IGVFDS9990NLDH

{
    "@context": "/terms/",
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    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS9990NLDH",
    "aliases": [
        "jesse-engreitz:measurement_set-scRNAseq_2kG_2PMDox2_2"
    ],
    "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 [IGVFDS9990NLDH](/measurement-sets/IGVFDS9990NLDH/) has sequence file(s): [IGVFFI5630OAME](/sequence-files/IGVFFI5630OAME/), [IGVFFI8377VRDR](/sequence-files/IGVFFI8377VRDR/), [IGVFFI9729ALBI](/sequence-files/IGVFFI9729ALBI/), [IGVFFI1729OFNZ](/sequence-files/IGVFFI1729OFNZ/), [IGVFFI0433KVBB](/sequence-files/IGVFFI0433KVBB/), [IGVFFI5850PMMU](/sequence-files/IGVFFI5850PMMU/), [IGVFFI3922SFRH](/sequence-files/IGVFFI3922SFRH/), [IGVFFI7055SNHD](/sequence-files/IGVFFI7055SNHD/), [IGVFFI0124DGXW](/sequence-files/IGVFFI0124DGXW/), [IGVFFI7978EKHA](/sequence-files/IGVFFI7978EKHA/), [IGVFFI5264PBTM](/sequence-files/IGVFFI5264PBTM/), [IGVFFI5241ZFKK](/sequence-files/IGVFFI5241ZFKK/), [IGVFFI4885HQOA](/sequence-files/IGVFFI4885HQOA/), [IGVFFI8854GPRU](/sequence-files/IGVFFI8854GPRU/), [IGVFFI5195LEZD](/sequence-files/IGVFFI5195LEZD/) 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/IGVFDS9990NLDH/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS7359MSBY](/auxiliary-sets/IGVFDS7359MSBY/) has sequence file(s): [IGVFFI0056ELXT](/sequence-files/IGVFFI0056ELXT/), [IGVFFI5659FYZA](/sequence-files/IGVFFI5659FYZA/), [IGVFFI4464QAQU](/sequence-files/IGVFFI4464QAQU/), [IGVFFI0326UVNH](/sequence-files/IGVFFI0326UVNH/) 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/IGVFDS7359MSBY/"
            },
            {
                "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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            ],
            "file_set_type": "gRNA sequencing",
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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": "2024-01-18T03:10:05.610962+00:00",
    "donors": [
        {
            "@id": "/human-donors/IGVFDO3459DFTW/",
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            "aliases": [
                "igvf:donor_of_teloHAEC"
            ],
            "sex": "female",
            "status": "released",
            "taxa": "Homo sapiens"
        }
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    "externally_hosted": false,
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            "submitted_file_name": "/seq/landerlabCE/Users/Helen/TeloHAEC_Perturb-seq_2kG/240210_IGVF_recombined_fastqs/scRNAseq_2kG_2PMDox2_2_L001_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI5195LEZD/",
            "accession": "IGVFFI5195LEZD",
            "aliases": [
                "jesse-engreitz:sequence_file-teloHAEC_2kG_library-NovaSeq2-scRNAseq_2kG_2PMDox2_2_b_GGTTCCTC_L001_R2_001.fastq.gz"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2023-12-20T23:58:08.039951+00:00",
            "file_format": "fastq",
            "file_size": 4313414491,
            "href": "/sequence-files/IGVFFI5195LEZD/@@download/IGVFFI5195LEZD.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/20/80d01d52-6eeb-49d1-8964-757054a2796e/IGVFFI5195LEZD.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_2_b_GGTTCCTC_L001_R2_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/IGVFSM3104QEEP/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM3104QEEP",
            "aliases": [
                "jesse-engreitz:in_vitro_systems-scRNAseq_2kG_2PMDox2_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": "2023-12-20T23:56:08.843094+00:00",
    "summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting genes in many genomic loci",
    "uuid": "11bc0bd1-70c1-4996-a9d5-3db831bbcc89"
}