IGVFDS4028IRAH

{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS4028IRAH/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS4028IRAH",
    "aliases": [
        "gary-hon:TF_Perturb_Seq_Pilot_Lenti_NPC_LW283"
    ],
    "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 [IGVFDS4028IRAH](/measurement-sets/IGVFDS4028IRAH/) has sequence file(s) [IGVFFI3964ARVE](/sequence-files/IGVFFI3964ARVE/), [IGVFFI3233FBMS](/sequence-files/IGVFFI3233FBMS/), [IGVFFI1317OLKM](/sequence-files/IGVFFI1317OLKM/), [IGVFFI6072QDBA](/sequence-files/IGVFFI6072QDBA/), [IGVFFI7655ZVVE](/sequence-files/IGVFFI7655ZVVE/), [IGVFFI8428EQHY](/sequence-files/IGVFFI8428EQHY/), [IGVFFI9367DVXT](/sequence-files/IGVFFI9367DVXT/), [IGVFFI5841BYNF](/sequence-files/IGVFFI5841BYNF/) 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/IGVFDS4028IRAH/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS4028IRAH](/measurement-sets/IGVFDS4028IRAH/) has sequence file(s): [IGVFFI3964ARVE](/sequence-files/IGVFFI3964ARVE/), [IGVFFI3233FBMS](/sequence-files/IGVFFI3233FBMS/), [IGVFFI1317OLKM](/sequence-files/IGVFFI1317OLKM/), [IGVFFI6072QDBA](/sequence-files/IGVFFI6072QDBA/), [IGVFFI7655ZVVE](/sequence-files/IGVFFI7655ZVVE/), [IGVFFI8428EQHY](/sequence-files/IGVFFI8428EQHY/), [IGVFFI9367DVXT](/sequence-files/IGVFFI9367DVXT/), [IGVFFI5841BYNF](/sequence-files/IGVFFI5841BYNF/) 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/IGVFDS4028IRAH/"
            },
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS2600XYHD](/auxiliary-sets/IGVFDS2600XYHD/) has sequence file(s) [IGVFFI5245DMCW](/sequence-files/IGVFFI5245DMCW/), [IGVFFI3918UPES](/sequence-files/IGVFFI3918UPES/), [IGVFFI7518XBAK](/sequence-files/IGVFFI7518XBAK/), [IGVFFI9972BHWI](/sequence-files/IGVFFI9972BHWI/), [IGVFFI8032BRVG](/sequence-files/IGVFFI8032BRVG/), [IGVFFI6392ULTE](/sequence-files/IGVFFI6392ULTE/), [IGVFFI2868ZCYM](/sequence-files/IGVFFI2868ZCYM/), [IGVFFI9747MXBT](/sequence-files/IGVFFI9747MXBT/) 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/IGVFDS2600XYHD/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS2600XYHD](/auxiliary-sets/IGVFDS2600XYHD/) has sequence file(s): [IGVFFI5245DMCW](/sequence-files/IGVFFI5245DMCW/), [IGVFFI3918UPES](/sequence-files/IGVFFI3918UPES/), [IGVFFI7518XBAK](/sequence-files/IGVFFI7518XBAK/), [IGVFFI9972BHWI](/sequence-files/IGVFFI9972BHWI/), [IGVFFI8032BRVG](/sequence-files/IGVFFI8032BRVG/), [IGVFFI6392ULTE](/sequence-files/IGVFFI6392ULTE/), [IGVFFI2868ZCYM](/sequence-files/IGVFFI2868ZCYM/), [IGVFFI9747MXBT](/sequence-files/IGVFFI9747MXBT/) 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/IGVFDS2600XYHD/"
            },
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS4262EBDF](/auxiliary-sets/IGVFDS4262EBDF/) has sequence file(s) [IGVFFI1665CADL](/sequence-files/IGVFFI1665CADL/), [IGVFFI3519VNMQ](/sequence-files/IGVFFI3519VNMQ/), [IGVFFI2060GRST](/sequence-files/IGVFFI2060GRST/), [IGVFFI8010OOFR](/sequence-files/IGVFFI8010OOFR/), [IGVFFI9758LRXH](/sequence-files/IGVFFI9758LRXH/), [IGVFFI6625XXQD](/sequence-files/IGVFFI6625XXQD/), [IGVFFI1976NIRG](/sequence-files/IGVFFI1976NIRG/), [IGVFFI1491BIMR](/sequence-files/IGVFFI1491BIMR/) 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/IGVFDS4262EBDF/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS4262EBDF](/auxiliary-sets/IGVFDS4262EBDF/) has sequence file(s): [IGVFFI1665CADL](/sequence-files/IGVFFI1665CADL/), [IGVFFI3519VNMQ](/sequence-files/IGVFFI3519VNMQ/), [IGVFFI2060GRST](/sequence-files/IGVFFI2060GRST/), [IGVFFI8010OOFR](/sequence-files/IGVFFI8010OOFR/), [IGVFFI9758LRXH](/sequence-files/IGVFFI9758LRXH/), [IGVFFI6625XXQD](/sequence-files/IGVFFI6625XXQD/), [IGVFFI1976NIRG](/sequence-files/IGVFFI1976NIRG/), [IGVFFI1491BIMR](/sequence-files/IGVFFI1491BIMR/) 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/IGVFDS4262EBDF/"
            }
        ]
    },
    "auxiliary_sets": [
        {
            "@id": "/auxiliary-sets/IGVFDS4262EBDF/",
            "accession": "IGVFDS4262EBDF",
            "aliases": [
                "gary-hon:TF_Perturb_Seq_Pilot_Lenti_NPC_sgRNA_LW283"
            ],
            "file_set_type": "gRNA sequencing",
            "status": "preview"
        },
        {
            "@id": "/auxiliary-sets/IGVFDS2600XYHD/",
            "accession": "IGVFDS2600XYHD",
            "aliases": [
                "gary-hon:TF_Perturb_Seq_Pilot_Lenti_NPC_HTO_LW283"
            ],
            "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": "2024-02-29T16:52:24.520021+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/IGVFFI3964ARVE/",
            "accession": "IGVFFI3964ARVE",
            "aliases": [
                "gary-hon:LW283_1_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:23:24.447593+00:00",
            "file_format": "fastq",
            "file_size": 93551303,
            "href": "/sequence-files/IGVFFI3964ARVE/@@download/IGVFFI3964ARVE.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/01/c52e92a5-5e4f-45ea-996b-f29d5cd66aa8/IGVFFI3964ARVE.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/LW283_S21_L001_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3233FBMS/",
            "accession": "IGVFFI3233FBMS",
            "aliases": [
                "gary-hon:LW283_1_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:23:29.500760+00:00",
            "file_format": "fastq",
            "file_size": 89256549,
            "href": "/sequence-files/IGVFFI3233FBMS/@@download/IGVFFI3233FBMS.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/01/ce58f204-71f3-491e-bd2a-3896680eaaa5/IGVFFI3233FBMS.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/LW283_S21_L001_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI1317OLKM/",
            "accession": "IGVFFI1317OLKM",
            "aliases": [
                "gary-hon:LW283_1_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:23:40.053726+00:00",
            "file_format": "fastq",
            "file_size": 573775618,
            "href": "/sequence-files/IGVFFI1317OLKM/@@download/IGVFFI1317OLKM.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/01/a9bdb1d2-96d1-4fe4-9d98-effbe68f85f2/IGVFFI1317OLKM.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/LW283_S21_L001_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI6072QDBA/",
            "accession": "IGVFFI6072QDBA",
            "aliases": [
                "gary-hon:LW283_2_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:23:53.253972+00:00",
            "file_format": "fastq",
            "file_size": 85255014,
            "href": "/sequence-files/IGVFFI6072QDBA/@@download/IGVFFI6072QDBA.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/01/c01c60f7-d5ec-4fd2-a23e-e6998b96c8d8/IGVFFI6072QDBA.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/LW283_S21_L002_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI7655ZVVE/",
            "accession": "IGVFFI7655ZVVE",
            "aliases": [
                "gary-hon:LW283_2_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:24:03.851896+00:00",
            "file_format": "fastq",
            "file_size": 566381073,
            "href": "/sequence-files/IGVFFI7655ZVVE/@@download/IGVFFI7655ZVVE.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/01/400aebae-b912-4217-97b1-7a9cbbeedaa2/IGVFFI7655ZVVE.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/LW283_S21_L002_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8428EQHY/",
            "accession": "IGVFFI8428EQHY",
            "aliases": [
                "gary-hon:LW283_1_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:23:34.097357+00:00",
            "file_format": "fastq",
            "file_size": 244502638,
            "href": "/sequence-files/IGVFFI8428EQHY/@@download/IGVFFI8428EQHY.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/01/3e84d951-97f0-4037-9004-6e71b7d0cfa3/IGVFFI8428EQHY.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/LW283_S21_L001_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9367DVXT/",
            "accession": "IGVFFI9367DVXT",
            "aliases": [
                "gary-hon:LW283_2_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:23:48.664693+00:00",
            "file_format": "fastq",
            "file_size": 93157501,
            "href": "/sequence-files/IGVFFI9367DVXT/@@download/IGVFFI9367DVXT.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/01/09eb5911-e144-42f5-a483-4ac8114b69e7/IGVFFI9367DVXT.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/LW283_S21_L002_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI5841BYNF/",
            "accession": "IGVFFI5841BYNF",
            "aliases": [
                "gary-hon:LW283_2_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:23:57.984352+00:00",
            "file_format": "fastq",
            "file_size": 242315493,
            "href": "/sequence-files/IGVFFI5841BYNF/@@download/IGVFFI5841BYNF.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/01/9ab36d55-1b2f-4d61-8235-041cd34b7c96/IGVFFI5841BYNF.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/LW283_S21_L002_R1_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/IGVFSM8464JMJS/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM8464JMJS",
            "aliases": [
                "nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_NPC_Lenti_LW283"
            ],
            "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_LW283), 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": "2024-03-01T17:21:38.396125+00:00",
    "submitter_comment": "Transcriptiome for LW283",
    "summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "6a2f8183-f3e1-4c79-aa03-fd20825599c2"
}