IGVFDS6988JXXY

{
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        "jesse-engreitz:measurement_set-scRNAseq_2kG_11AMDox_2"
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        "@id": "/assay-terms/OBI_0003660/",
        "status": "released",
        "term_name": "in vitro CRISPR screen using single-cell RNA-seq"
    },
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        "INTERNAL_ACTION": [
            {
                "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",
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            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS6988JXXY](/measurement-sets/IGVFDS6988JXXY/) has sequence file(s): [IGVFFI2630DHSW](/sequence-files/IGVFFI2630DHSW/), [IGVFFI7010OHYN](/sequence-files/IGVFFI7010OHYN/), [IGVFFI6039XWXL](/sequence-files/IGVFFI6039XWXL/), [IGVFFI9123MXUQ](/sequence-files/IGVFFI9123MXUQ/), [IGVFFI4457IIQJ](/sequence-files/IGVFFI4457IIQJ/), [IGVFFI2083YGXI](/sequence-files/IGVFFI2083YGXI/), [IGVFFI6377KSCX](/sequence-files/IGVFFI6377KSCX/), [IGVFFI2750MKBC](/sequence-files/IGVFFI2750MKBC/), [IGVFFI7760CULU](/sequence-files/IGVFFI7760CULU/), [IGVFFI4236KWOZ](/sequence-files/IGVFFI4236KWOZ/), [IGVFFI0543XYDB](/sequence-files/IGVFFI0543XYDB/), [IGVFFI5923PWYI](/sequence-files/IGVFFI5923PWYI/), [IGVFFI2076YYYQ](/sequence-files/IGVFFI2076YYYQ/), [IGVFFI5220PBRZ](/sequence-files/IGVFFI5220PBRZ/), [IGVFFI2975TGMY](/sequence-files/IGVFFI2975TGMY/) 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/IGVFDS6988JXXY/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS6454USPN](/auxiliary-sets/IGVFDS6454USPN/) has sequence file(s): [IGVFFI7088MWDI](/sequence-files/IGVFFI7088MWDI/), [IGVFFI2366TACA](/sequence-files/IGVFFI2366TACA/), [IGVFFI2902MSBX](/sequence-files/IGVFFI2902MSBX/), [IGVFFI7579ADQD](/sequence-files/IGVFFI7579ADQD/) 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",
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            "title": "Jesse Engreitz"
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        "title": "Stanford Center for Connecting DNA Variants to Function and Phenotype"
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            "@id": "/sequence-files/IGVFFI2975TGMY/",
            "accession": "IGVFFI2975TGMY",
            "aliases": [
                "jesse-engreitz:sequence_file-teloHAEC_2kG_library-NovaSeq2-scRNAseq_2kG_11AMDox_2_d_ATGAGAAA_L001_I1_001.fastq.gz"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2023-12-20T22:05:29.547763+00:00",
            "file_format": "fastq",
            "file_size": 552665487,
            "href": "/sequence-files/IGVFFI2975TGMY/@@download/IGVFFI2975TGMY.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/20/5b6a9702-cb4f-408b-8820-44439c8270bc/IGVFFI2975TGMY.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_11AMDox_2_d_ATGAGAAA_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/IGVFSM1575CPXR/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM1575CPXR",
            "aliases": [
                "jesse-engreitz:in_vitro_systems-scRNAseq_2kG_11AMDox_2"
            ],
            "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": "2023-12-20T22:03:00.388908+00:00",
    "summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting genes in many genomic loci",
    "uuid": "175a8ad8-28a7-4aff-b98d-c8f6df27ff82"
}