IGVFDS8810ABUD

{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS8810ABUD/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS8810ABUD",
    "aliases": [
        "gary-hon:TF_Perturb_Seq_Pilot_Lenti_NPC_LW282"
    ],
    "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": "Measurement set [IGVFDS8810ABUD](/measurement-sets/IGVFDS8810ABUD/) has sequence file(s) [IGVFFI5962SCOE](/sequence-files/IGVFFI5962SCOE/), [IGVFFI0480OGUQ](/sequence-files/IGVFFI0480OGUQ/), [IGVFFI0724COUK](/sequence-files/IGVFFI0724COUK/), [IGVFFI6944QPBK](/sequence-files/IGVFFI6944QPBK/), [IGVFFI2488TFIW](/sequence-files/IGVFFI2488TFIW/), [IGVFFI5032ZZGX](/sequence-files/IGVFFI5032ZZGX/), [IGVFFI6517QDFT](/sequence-files/IGVFFI6517QDFT/), [IGVFFI9269XLGJ](/sequence-files/IGVFFI9269XLGJ/) 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/IGVFDS8810ABUD/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS8810ABUD](/measurement-sets/IGVFDS8810ABUD/) has sequence file(s): [IGVFFI5962SCOE](/sequence-files/IGVFFI5962SCOE/), [IGVFFI0480OGUQ](/sequence-files/IGVFFI0480OGUQ/), [IGVFFI0724COUK](/sequence-files/IGVFFI0724COUK/), [IGVFFI6944QPBK](/sequence-files/IGVFFI6944QPBK/), [IGVFFI2488TFIW](/sequence-files/IGVFFI2488TFIW/), [IGVFFI5032ZZGX](/sequence-files/IGVFFI5032ZZGX/), [IGVFFI6517QDFT](/sequence-files/IGVFFI6517QDFT/), [IGVFFI9269XLGJ](/sequence-files/IGVFFI9269XLGJ/) 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/IGVFDS8810ABUD/"
            },
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS7986GKWR](/auxiliary-sets/IGVFDS7986GKWR/) has sequence file(s) [IGVFFI9536AHMJ](/sequence-files/IGVFFI9536AHMJ/), [IGVFFI2700GHXT](/sequence-files/IGVFFI2700GHXT/), [IGVFFI9141KKTA](/sequence-files/IGVFFI9141KKTA/), [IGVFFI3164PDJY](/sequence-files/IGVFFI3164PDJY/), [IGVFFI3852EJBS](/sequence-files/IGVFFI3852EJBS/), [IGVFFI3491WALI](/sequence-files/IGVFFI3491WALI/), [IGVFFI2014MVWI](/sequence-files/IGVFFI2014MVWI/), [IGVFFI3418CTXX](/sequence-files/IGVFFI3418CTXX/) 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/IGVFDS7986GKWR/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS7986GKWR](/auxiliary-sets/IGVFDS7986GKWR/) has sequence file(s): [IGVFFI9536AHMJ](/sequence-files/IGVFFI9536AHMJ/), [IGVFFI2700GHXT](/sequence-files/IGVFFI2700GHXT/), [IGVFFI9141KKTA](/sequence-files/IGVFFI9141KKTA/), [IGVFFI3164PDJY](/sequence-files/IGVFFI3164PDJY/), [IGVFFI3852EJBS](/sequence-files/IGVFFI3852EJBS/), [IGVFFI3491WALI](/sequence-files/IGVFFI3491WALI/), [IGVFFI2014MVWI](/sequence-files/IGVFFI2014MVWI/), [IGVFFI3418CTXX](/sequence-files/IGVFFI3418CTXX/) 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/IGVFDS7986GKWR/"
            },
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS3567LQMB](/auxiliary-sets/IGVFDS3567LQMB/) has sequence file(s) [IGVFFI1692PBQW](/sequence-files/IGVFFI1692PBQW/), [IGVFFI5482BVUW](/sequence-files/IGVFFI5482BVUW/), [IGVFFI9298IPBX](/sequence-files/IGVFFI9298IPBX/), [IGVFFI0409KOWK](/sequence-files/IGVFFI0409KOWK/), [IGVFFI3785WYDT](/sequence-files/IGVFFI3785WYDT/), [IGVFFI5436EVPV](/sequence-files/IGVFFI5436EVPV/), [IGVFFI2912RLLI](/sequence-files/IGVFFI2912RLLI/), [IGVFFI4099YBZW](/sequence-files/IGVFFI4099YBZW/) 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/IGVFDS3567LQMB/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS3567LQMB](/auxiliary-sets/IGVFDS3567LQMB/) has sequence file(s): [IGVFFI1692PBQW](/sequence-files/IGVFFI1692PBQW/), [IGVFFI5482BVUW](/sequence-files/IGVFFI5482BVUW/), [IGVFFI9298IPBX](/sequence-files/IGVFFI9298IPBX/), [IGVFFI0409KOWK](/sequence-files/IGVFFI0409KOWK/), [IGVFFI3785WYDT](/sequence-files/IGVFFI3785WYDT/), [IGVFFI5436EVPV](/sequence-files/IGVFFI5436EVPV/), [IGVFFI2912RLLI](/sequence-files/IGVFFI2912RLLI/), [IGVFFI4099YBZW](/sequence-files/IGVFFI4099YBZW/) 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/IGVFDS3567LQMB/"
            }
        ]
    },
    "auxiliary_sets": [
        {
            "@id": "/auxiliary-sets/IGVFDS7986GKWR/",
            "accession": "IGVFDS7986GKWR",
            "aliases": [
                "gary-hon:TF_Perturb_Seq_Pilot_Lenti_NPC_sgRNA_LW282"
            ],
            "file_set_type": "gRNA sequencing",
            "status": "preview"
        },
        {
            "@id": "/auxiliary-sets/IGVFDS3567LQMB/",
            "accession": "IGVFDS3567LQMB",
            "aliases": [
                "gary-hon:TF_Perturb_Seq_Pilot_Lenti_NPC_HTO_LW282"
            ],
            "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": "2024-02-29T16:52:22.949040+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/IGVFFI5962SCOE/",
            "accession": "IGVFFI5962SCOE",
            "aliases": [
                "gary-hon:LW282_1_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:20:32.454723+00:00",
            "file_format": "fastq",
            "file_size": 122064232,
            "href": "/sequence-files/IGVFFI5962SCOE/@@download/IGVFFI5962SCOE.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/01/2fc298a1-ee2c-4afd-a5ac-7c6d1d7583e7/IGVFFI5962SCOE.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/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW282_S20_L001_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI0480OGUQ/",
            "accession": "IGVFFI0480OGUQ",
            "aliases": [
                "gary-hon:LW282_2_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:21:16.939592+00:00",
            "file_format": "fastq",
            "file_size": 304514898,
            "href": "/sequence-files/IGVFFI0480OGUQ/@@download/IGVFFI0480OGUQ.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/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW282_S20_L002_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI0724COUK/",
            "accession": "IGVFFI0724COUK",
            "aliases": [
                "gary-hon:LW282_1_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:20:52.491254+00:00",
            "file_format": "fastq",
            "file_size": 731632297,
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            "s3_uri": "s3://igvf-files/2024/03/01/67273e74-4f7e-4861-81f0-41618e1144ed/IGVFFI0724COUK.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/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW282_S20_L001_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI6944QPBK/",
            "accession": "IGVFFI6944QPBK",
            "aliases": [
                "gary-hon:LW282_2_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:21:02.657642+00:00",
            "file_format": "fastq",
            "file_size": 120960878,
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            "s3_uri": "s3://igvf-files/2024/03/01/a249ac07-05b0-41f4-9f62-28884ef1b18d/IGVFFI6944QPBK.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/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW282_S20_L002_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI2488TFIW/",
            "accession": "IGVFFI2488TFIW",
            "aliases": [
                "gary-hon:LW282_1_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:20:46.000947+00:00",
            "file_format": "fastq",
            "file_size": 310580740,
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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/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW282_S20_L001_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI5032ZZGX/",
            "accession": "IGVFFI5032ZZGX",
            "aliases": [
                "gary-hon:LW282_2_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:21:12.402547+00:00",
            "file_format": "fastq",
            "file_size": 98099201,
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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/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW282_S20_L002_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI6517QDFT/",
            "accession": "IGVFFI6517QDFT",
            "aliases": [
                "gary-hon:LW282_1_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:20:40.962973+00:00",
            "file_format": "fastq",
            "file_size": 101970876,
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            "s3_uri": "s3://igvf-files/2024/03/01/bff287f1-b598-4599-8e75-0dba5af0864c/IGVFFI6517QDFT.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/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW282_S20_L001_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9269XLGJ/",
            "accession": "IGVFFI9269XLGJ",
            "aliases": [
                "gary-hon:LW282_2_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:21:28.430862+00:00",
            "file_format": "fastq",
            "file_size": 713673212,
            "href": "/sequence-files/IGVFFI9269XLGJ/@@download/IGVFFI9269XLGJ.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/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW282_S20_L002_R2_001.fastq.gz",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS1588TVKF/"
    ],
    "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/IGVFSM1288TQKF/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM1288TQKF",
            "aliases": [
                "nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_NPC_Lenti_LW282"
            ],
            "classifications": [
                "differentiated cell specimen"
            ],
            "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) differentiated cell specimen induced to neural stem cell for 20 days (cellular sub pool: subpool_LW282), male, Homo sapiens modified with CRISPRi Sp-dCas9, transduced (lentivirus) with a guide library",
            "targeted_sample_term": {
                "@id": "/sample-terms/CL_0000047/",
                "status": "preview",
                "term_name": "neural stem cell"
            },
            "taxa": "Homo sapiens"
        }
    ],
    "schema_version": "23",
    "status": "preview",
    "submitted_by": {
        "@id": "/users/b05645f1-2d56-4a5e-b272-4601e555a3fa/",
        "title": "Mpathi Nzima"
    },
    "submitted_files_timestamp": "2024-03-01T17:18:46.886742+00:00",
    "submitter_comment": "Transcriptiome for LW282",
    "summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "72de59a0-1f71-4b6b-a0eb-6f062c62afc4"
}