ce4a9fb7ff4b/IGVFFI1876MOKD.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//LW424_S2_L004_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI0952BGMF/",
            "accession": "IGVFFI0952BGMF",
            "aliases": [
                "gary-hon:LW424_4_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-13T21:28:43.203234+00:00",
            "file_format": "fastq",
            "file_size": 2636479741,
            "href": "/sequence-files/IGVFFI0952BGMF/@@download/IGVFFI0952BGMF.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/11/13/2bb7db40-e790-4576-ab69-90ed1ba4b323/IGVFFI0952BGMF.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//LW424_S2_L004_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI6632FFZB/",
            "accession": "IGVFFI6632FFZB",
            "aliases": [
                "gary-hon:LW424_4_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-13T21:33:19.039925+00:00",
            "file_format": "fastq",
            "file_size": 27590644970,
            "href": "/sequence-files/IGVFFI6632FFZB/@@download/IGVFFI6632FFZB.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/11/13/3222edbb-f017-47ff-ad4b-8e74cd457f7b/IGVFFI6632FFZB.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//LW424_S2_L004_R2_001.fastq.gz",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS6924DJAZ/"
    ],
    "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/IGVFSM3002CFHI/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM3002CFHI",
            "aliases": [
                "nikhil-munshi:differentited_H9_CM_Pilot2_Mini_Inducible_LW424"
            ],
            "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_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_LW424), 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": "2024-11-13T21:01:26.842204+00:00",
    "submitter_comment": "Transcriptiome for LW424",
    "summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "c0462885-be6a-4eeb-903b-ffef714c4035"
}