IGVFDS0657YBVN

{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS0657YBVN/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS0657YBVN",
    "aliases": [
        "gary-hon:TF_Perturb_Seq_Pilot_Lenti_NPC_LW284"
    ],
    "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 [IGVFDS2693DPLW](/auxiliary-sets/IGVFDS2693DPLW/) has sequence file(s) [IGVFFI7707CNCP](/sequence-files/IGVFFI7707CNCP/), [IGVFFI7180TCQN](/sequence-files/IGVFFI7180TCQN/), [IGVFFI4098UEYI](/sequence-files/IGVFFI4098UEYI/), [IGVFFI0338ZIDU](/sequence-files/IGVFFI0338ZIDU/), [IGVFFI2183YERZ](/sequence-files/IGVFFI2183YERZ/), [IGVFFI2451CCHU](/sequence-files/IGVFFI2451CCHU/), [IGVFFI7688VJBW](/sequence-files/IGVFFI7688VJBW/), [IGVFFI7643DOED](/sequence-files/IGVFFI7643DOED/) 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/IGVFDS2693DPLW/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS2693DPLW](/auxiliary-sets/IGVFDS2693DPLW/) has sequence file(s): [IGVFFI7707CNCP](/sequence-files/IGVFFI7707CNCP/), [IGVFFI7180TCQN](/sequence-files/IGVFFI7180TCQN/), [IGVFFI4098UEYI](/sequence-files/IGVFFI4098UEYI/), [IGVFFI0338ZIDU](/sequence-files/IGVFFI0338ZIDU/), [IGVFFI2183YERZ](/sequence-files/IGVFFI2183YERZ/), [IGVFFI2451CCHU](/sequence-files/IGVFFI2451CCHU/), [IGVFFI7688VJBW](/sequence-files/IGVFFI7688VJBW/), [IGVFFI7643DOED](/sequence-files/IGVFFI7643DOED/) 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/IGVFDS2693DPLW/"
            },
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS5339UNRP](/auxiliary-sets/IGVFDS5339UNRP/) has sequence file(s) [IGVFFI2235WFJR](/sequence-files/IGVFFI2235WFJR/), [IGVFFI3240FCBJ](/sequence-files/IGVFFI3240FCBJ/), [IGVFFI5213ZPGN](/sequence-files/IGVFFI5213ZPGN/), [IGVFFI7051FHND](/sequence-files/IGVFFI7051FHND/), [IGVFFI8462WRNK](/sequence-files/IGVFFI8462WRNK/), [IGVFFI1428MDRF](/sequence-files/IGVFFI1428MDRF/), [IGVFFI8576TNCS](/sequence-files/IGVFFI8576TNCS/), [IGVFFI9815IGUY](/sequence-files/IGVFFI9815IGUY/) 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/IGVFDS5339UNRP/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS5339UNRP](/auxiliary-sets/IGVFDS5339UNRP/) has sequence file(s): [IGVFFI2235WFJR](/sequence-files/IGVFFI2235WFJR/), [IGVFFI3240FCBJ](/sequence-files/IGVFFI3240FCBJ/), [IGVFFI5213ZPGN](/sequence-files/IGVFFI5213ZPGN/), [IGVFFI7051FHND](/sequence-files/IGVFFI7051FHND/), [IGVFFI8462WRNK](/sequence-files/IGVFFI8462WRNK/), [IGVFFI1428MDRF](/sequence-files/IGVFFI1428MDRF/), [IGVFFI8576TNCS](/sequence-files/IGVFFI8576TNCS/), [IGVFFI9815IGUY](/sequence-files/IGVFFI9815IGUY/) 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/IGVFDS5339UNRP/"
            },
            {
                "category": "missing sequencing kit",
                "detail": "Measurement set [IGVFDS0657YBVN](/measurement-sets/IGVFDS0657YBVN/) has sequence file(s) [IGVFFI0567LHAG](/sequence-files/IGVFFI0567LHAG/), [IGVFFI0729NJWD](/sequence-files/IGVFFI0729NJWD/), [IGVFFI5586QFMY](/sequence-files/IGVFFI5586QFMY/), [IGVFFI2725QQFG](/sequence-files/IGVFFI2725QQFG/), [IGVFFI0060LELM](/sequence-files/IGVFFI0060LELM/), [IGVFFI9833YXEJ](/sequence-files/IGVFFI9833YXEJ/), [IGVFFI3869NPKN](/sequence-files/IGVFFI3869NPKN/), [IGVFFI2466VXVK](/sequence-files/IGVFFI2466VXVK/) 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/IGVFDS0657YBVN/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS0657YBVN](/measurement-sets/IGVFDS0657YBVN/) has sequence file(s): [IGVFFI0567LHAG](/sequence-files/IGVFFI0567LHAG/), [IGVFFI0729NJWD](/sequence-files/IGVFFI0729NJWD/), [IGVFFI5586QFMY](/sequence-files/IGVFFI5586QFMY/), [IGVFFI2725QQFG](/sequence-files/IGVFFI2725QQFG/), [IGVFFI0060LELM](/sequence-files/IGVFFI0060LELM/), [IGVFFI9833YXEJ](/sequence-files/IGVFFI9833YXEJ/), [IGVFFI3869NPKN](/sequence-files/IGVFFI3869NPKN/), [IGVFFI2466VXVK](/sequence-files/IGVFFI2466VXVK/) 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/IGVFDS0657YBVN/"
            }
        ]
    },
    "auxiliary_sets": [
        {
            "@id": "/auxiliary-sets/IGVFDS5339UNRP/",
            "accession": "IGVFDS5339UNRP",
            "aliases": [
                "gary-hon:TF_Perturb_Seq_Pilot_Lenti_NPC_sgRNA_LW284"
            ],
            "file_set_type": "gRNA sequencing",
            "status": "preview"
        },
        {
            "@id": "/auxiliary-sets/IGVFDS2693DPLW/",
            "accession": "IGVFDS2693DPLW",
            "aliases": [
                "gary-hon:TF_Perturb_Seq_Pilot_Lenti_NPC_HTO_LW284"
            ],
            "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": "2024-02-29T16:52:25.937545+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/IGVFFI0567LHAG/",
            "accession": "IGVFFI0567LHAG",
            "aliases": [
                "gary-hon:LW284_1_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:26:00.677040+00:00",
            "file_format": "fastq",
            "file_size": 79014274,
            "href": "/sequence-files/IGVFFI0567LHAG/@@download/IGVFFI0567LHAG.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/01/5f7898b5-2e90-4070-adeb-a0715cf6c822/IGVFFI0567LHAG.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/LW284_S22_L001_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI0729NJWD/",
            "accession": "IGVFFI0729NJWD",
            "aliases": [
                "gary-hon:LW284_1_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:26:05.335885+00:00",
            "file_format": "fastq",
            "file_size": 233700193,
            "href": "/sequence-files/IGVFFI0729NJWD/@@download/IGVFFI0729NJWD.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/01/3ebf2fe7-b3e6-4bdd-b5f5-1d84e600b497/IGVFFI0729NJWD.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/LW284_S22_L001_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI5586QFMY/",
            "accession": "IGVFFI5586QFMY",
            "aliases": [
                "gary-hon:LW284_1_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:26:11.130914+00:00",
            "file_format": "fastq",
            "file_size": 549762093,
            "href": "/sequence-files/IGVFFI5586QFMY/@@download/IGVFFI5586QFMY.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/01/a9fdeb0c-a5da-4a1d-b396-955dce43c07e/IGVFFI5586QFMY.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/LW284_S22_L001_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI2725QQFG/",
            "accession": "IGVFFI2725QQFG",
            "aliases": [
                "gary-hon:LW284_1_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:25:55.994242+00:00",
            "file_format": "fastq",
            "file_size": 90886916,
            "href": "/sequence-files/IGVFFI2725QQFG/@@download/IGVFFI2725QQFG.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/01/15da4ef2-37b2-4bd9-94ba-8125f58b1eef/IGVFFI2725QQFG.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/LW284_S22_L001_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI0060LELM/",
            "accession": "IGVFFI0060LELM",
            "aliases": [
                "gary-hon:LW284_2_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:26:28.919041+00:00",
            "file_format": "fastq",
            "file_size": 227740653,
            "href": "/sequence-files/IGVFFI0060LELM/@@download/IGVFFI0060LELM.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/01/2f06f109-2bb7-42b4-8527-0b81e622e647/IGVFFI0060LELM.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/LW284_S22_L002_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9833YXEJ/",
            "accession": "IGVFFI9833YXEJ",
            "aliases": [
                "gary-hon:LW284_2_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:26:34.758996+00:00",
            "file_format": "fastq",
            "file_size": 534301779,
            "href": "/sequence-files/IGVFFI9833YXEJ/@@download/IGVFFI9833YXEJ.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/LW284_S22_L002_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3869NPKN/",
            "accession": "IGVFFI3869NPKN",
            "aliases": [
                "gary-hon:LW284_2_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:26:19.734140+00:00",
            "file_format": "fastq",
            "file_size": 89132503,
            "href": "/sequence-files/IGVFFI3869NPKN/@@download/IGVFFI3869NPKN.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/01/38570c44-7c1d-4d6d-90d9-bc24c7a069d3/IGVFFI3869NPKN.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/LW284_S22_L002_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI2466VXVK/",
            "accession": "IGVFFI2466VXVK",
            "aliases": [
                "gary-hon:LW284_2_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:26:24.360058+00:00",
            "file_format": "fastq",
            "file_size": 75842540,
            "href": "/sequence-files/IGVFFI2466VXVK/@@download/IGVFFI2466VXVK.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/01/1310287b-5377-413c-994c-5e7bb5e7ef5a/IGVFFI2466VXVK.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/LW284_S22_L002_I2_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/IGVFSM2597WGYB/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM2597WGYB",
            "aliases": [
                "nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_NPC_Lenti_LW284"
            ],
            "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_LW284), 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": "2024-03-01T17:24:12.594077+00:00",
    "submitter_comment": "Transcriptiome for LW284",
    "summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "51b9b19c-0504-4fae-8c89-2d40067a2e50"
}