IGVFDS5429CXNB

{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS5429CXNB/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS5429CXNB",
    "aliases": [
        "gary-hon:TF_Perturb_Seq_Pilot_Lenti_iPSC_LW286"
    ],
    "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 [IGVFDS3465KEWH](/auxiliary-sets/IGVFDS3465KEWH/) has sequence file(s) [IGVFFI3046CEDS](/sequence-files/IGVFFI3046CEDS/), [IGVFFI2095GWCE](/sequence-files/IGVFFI2095GWCE/), [IGVFFI4014VOTR](/sequence-files/IGVFFI4014VOTR/), [IGVFFI6603ZNLC](/sequence-files/IGVFFI6603ZNLC/) 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/IGVFDS3465KEWH/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS3465KEWH](/auxiliary-sets/IGVFDS3465KEWH/) has sequence file(s): [IGVFFI3046CEDS](/sequence-files/IGVFFI3046CEDS/), [IGVFFI2095GWCE](/sequence-files/IGVFFI2095GWCE/), [IGVFFI4014VOTR](/sequence-files/IGVFFI4014VOTR/), [IGVFFI6603ZNLC](/sequence-files/IGVFFI6603ZNLC/) 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/IGVFDS3465KEWH/"
            },
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS1128FXRR](/auxiliary-sets/IGVFDS1128FXRR/) has sequence file(s) [IGVFFI9511EKXQ](/sequence-files/IGVFFI9511EKXQ/), [IGVFFI6053YIFW](/sequence-files/IGVFFI6053YIFW/), [IGVFFI6212DKTA](/sequence-files/IGVFFI6212DKTA/), [IGVFFI6700ENLR](/sequence-files/IGVFFI6700ENLR/) 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/IGVFDS1128FXRR/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS1128FXRR](/auxiliary-sets/IGVFDS1128FXRR/) has sequence file(s): [IGVFFI9511EKXQ](/sequence-files/IGVFFI9511EKXQ/), [IGVFFI6053YIFW](/sequence-files/IGVFFI6053YIFW/), [IGVFFI6212DKTA](/sequence-files/IGVFFI6212DKTA/), [IGVFFI6700ENLR](/sequence-files/IGVFFI6700ENLR/) 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/IGVFDS1128FXRR/"
            },
            {
                "category": "missing sequencing kit",
                "detail": "Measurement set [IGVFDS5429CXNB](/measurement-sets/IGVFDS5429CXNB/) has sequence file(s) [IGVFFI2177DFRH](/sequence-files/IGVFFI2177DFRH/), [IGVFFI3868KDUU](/sequence-files/IGVFFI3868KDUU/), [IGVFFI8142CIDW](/sequence-files/IGVFFI8142CIDW/), [IGVFFI5020EGXD](/sequence-files/IGVFFI5020EGXD/), [IGVFFI0160DJHO](/sequence-files/IGVFFI0160DJHO/), [IGVFFI8734WGHA](/sequence-files/IGVFFI8734WGHA/), [IGVFFI0871LPRK](/sequence-files/IGVFFI0871LPRK/), [IGVFFI7095FECZ](/sequence-files/IGVFFI7095FECZ/) 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/IGVFDS5429CXNB/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS5429CXNB](/measurement-sets/IGVFDS5429CXNB/) has sequence file(s): [IGVFFI2177DFRH](/sequence-files/IGVFFI2177DFRH/), [IGVFFI3868KDUU](/sequence-files/IGVFFI3868KDUU/), [IGVFFI8142CIDW](/sequence-files/IGVFFI8142CIDW/), [IGVFFI5020EGXD](/sequence-files/IGVFFI5020EGXD/), [IGVFFI0160DJHO](/sequence-files/IGVFFI0160DJHO/), [IGVFFI8734WGHA](/sequence-files/IGVFFI8734WGHA/), [IGVFFI0871LPRK](/sequence-files/IGVFFI0871LPRK/), [IGVFFI7095FECZ](/sequence-files/IGVFFI7095FECZ/) 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/IGVFDS5429CXNB/"
            }
        ]
    },
    "auxiliary_sets": [
        {
            "@id": "/auxiliary-sets/IGVFDS1128FXRR/",
            "accession": "IGVFDS1128FXRR",
            "aliases": [
                "gary-hon:TF_Perturb_Seq_Pilot_Lenti_iPSC_sgRNA_LW286"
            ],
            "file_set_type": "gRNA sequencing",
            "status": "preview"
        },
        {
            "@id": "/auxiliary-sets/IGVFDS3465KEWH/",
            "accession": "IGVFDS3465KEWH",
            "aliases": [
                "gary-hon:TF_Perturb_Seq_Pilot_Lenti_iPSC_HTO_LW286"
            ],
            "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": "2024-02-21T21:28:50.109383+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/IGVFFI2177DFRH/",
            "accession": "IGVFFI2177DFRH",
            "aliases": [
                "gary-hon:LW286_1_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-04T19:48:05.129836+00:00",
            "file_format": "fastq",
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            "s3_uri": "s3://igvf-files/2024/03/04/3cb44fcd-6dba-46f6-a4cd-2a625686c245/IGVFFI2177DFRH.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/2023/2023-11-03-McDermott-NextSeq.10X.run1/2023-11-03/outs/fastq_path/AAC7TGLHV//LW286_S1_L001_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3868KDUU/",
            "accession": "IGVFFI3868KDUU",
            "aliases": [
                "gary-hon:LW286_1_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-04T19:48:17.114209+00:00",
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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/2023/2023-11-03-McDermott-NextSeq.10X.run1/2023-11-03/outs/fastq_path/AAC7TGLHV//LW286_S1_L001_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8142CIDW/",
            "accession": "IGVFFI8142CIDW",
            "aliases": [
                "gary-hon:LW286_1_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-04T19:48:28.505387+00:00",
            "file_format": "fastq",
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            "sequencing_platform": {
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                "status": "released",
                "term_name": "Illumina NextSeq 2000"
            },
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            "submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-11-03-McDermott-NextSeq.10X.run1/2023-11-03/outs/fastq_path/AAC7TGLHV//LW286_S1_L001_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI5020EGXD/",
            "accession": "IGVFFI5020EGXD",
            "aliases": [
                "gary-hon:LW286_1_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-04T19:48:53.851358+00:00",
            "file_format": "fastq",
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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/2023/2023-11-03-McDermott-NextSeq.10X.run1/2023-11-03/outs/fastq_path/AAC7TGLHV//LW286_S1_L001_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI0160DJHO/",
            "accession": "IGVFFI0160DJHO",
            "aliases": [
                "gary-hon:LW286_2_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-04T19:49:53.128618+00:00",
            "file_format": "fastq",
            "file_size": 787212709,
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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/2023/2023-11-03-McDermott-NextSeq.10X.run1/2023-11-03/outs/fastq_path/AAC7TGLHV//LW286_S1_L002_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8734WGHA/",
            "accession": "IGVFFI8734WGHA",
            "aliases": [
                "gary-hon:LW286_2_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-04T19:50:03.826342+00:00",
            "file_format": "fastq",
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            "sequencing_platform": {
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                "status": "released",
                "term_name": "Illumina NextSeq 2000"
            },
            "status": "preview",
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            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI0871LPRK/",
            "accession": "IGVFFI0871LPRK",
            "aliases": [
                "gary-hon:LW286_2_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-04T19:50:14.966303+00:00",
            "file_format": "fastq",
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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/2023/2023-11-03-McDermott-NextSeq.10X.run1/2023-11-03/outs/fastq_path/AAC7TGLHV//LW286_S1_L002_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI7095FECZ/",
            "accession": "IGVFFI7095FECZ",
            "aliases": [
                "gary-hon:LW286_2_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-04T19:50:39.001783+00:00",
            "file_format": "fastq",
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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/2023/2023-11-03-McDermott-NextSeq.10X.run1/2023-11-03/outs/fastq_path/AAC7TGLHV//LW286_S1_L002_R2_001.fastq.gz",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS7340YDHF/"
    ],
    "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/IGVFSM2726ORRN/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM2726ORRN",
            "aliases": [
                "nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_iPSC_Lenti_LW286"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                {
                    "@id": "/construct-library-sets/IGVFDS2302LCEO/",
                    "accession": "IGVFDS2302LCEO",
                    "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) cell line (cellular sub pool: subpool_LW286), male, Homo sapiens modified with CRISPRi Sp-dCas9, transduced (lentivirus) with a guide library",
            "taxa": "Homo sapiens"
        }
    ],
    "schema_version": "23",
    "status": "preview",
    "submitted_by": {
        "@id": "/users/b05645f1-2d56-4a5e-b272-4601e555a3fa/",
        "title": "Mpathi Nzima"
    },
    "submitted_files_timestamp": "2024-03-04T19:48:05.129836+00:00",
    "submitter_comment": "Transcriptiome for LW286",
    "summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "acb59998-eb3d-4a8e-9afa-9a8a110c1a9d"
}