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IGVFDS8841TWDX

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{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS8841TWDX/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS8841TWDX",
    "aliases": [
        "jesse-engreitz:measurement_set-scRNAseq_2kG_2PMDox2_5"
    ],
    "assay_term": {
        "@id": "/assay-terms/OBI_0003660/",
        "assay_slims": [
            "CRISPR screens"
        ],
        "status": "released",
        "term_name": "in vitro CRISPR screen using single-cell RNA-seq"
    },
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "mismatched status",
                "detail": "Preview measurement set [IGVFDS8841TWDX](/measurement-sets/IGVFDS8841TWDX/) has in progress subobject publication [2e37380f-fb50-4dbc-a7ec-e9e6532c9f99](/publications/2e37380f-fb50-4dbc-a7ec-e9e6532c9f99/).",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_item_status",
                "path": "/measurement-sets/IGVFDS8841TWDX/"
            },
            {
                "category": "mismatched status",
                "detail": "Preview measurement set [IGVFDS8841TWDX](/measurement-sets/IGVFDS8841TWDX/) has in progress subobject tabular file [IGVFFI4695IKAL](/tabular-files/IGVFFI4695IKAL/).",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_item_status",
                "path": "/measurement-sets/IGVFDS8841TWDX/"
            },
            {
                "category": "NTR term ID",
                "detail": "Sample term for [NTR_0000753](/sample-terms/NTR_0000753/) has been newly requested. Ontology terms with a newly requested term ID are expected to have it updated following its addition to the appropriate ontology database.",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_ntr_term_id",
                "path": "/sample-terms/NTR_0000753/"
            }
        ],
        "NOT_COMPLIANT": [
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS7498VOOU](/auxiliary-sets/IGVFDS7498VOOU/) has sequence file(s): [IGVFFI9018CEVP](/sequence-files/IGVFFI9018CEVP/), [IGVFFI0070PCWW](/sequence-files/IGVFFI0070PCWW/), [IGVFFI4437QXSH](/sequence-files/IGVFFI4437QXSH/), [IGVFFI6893DOBJ](/sequence-files/IGVFFI6893DOBJ/) which do not have any `seqspecs`. Sequence files in a file set associated with single cell data are expected to link to a sequence specification file.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_missing_seqspec",
                "path": "/auxiliary-sets/IGVFDS7498VOOU/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS8841TWDX](/measurement-sets/IGVFDS8841TWDX/) has sequence file(s): [IGVFFI3762BSGQ](/sequence-files/IGVFFI3762BSGQ/), [IGVFFI3401QKMA](/sequence-files/IGVFFI3401QKMA/), [IGVFFI6094RPZX](/sequence-files/IGVFFI6094RPZX/), [IGVFFI2897CYDA](/sequence-files/IGVFFI2897CYDA/), [IGVFFI8688YIFV](/sequence-files/IGVFFI8688YIFV/), [IGVFFI8556VPTP](/sequence-files/IGVFFI8556VPTP/), [IGVFFI2524TDDH](/sequence-files/IGVFFI2524TDDH/), [IGVFFI5193KFUL](/sequence-files/IGVFFI5193KFUL/), [IGVFFI9303KSLM](/sequence-files/IGVFFI9303KSLM/), [IGVFFI8820RZOX](/sequence-files/IGVFFI8820RZOX/), [IGVFFI9103ZOPV](/sequence-files/IGVFFI9103ZOPV/), [IGVFFI7582WACA](/sequence-files/IGVFFI7582WACA/), [IGVFFI3915VCBQ](/sequence-files/IGVFFI3915VCBQ/), [IGVFFI6446GHWG](/sequence-files/IGVFFI6446GHWG/), [IGVFFI5649YCIZ](/sequence-files/IGVFFI5649YCIZ/) which do not have any `seqspecs`. Sequence files in a file set associated with single cell data are expected to link to a sequence specification file.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_missing_seqspec",
                "path": "/measurement-sets/IGVFDS8841TWDX/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS8841TWDX](/measurement-sets/IGVFDS8841TWDX/) has a sequence file [IGVFFI3762BSGQ](/sequence-files/IGVFFI3762BSGQ/) missing `read_names`. Sequence files are expected to have read names.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_single_cell_read_names",
                "path": "/measurement-sets/IGVFDS8841TWDX/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS8841TWDX](/measurement-sets/IGVFDS8841TWDX/) has a sequence file [IGVFFI3401QKMA](/sequence-files/IGVFFI3401QKMA/) missing `read_names`. Sequence files are expected to have read names.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_single_cell_read_names",
                "path": "/measurement-sets/IGVFDS8841TWDX/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS8841TWDX](/measurement-sets/IGVFDS8841TWDX/) has a sequence file [IGVFFI2897CYDA](/sequence-files/IGVFFI2897CYDA/) missing `read_names`. Sequence files are expected to have read names.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_single_cell_read_names",
                "path": "/measurement-sets/IGVFDS8841TWDX/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS8841TWDX](/measurement-sets/IGVFDS8841TWDX/) has a sequence file [IGVFFI8688YIFV](/sequence-files/IGVFFI8688YIFV/) missing `read_names`. Sequence files are expected to have read names.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_single_cell_read_names",
                "path": "/measurement-sets/IGVFDS8841TWDX/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS8841TWDX](/measurement-sets/IGVFDS8841TWDX/) has a sequence file [IGVFFI2524TDDH](/sequence-files/IGVFFI2524TDDH/) missing `read_names`. Sequence files are expected to have read names.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_single_cell_read_names",
                "path": "/measurement-sets/IGVFDS8841TWDX/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS8841TWDX](/measurement-sets/IGVFDS8841TWDX/) has a sequence file [IGVFFI5193KFUL](/sequence-files/IGVFFI5193KFUL/) missing `read_names`. Sequence files are expected to have read names.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_single_cell_read_names",
                "path": "/measurement-sets/IGVFDS8841TWDX/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS8841TWDX](/measurement-sets/IGVFDS8841TWDX/) has a sequence file [IGVFFI8820RZOX](/sequence-files/IGVFFI8820RZOX/) missing `read_names`. Sequence files are expected to have read names.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_single_cell_read_names",
                "path": "/measurement-sets/IGVFDS8841TWDX/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS8841TWDX](/measurement-sets/IGVFDS8841TWDX/) has a sequence file [IGVFFI9103ZOPV](/sequence-files/IGVFFI9103ZOPV/) missing `read_names`. Sequence files are expected to have read names.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_single_cell_read_names",
                "path": "/measurement-sets/IGVFDS8841TWDX/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS8841TWDX](/measurement-sets/IGVFDS8841TWDX/) has a sequence file [IGVFFI7582WACA](/sequence-files/IGVFFI7582WACA/) missing `read_names`. Sequence files are expected to have read names.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_single_cell_read_names",
                "path": "/measurement-sets/IGVFDS8841TWDX/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS8841TWDX](/measurement-sets/IGVFDS8841TWDX/) has a sequence file [IGVFFI6446GHWG](/sequence-files/IGVFFI6446GHWG/) missing `read_names`. Sequence files are expected to have read names.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_single_cell_read_names",
                "path": "/measurement-sets/IGVFDS8841TWDX/"
            }
        ],
        "WARNING": [
            {
                "category": "missing nucleic acid delivery",
                "detail": "In vitro system [IGVFSM6643KIQQ](/in-vitro-systems/IGVFSM6643KIQQ/) has `construct_library_sets` but is missing `nucleic_acid_delivery`. Samples linked to construct library sets are expected to specify nucleic acid delivery method.",
                "level": 40,
                "level_name": "WARNING",
                "name": "audit_missing_nucleic_acid_delivery",
                "path": "/in-vitro-systems/IGVFSM6643KIQQ/"
            }
        ]
    },
    "auxiliary_sets": [
        {
            "@id": "/auxiliary-sets/IGVFDS7498VOOU/",
            "accession": "IGVFDS7498VOOU",
            "aliases": [
                "jesse-engreitz:auxiliary_sets-scRNAseq_2kG_2PMDox2_5"
            ],
            "file_set_type": "gRNA sequencing",
            "status": "preview"
        }
    ],
    "award": {
        "@id": "/awards/HG011972/",
        "component": "functional characterization",
        "contact_pi": {
            "@id": "/users/6c75dbfa-635e-4a7a-8ec8-9e51e9c380a4/",
            "title": "Jesse Engreitz"
        },
        "title": "Stanford Center for Connecting DNA Variants to Function and Phenotype"
    },
    "construct_library_sets": [
        {
            "@id": "/construct-library-sets/IGVFDS1298TUYG/",
            "accession": "IGVFDS1298TUYG",
            "file_set_type": "guide library",
            "integrated_content_files": [
                {
                    "@id": "/tabular-files/IGVFFI9754AGFB/",
                    "accession": "IGVFFI9754AGFB",
                    "content_type": "guide RNA sequences",
                    "status": "in progress",
                    "summary": "GRCh38 guide RNA sequences"
                }
            ],
            "status": "preview",
            "summary": "guide (sgRNA) library targeting genes in many genomic loci"
        }
    ],
    "control_for": [],
    "creation_timestamp": "2024-01-18T03:10:06.609472+00:00",
    "data_use_limitation_summaries": [
        "no certificate"
    ],
    "donors": [
        {
            "@id": "/human-donors/IGVFDO3459DFTW/",
            "accession": "IGVFDO3459DFTW",
            "aliases": [
                "igvf:donor_of_teloHAEC"
            ],
            "sex": "female",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "externally_hosted": false,
    "file_set_type": "experimental data",
    "files": [
        {
            "@id": "/sequence-files/IGVFFI3762BSGQ/",
            "accession": "IGVFFI3762BSGQ",
            "aliases": [
                "jesse-engreitz:sequence_file-teloHAEC_2kG_library-NovaSeq2-scRNAseq_2kG_2PMDox2_5_b_GATCAGCA_L001_R1_001.fastq.gz"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2023-12-21T00:27:13.011515+00:00",
            "file_format": "fastq",
            "file_size": 3710939134,
            "href": "/sequence-files/IGVFFI3762BSGQ/@@download/IGVFFI3762BSGQ.fastq.gz",
            "md5sum": "400507d880e83b131c118c278167ab74",
            "s3_uri": "s3://igvf-files/2023/12/21/0db2a6d2-b7b7-4962-ad48-676fcccd43f5/IGVFFI3762BSGQ.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0008637/",
                "status": "released",
                "term_name": "Illumina NovaSeq 6000"
            },
            "status": "preview",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Users/kangh/TeloHAEC_Perturb-seq_2kG/210616_Broad_fastq/scRNAseq_2kG_2PMDox2_5_b_GATCAGCA_L001_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3401QKMA/",
            "accession": "IGVFFI3401QKMA",
            "aliases": [
                "jesse-engreitz:sequence_file-teloHAEC_2kG_library-NovaSeq2-scRNAseq_2kG_2PMDox2_5_b_GATCAGCA_L001_R2_001.fastq.gz"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2023-12-21T00:26:25.591676+00:00",
            "file_format": "fastq",
            "file_size": 5195931578,
            "href": "/sequence-files/IGVFFI3401QKMA/@@download/IGVFFI3401QKMA.fastq.gz",
            "md5sum": "33fe77c021e679008581ae4f9f2d52b7",
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            "sequencing_platform": {
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                "status": "released",
                "term_name": "Illumina NovaSeq 6000"
            },
            "status": "preview",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Users/kangh/TeloHAEC_Perturb-seq_2kG/210616_Broad_fastq/scRNAseq_2kG_2PMDox2_5_b_GATCAGCA_L001_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI6094RPZX/",
            "accession": "IGVFFI6094RPZX",
            "aliases": [
                "jesse-engreitz:sequence_file-teloHAEC_2kG_library-NovaSeq2-scRNAseq_2kG_2PMDox2_5_c_ACAACAGG_L001_I1_001.fastq.gz"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2023-12-21T00:29:18.463734+00:00",
            "file_format": "fastq",
            "file_size": 1144327977,
            "href": "/sequence-files/IGVFFI6094RPZX/@@download/IGVFFI6094RPZX.fastq.gz",
            "md5sum": "5692d6867ba182b897c036661e42bd47",
            "s3_uri": "s3://igvf-files/2023/12/21/1fcc0390-86e8-4e13-aaf9-f37e123f7235/IGVFFI6094RPZX.fastq.gz",
            "sequencing_platform": {
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                "status": "released",
                "term_name": "Illumina NovaSeq 6000"
            },
            "status": "preview",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Users/kangh/TeloHAEC_Perturb-seq_2kG/210616_Broad_fastq/scRNAseq_2kG_2PMDox2_5_c_ACAACAGG_L001_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI2897CYDA/",
            "accession": "IGVFFI2897CYDA",
            "aliases": [
                "jesse-engreitz:sequence_file-teloHAEC_2kG_library-NovaSeq2-scRNAseq_2kG_2PMDox2_5_c_ACAACAGG_L001_R1_001.fastq.gz"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2023-12-21T00:28:40.464298+00:00",
            "file_format": "fastq",
            "file_size": 4066341873,
            "href": "/sequence-files/IGVFFI2897CYDA/@@download/IGVFFI2897CYDA.fastq.gz",
            "md5sum": "f251a13af6f689b6c757da3d6bcdd9c6",
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            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0008637/",
                "status": "released",
                "term_name": "Illumina NovaSeq 6000"
            },
            "status": "preview",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Users/kangh/TeloHAEC_Perturb-seq_2kG/210616_Broad_fastq/scRNAseq_2kG_2PMDox2_5_c_ACAACAGG_L001_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8688YIFV/",
            "accession": "IGVFFI8688YIFV",
            "aliases": [
                "jesse-engreitz:sequence_file-teloHAEC_2kG_library-NovaSeq2-scRNAseq_2kG_2PMDox2_5_c_ACAACAGG_L001_R2_001.fastq.gz"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2023-12-21T00:27:49.014747+00:00",
            "file_format": "fastq",
            "file_size": 5687951295,
            "href": "/sequence-files/IGVFFI8688YIFV/@@download/IGVFFI8688YIFV.fastq.gz",
            "md5sum": "b1239257eb427422da7a40a99c13b3b9",
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            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0008637/",
                "status": "released",
                "term_name": "Illumina NovaSeq 6000"
            },
            "status": "preview",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Users/kangh/TeloHAEC_Perturb-seq_2kG/210616_Broad_fastq/scRNAseq_2kG_2PMDox2_5_c_ACAACAGG_L001_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8556VPTP/",
            "accession": "IGVFFI8556VPTP",
            "aliases": [
                "jesse-engreitz:sequence_file-teloHAEC_2kG_library-NovaSeq2-scRNAseq_2kG_2PMDox2_5_a_CTCGTCAC_L001_I1_001.fastq.gz"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2023-12-21T00:26:03.502261+00:00",
            "file_format": "fastq",
            "file_size": 794893135,
            "href": "/sequence-files/IGVFFI8556VPTP/@@download/IGVFFI8556VPTP.fastq.gz",
            "md5sum": "53985aa5f5f94ab1511193b5c13c3544",
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            "sequencing_platform": {
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                "status": "released",
                "term_name": "Illumina NovaSeq 6000"
            },
            "status": "preview",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Users/kangh/TeloHAEC_Perturb-seq_2kG/210616_Broad_fastq/scRNAseq_2kG_2PMDox2_5_a_CTCGTCAC_L001_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI2524TDDH/",
            "accession": "IGVFFI2524TDDH",
            "aliases": [
                "jesse-engreitz:sequence_file-teloHAEC_2kG_library-NovaSeq2-scRNAseq_2kG_2PMDox2_5_a_CTCGTCAC_L001_R1_001.fastq.gz"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2023-12-21T00:24:55.317422+00:00",
            "file_format": "fastq",
            "file_size": 2980248807,
            "href": "/sequence-files/IGVFFI2524TDDH/@@download/IGVFFI2524TDDH.fastq.gz",
            "md5sum": "7509ae43361f3149369c42bc16091826",
            "s3_uri": "s3://igvf-files/2023/12/21/e5fa59eb-88d3-409a-ba67-8fa6fb1e3454/IGVFFI2524TDDH.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0008637/",
                "status": "released",
                "term_name": "Illumina NovaSeq 6000"
            },
            "status": "preview",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Users/kangh/TeloHAEC_Perturb-seq_2kG/210616_Broad_fastq/scRNAseq_2kG_2PMDox2_5_a_CTCGTCAC_L001_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI5193KFUL/",
            "accession": "IGVFFI5193KFUL",
            "aliases": [
                "jesse-engreitz:sequence_file-teloHAEC_2kG_library-NovaSeq2-scRNAseq_2kG_2PMDox2_5_a_CTCGTCAC_L001_R2_001.fastq.gz"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2023-12-21T00:25:24.866566+00:00",
            "file_format": "fastq",
            "file_size": 4159186202,
            "href": "/sequence-files/IGVFFI5193KFUL/@@download/IGVFFI5193KFUL.fastq.gz",
            "md5sum": "826212fd7333b1919d4b028e2f318065",
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            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0008637/",
                "status": "released",
                "term_name": "Illumina NovaSeq 6000"
            },
            "status": "preview",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Users/kangh/TeloHAEC_Perturb-seq_2kG/210616_Broad_fastq/scRNAseq_2kG_2PMDox2_5_a_CTCGTCAC_L001_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9303KSLM/",
            "accession": "IGVFFI9303KSLM",
            "aliases": [
                "jesse-engreitz:sequence_file-teloHAEC_2kG_library-NovaSeq2-scRNAseq_2kG_2PMDox2_5_d_TGGTGTTT_L001_I1_001.fastq.gz"
            ],
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