IGVFDS6054GEKL

{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS6054GEKL/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS6054GEKL",
    "aliases": [
        "gary-hon:CM_Pilot_2_Lenti_RNA_LW264"
    ],
    "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 [IGVFDS3533NRTW](/auxiliary-sets/IGVFDS3533NRTW/) has sequence file(s) [IGVFFI2147OLQC](/sequence-files/IGVFFI2147OLQC/), [IGVFFI8172KHSP](/sequence-files/IGVFFI8172KHSP/), [IGVFFI9339EFZQ](/sequence-files/IGVFFI9339EFZQ/), [IGVFFI2974UJYR](/sequence-files/IGVFFI2974UJYR/) 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/IGVFDS3533NRTW/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS3533NRTW](/auxiliary-sets/IGVFDS3533NRTW/) has sequence file(s): [IGVFFI2147OLQC](/sequence-files/IGVFFI2147OLQC/), [IGVFFI8172KHSP](/sequence-files/IGVFFI8172KHSP/), [IGVFFI9339EFZQ](/sequence-files/IGVFFI9339EFZQ/), [IGVFFI2974UJYR](/sequence-files/IGVFFI2974UJYR/) 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/IGVFDS3533NRTW/"
            },
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS4926IAGY](/auxiliary-sets/IGVFDS4926IAGY/) has sequence file(s) [IGVFFI5091VQUO](/sequence-files/IGVFFI5091VQUO/), [IGVFFI9705OPKD](/sequence-files/IGVFFI9705OPKD/), [IGVFFI9390TIHO](/sequence-files/IGVFFI9390TIHO/), [IGVFFI3694DSSY](/sequence-files/IGVFFI3694DSSY/) 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/IGVFDS4926IAGY/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS4926IAGY](/auxiliary-sets/IGVFDS4926IAGY/) has sequence file(s): [IGVFFI5091VQUO](/sequence-files/IGVFFI5091VQUO/), [IGVFFI9705OPKD](/sequence-files/IGVFFI9705OPKD/), [IGVFFI9390TIHO](/sequence-files/IGVFFI9390TIHO/), [IGVFFI3694DSSY](/sequence-files/IGVFFI3694DSSY/) 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/IGVFDS4926IAGY/"
            },
            {
                "category": "missing sequencing kit",
                "detail": "Measurement set [IGVFDS6054GEKL](/measurement-sets/IGVFDS6054GEKL/) has sequence file(s) [IGVFFI0832KEPC](/sequence-files/IGVFFI0832KEPC/), [IGVFFI3005ICNR](/sequence-files/IGVFFI3005ICNR/), [IGVFFI6995CWOO](/sequence-files/IGVFFI6995CWOO/), [IGVFFI1648TSYB](/sequence-files/IGVFFI1648TSYB/), [IGVFFI5883BJSS](/sequence-files/IGVFFI5883BJSS/), [IGVFFI1664QUMY](/sequence-files/IGVFFI1664QUMY/), [IGVFFI8141LWAA](/sequence-files/IGVFFI8141LWAA/), [IGVFFI5887SCUI](/sequence-files/IGVFFI5887SCUI/) 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/IGVFDS6054GEKL/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS6054GEKL](/measurement-sets/IGVFDS6054GEKL/) has sequence file(s): [IGVFFI0832KEPC](/sequence-files/IGVFFI0832KEPC/), [IGVFFI3005ICNR](/sequence-files/IGVFFI3005ICNR/), [IGVFFI6995CWOO](/sequence-files/IGVFFI6995CWOO/), [IGVFFI1648TSYB](/sequence-files/IGVFFI1648TSYB/), [IGVFFI5883BJSS](/sequence-files/IGVFFI5883BJSS/), [IGVFFI1664QUMY](/sequence-files/IGVFFI1664QUMY/), [IGVFFI8141LWAA](/sequence-files/IGVFFI8141LWAA/), [IGVFFI5887SCUI](/sequence-files/IGVFFI5887SCUI/) 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/IGVFDS6054GEKL/"
            }
        ]
    },
    "auxiliary_sets": [
        {
            "@id": "/auxiliary-sets/IGVFDS4926IAGY/",
            "accession": "IGVFDS4926IAGY",
            "aliases": [
                "gary-hon:CM_Pilot_2_Lenti_HTO_LW264"
            ],
            "file_set_type": "cell hashing barcode sequencing",
            "status": "preview"
        },
        {
            "@id": "/auxiliary-sets/IGVFDS3533NRTW/",
            "accession": "IGVFDS3533NRTW",
            "aliases": [
                "gary-hon:CM_Pilot_2_Lenti_sgRNA_LW264"
            ],
            "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": "2024-02-15T23:43:23.889970+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": [
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            "@id": "/sequence-files/IGVFFI0832KEPC/",
            "accession": "IGVFFI0832KEPC",
            "aliases": [
                "gary-hon:LW264_2_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-20T17:56:28.336440+00:00",
            "file_format": "fastq",
            "file_size": 417181900,
            "href": "/sequence-files/IGVFFI0832KEPC/@@download/IGVFFI0832KEPC.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/02/20/b5c5d09e-a245-418e-b731-fab8dd068f9c/IGVFFI0832KEPC.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/LW264_S4_L002_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3005ICNR/",
            "accession": "IGVFFI3005ICNR",
            "aliases": [
                "gary-hon:LW264_2_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-20T17:56:59.914154+00:00",
            "file_format": "fastq",
            "file_size": 3455036767,
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            "s3_uri": "s3://igvf-files/2024/02/20/ebfd514b-b176-4ce5-8352-9b121088eba9/IGVFFI3005ICNR.fastq.gz",
            "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/LW264_S4_L002_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI6995CWOO/",
            "accession": "IGVFFI6995CWOO",
            "aliases": [
                "gary-hon:LW264_1_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-20T17:55:52.799875+00:00",
            "file_format": "fastq",
            "file_size": 3685964399,
            "href": "/sequence-files/IGVFFI6995CWOO/@@download/IGVFFI6995CWOO.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/02/20/6c91636a-3acd-4042-8aca-bf3221c6e27b/IGVFFI6995CWOO.fastq.gz",
            "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/LW264_S4_L001_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI1648TSYB/",
            "accession": "IGVFFI1648TSYB",
            "aliases": [
                "gary-hon:LW264_1_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-20T17:55:16.009937+00:00",
            "file_format": "fastq",
            "file_size": 451427783,
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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/LW264_S4_L001_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI5883BJSS/",
            "accession": "IGVFFI5883BJSS",
            "aliases": [
                "gary-hon:LW264_1_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-20T17:55:27.653706+00:00",
            "file_format": "fastq",
            "file_size": 436308416,
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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/LW264_S4_L001_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI1664QUMY/",
            "accession": "IGVFFI1664QUMY",
            "aliases": [
                "gary-hon:LW264_1_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-20T17:55:35.624649+00:00",
            "file_format": "fastq",
            "file_size": 1495286089,
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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/LW264_S4_L001_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8141LWAA/",
            "accession": "IGVFFI8141LWAA",
            "aliases": [
                "gary-hon:LW264_2_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-20T17:56:36.256702+00:00",
            "file_format": "fastq",
            "file_size": 402147296,
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            "s3_uri": "s3://igvf-files/2024/02/20/8fd79159-80e0-4d6c-b976-5a3ff3d7cc2a/IGVFFI8141LWAA.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/LW264_S4_L002_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI5887SCUI/",
            "accession": "IGVFFI5887SCUI",
            "aliases": [
                "gary-hon:LW264_2_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-20T17:56:44.040728+00:00",
            "file_format": "fastq",
            "file_size": 1372770915,
            "href": "/sequence-files/IGVFFI5887SCUI/@@download/IGVFFI5887SCUI.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/02/20/481ad059-819f-42c0-bb51-eb8a86e6cb58/IGVFFI5887SCUI.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/LW264_S4_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/IGVFSM0981UTUA/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM0981UTUA",
            "aliases": [
                "nikhil-munshi:differentited_WTC11_CM_Pilot1_Lenti_LW264"
            ],
            "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_LW264), 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": "2024-02-20T17:55:16.009937+00:00",
    "submitter_comment": "Transcriptiome for LW264'",
    "summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "de5e46b9-d343-40f4-8725-6facd3ccabb5"
}