IGVFDS4965SLDK

{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS4965SLDK/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS4965SLDK",
    "aliases": [
        "gary-hon:CM_Pilot_2_Lenti_RNA_LW263"
    ],
    "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 [IGVFDS1349DIMY](/auxiliary-sets/IGVFDS1349DIMY/) has sequence file(s) [IGVFFI5886EXSK](/sequence-files/IGVFFI5886EXSK/), [IGVFFI5666YZNA](/sequence-files/IGVFFI5666YZNA/), [IGVFFI4467KSXD](/sequence-files/IGVFFI4467KSXD/), [IGVFFI0207DWDS](/sequence-files/IGVFFI0207DWDS/) 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/IGVFDS1349DIMY/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS1349DIMY](/auxiliary-sets/IGVFDS1349DIMY/) has sequence file(s): [IGVFFI5886EXSK](/sequence-files/IGVFFI5886EXSK/), [IGVFFI5666YZNA](/sequence-files/IGVFFI5666YZNA/), [IGVFFI4467KSXD](/sequence-files/IGVFFI4467KSXD/), [IGVFFI0207DWDS](/sequence-files/IGVFFI0207DWDS/) 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/IGVFDS1349DIMY/"
            },
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS3499IMSW](/auxiliary-sets/IGVFDS3499IMSW/) has sequence file(s) [IGVFFI3413ZJXI](/sequence-files/IGVFFI3413ZJXI/), [IGVFFI7275XULX](/sequence-files/IGVFFI7275XULX/), [IGVFFI8393MYLT](/sequence-files/IGVFFI8393MYLT/), [IGVFFI7485JXZQ](/sequence-files/IGVFFI7485JXZQ/) 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/IGVFDS3499IMSW/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS3499IMSW](/auxiliary-sets/IGVFDS3499IMSW/) has sequence file(s): [IGVFFI3413ZJXI](/sequence-files/IGVFFI3413ZJXI/), [IGVFFI7275XULX](/sequence-files/IGVFFI7275XULX/), [IGVFFI8393MYLT](/sequence-files/IGVFFI8393MYLT/), [IGVFFI7485JXZQ](/sequence-files/IGVFFI7485JXZQ/) 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/IGVFDS3499IMSW/"
            },
            {
                "category": "missing sequencing kit",
                "detail": "Measurement set [IGVFDS4965SLDK](/measurement-sets/IGVFDS4965SLDK/) has sequence file(s) [IGVFFI3835DQFV](/sequence-files/IGVFFI3835DQFV/), [IGVFFI2480DXKX](/sequence-files/IGVFFI2480DXKX/), [IGVFFI9227QJVY](/sequence-files/IGVFFI9227QJVY/), [IGVFFI8530NRGN](/sequence-files/IGVFFI8530NRGN/), [IGVFFI6673PFDE](/sequence-files/IGVFFI6673PFDE/), [IGVFFI3950HPMX](/sequence-files/IGVFFI3950HPMX/), [IGVFFI5242ONUU](/sequence-files/IGVFFI5242ONUU/), [IGVFFI9286IOQJ](/sequence-files/IGVFFI9286IOQJ/) 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/IGVFDS4965SLDK/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS4965SLDK](/measurement-sets/IGVFDS4965SLDK/) has sequence file(s): [IGVFFI3835DQFV](/sequence-files/IGVFFI3835DQFV/), [IGVFFI2480DXKX](/sequence-files/IGVFFI2480DXKX/), [IGVFFI9227QJVY](/sequence-files/IGVFFI9227QJVY/), [IGVFFI8530NRGN](/sequence-files/IGVFFI8530NRGN/), [IGVFFI6673PFDE](/sequence-files/IGVFFI6673PFDE/), [IGVFFI3950HPMX](/sequence-files/IGVFFI3950HPMX/), [IGVFFI5242ONUU](/sequence-files/IGVFFI5242ONUU/), [IGVFFI9286IOQJ](/sequence-files/IGVFFI9286IOQJ/) 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/IGVFDS4965SLDK/"
            }
        ]
    },
    "auxiliary_sets": [
        {
            "@id": "/auxiliary-sets/IGVFDS3499IMSW/",
            "accession": "IGVFDS3499IMSW",
            "aliases": [
                "gary-hon:CM_Pilot_2_Lenti_HTO_LW263"
            ],
            "file_set_type": "cell hashing barcode sequencing",
            "status": "preview"
        },
        {
            "@id": "/auxiliary-sets/IGVFDS1349DIMY/",
            "accession": "IGVFDS1349DIMY",
            "aliases": [
                "gary-hon:CM_Pilot_2_Lenti_sgRNA_LW263"
            ],
            "file_set_type": "gRNA 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": "2024-02-15T23:43:22.918980+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/IGVFFI3835DQFV/",
            "accession": "IGVFFI3835DQFV",
            "aliases": [
                "gary-hon:LW263_1_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-20T17:52:59.793968+00:00",
            "file_format": "fastq",
            "file_size": 464312119,
            "href": "/sequence-files/IGVFFI3835DQFV/@@download/IGVFFI3835DQFV.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/02/20/9314f008-fce7-4250-bb08-30ae4d5159f7/IGVFFI3835DQFV.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/2023/2023-07-13-McDermott-NextSeq.10X.run3.transcriptome/2023-07-13/outs/fastq_path/AAC5GH5HV/LW263_S3_L001_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI2480DXKX/",
            "accession": "IGVFFI2480DXKX",
            "aliases": [
                "gary-hon:LW263_1_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-20T17:53:08.016870+00:00",
            "file_format": "fastq",
            "file_size": 458230732,
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            "sequencing_platform": {
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                "status": "released",
                "term_name": "Illumina NextSeq 2000"
            },
            "status": "preview",
            "submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-07-13-McDermott-NextSeq.10X.run3.transcriptome/2023-07-13/outs/fastq_path/AAC5GH5HV/LW263_S3_L001_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9227QJVY/",
            "accession": "IGVFFI9227QJVY",
            "aliases": [
                "gary-hon:LW263_1_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-20T17:53:19.368361+00:00",
            "file_format": "fastq",
            "file_size": 1440579873,
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            "sequencing_platform": {
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                "status": "released",
                "term_name": "Illumina NextSeq 2000"
            },
            "status": "preview",
            "submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-07-13-McDermott-NextSeq.10X.run3.transcriptome/2023-07-13/outs/fastq_path/AAC5GH5HV/LW263_S3_L001_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8530NRGN/",
            "accession": "IGVFFI8530NRGN",
            "aliases": [
                "gary-hon:LW263_1_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-20T17:53:35.981641+00:00",
            "file_format": "fastq",
            "file_size": 3539853202,
            "href": "/sequence-files/IGVFFI8530NRGN/@@download/IGVFFI8530NRGN.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/02/20/3a108809-966d-486c-8a5c-567441c74d4c/IGVFFI8530NRGN.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/2023/2023-07-13-McDermott-NextSeq.10X.run3.transcriptome/2023-07-13/outs/fastq_path/AAC5GH5HV/LW263_S3_L001_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI6673PFDE/",
            "accession": "IGVFFI6673PFDE",
            "aliases": [
                "gary-hon:LW263_2_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-20T17:54:10.484955+00:00",
            "file_format": "fastq",
            "file_size": 447603132,
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            "sequencing_platform": {
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                "status": "released",
                "term_name": "Illumina NextSeq 2000"
            },
            "status": "preview",
            "submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-07-13-McDermott-NextSeq.10X.run3.transcriptome/2023-07-13/outs/fastq_path/AAC5GH5HV/LW263_S3_L002_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3950HPMX/",
            "accession": "IGVFFI3950HPMX",
            "aliases": [
                "gary-hon:LW263_2_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-20T17:54:18.626567+00:00",
            "file_format": "fastq",
            "file_size": 423153296,
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            "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/2023/2023-07-13-McDermott-NextSeq.10X.run3.transcriptome/2023-07-13/outs/fastq_path/AAC5GH5HV/LW263_S3_L002_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI5242ONUU/",
            "accession": "IGVFFI5242ONUU",
            "aliases": [
                "gary-hon:LW263_2_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-20T17:54:42.345710+00:00",
            "file_format": "fastq",
            "file_size": 3461324309,
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            "s3_uri": "s3://igvf-files/2024/02/20/d19f4fb8-52dc-466c-adeb-8123cadd7582/IGVFFI5242ONUU.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/2023/2023-07-13-McDermott-NextSeq.10X.run3.transcriptome/2023-07-13/outs/fastq_path/AAC5GH5HV/LW263_S3_L002_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9286IOQJ/",
            "accession": "IGVFFI9286IOQJ",
            "aliases": [
                "gary-hon:LW263_2_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-20T17:54:26.382307+00:00",
            "file_format": "fastq",
            "file_size": 1379552254,
            "href": "/sequence-files/IGVFFI9286IOQJ/@@download/IGVFFI9286IOQJ.fastq.gz",
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            "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/2023/2023-07-13-McDermott-NextSeq.10X.run3.transcriptome/2023-07-13/outs/fastq_path/AAC5GH5HV/LW263_S3_L002_R1_001.fastq.gz",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS4003HZAB/"
    ],
    "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/IGVFSM0333RWYR/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM0333RWYR",
            "aliases": [
                "nikhil-munshi:differentited_WTC11_CM_Pilot1_Lenti_LW263"
            ],
            "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_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_LW263), 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": "2024-02-20T17:52:59.793968+00:00",
    "submitter_comment": "Transcriptiome for LW263'",
    "summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "16d2bf43-4efb-434f-8f46-24e2fd65e76d"
}