IGVFDS8841TWDX

{
    "@context": "/terms/",
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    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS8841TWDX",
    "aliases": [
        "jesse-engreitz:measurement_set-scRNAseq_2kG_2PMDox2_5"
    ],
    "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 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 are expected to link to a sequence specification file.",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_missing_seqspec",
                "path": "/measurement-sets/IGVFDS8841TWDX/"
            },
            {
                "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 are expected to link to a sequence specification file.",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_missing_seqspec",
                "path": "/auxiliary-sets/IGVFDS7498VOOU/"
            },
            {
                "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/"
            }
        ]
    },
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            ],
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    ],
    "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"
    },
    "control_for": [],
    "creation_timestamp": "2024-01-18T03:10:06.609472+00:00",
    "donors": [
        {
            "@id": "/human-donors/IGVFDO3459DFTW/",
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            "sex": "female",
            "status": "released",
            "taxa": "Homo sapiens"
        }
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            "submitted_file_name": "/oak/stanford/groups/engreitz/Users/kangh/TeloHAEC_Perturb-seq_2kG/210528_Broad_fastq/scRNAseq_2kG_2PMDox2_5_S1_L001_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI5649YCIZ/",
            "accession": "IGVFFI5649YCIZ",
            "aliases": [
                "jesse-engreitz:sequence_file-teloHAEC_2kG_library-NovaSeq1-scRNAseq_2kG_2PMDox2_5_S1_L001_I1_001.fastq.gz"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2023-12-21T00:31:34.621336+00:00",
            "file_format": "fastq",
            "file_size": 2652887925,
            "href": "/sequence-files/IGVFFI5649YCIZ/@@download/IGVFFI5649YCIZ.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/21/4bd1c58c-ea13-41a4-bcf3-209383a7feb5/IGVFFI5649YCIZ.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/210528_Broad_fastq/scRNAseq_2kG_2PMDox2_5_S1_L001_I1_001.fastq.gz",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS7943IIWZ/"
    ],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "notes": "The readout 86015c12-b9a6-43ba-9601-5d75aab4d39c was removed from this measurement set.",
    "preferred_assay_title": "Perturb-seq",
    "protocols": [
        "https://www.protocols.io/view/systematic-perturb-seq-to-discover-endothelial-cel-261ged73yv47/v1"
    ],
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM6643KIQQ/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM6643KIQQ",
            "aliases": [
                "jesse-engreitz:in_vitro_systems-scRNAseq_2kG_2PMDox2_5"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                {
                    "@id": "/construct-library-sets/IGVFDS1298TUYG/",
                    "accession": "IGVFDS1298TUYG",
                    "file_set_type": "guide library",
                    "status": "preview",
                    "summary": "guide (sgRNA) library targeting genes in many genomic loci"
                }
            ],
            "modifications": [
                {
                    "@id": "/crispr-modifications/b4bc725a-8eeb-4180-9789-bece3516c0c1/",
                    "modality": "interference",
                    "status": "released"
                }
            ],
            "sample_terms": [
                {
                    "@id": "/sample-terms/NTR_0000753/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
                        "Item"
                    ],
                    "aliases": [
                        "igvf:TeloHAEC"
                    ],
                    "status": "released",
                    "summary": "TeloHAEC",
                    "term_name": "TeloHAEC"
                }
            ],
            "status": "preview",
            "summary": "TeloHAEC cell line, female, Homo sapiens modified with CRISPRi Sp-dCas9-KOX1-KRAB, transfected with a guide library",
            "taxa": "Homo sapiens"
        }
    ],
    "schema_version": "23",
    "status": "preview",
    "submitted_by": {
        "@id": "/users/05fa0dc9-0e33-427c-9d1f-82393edc4a03/",
        "title": "Helen Kang"
    },
    "submitted_files_timestamp": "2023-12-21T00:24:55.317422+00:00",
    "summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting genes in many genomic loci",
    "uuid": "e64f51eb-1522-4118-ad43-c0d10d3070a9"
}