IGVFDS7600PZYR

{
    "@context": "/terms/",
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    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS7600PZYR",
    "aliases": [
        "jesse-engreitz:measurement_set-scRNAseq_2kG_2PMDox2_1"
    ],
    "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": "Auxiliary set [IGVFDS4784DDTU](/auxiliary-sets/IGVFDS4784DDTU/) has sequence file(s): [IGVFFI4092GRZQ](/sequence-files/IGVFFI4092GRZQ/), [IGVFFI1378RGUV](/sequence-files/IGVFFI1378RGUV/), [IGVFFI7575DTDH](/sequence-files/IGVFFI7575DTDH/), [IGVFFI4619DNJG](/sequence-files/IGVFFI4619DNJG/) 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/IGVFDS4784DDTU/"
            },
            {
                "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/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS7600PZYR](/measurement-sets/IGVFDS7600PZYR/) has sequence file(s): [IGVFFI4487DHRU](/sequence-files/IGVFFI4487DHRU/), [IGVFFI9049JPTY](/sequence-files/IGVFFI9049JPTY/), [IGVFFI6125WLFU](/sequence-files/IGVFFI6125WLFU/), [IGVFFI2912EVSN](/sequence-files/IGVFFI2912EVSN/), [IGVFFI2157LCVI](/sequence-files/IGVFFI2157LCVI/), [IGVFFI2426GZJV](/sequence-files/IGVFFI2426GZJV/), [IGVFFI8328SBXI](/sequence-files/IGVFFI8328SBXI/), [IGVFFI7882CEIW](/sequence-files/IGVFFI7882CEIW/), [IGVFFI4775GVGW](/sequence-files/IGVFFI4775GVGW/), [IGVFFI5607YHVQ](/sequence-files/IGVFFI5607YHVQ/), [IGVFFI1492IMBA](/sequence-files/IGVFFI1492IMBA/), [IGVFFI4544QBUW](/sequence-files/IGVFFI4544QBUW/), [IGVFFI8003RIWJ](/sequence-files/IGVFFI8003RIWJ/), [IGVFFI6612DJXQ](/sequence-files/IGVFFI6612DJXQ/), [IGVFFI1024CKHO](/sequence-files/IGVFFI1024CKHO/) 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/IGVFDS7600PZYR/"
            }
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            "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"
    },
    "control_for": [],
    "creation_timestamp": "2024-01-18T03:10:05.300543+00:00",
    "donors": [
        {
            "@id": "/human-donors/IGVFDO3459DFTW/",
            "accession": "IGVFDO3459DFTW",
            "aliases": [
                "igvf:donor_of_teloHAEC"
            ],
            "sex": "female",
            "status": "released",
            "taxa": "Homo sapiens"
        }
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            "submitted_file_name": "/seq/landerlabCE/Users/Helen/TeloHAEC_Perturb-seq_2kG/240210_IGVF_recombined_fastqs/scRNAseq_2kG_2PMDox2_1_L001_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI1024CKHO/",
            "accession": "IGVFFI1024CKHO",
            "aliases": [
                "jesse-engreitz:sequence_file-teloHAEC_2kG_library-NovaSeq2-scRNAseq_2kG_2PMDox2_1_c_TGAAGTAC_L001_R2_001.fastq.gz"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2023-12-20T23:50:32.153016+00:00",
            "file_format": "fastq",
            "file_size": 4839299181,
            "href": "/sequence-files/IGVFFI1024CKHO/@@download/IGVFFI1024CKHO.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/20/b2285241-d706-4795-abbc-ec2506873699/IGVFFI1024CKHO.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_1_c_TGAAGTAC_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/IGVFSM0862BZMH/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM0862BZMH",
            "aliases": [
                "jesse-engreitz:in_vitro_systems-scRNAseq_2kG_2PMDox2_1"
            ],
            "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": "2023-12-20T23:46:39.750209+00:00",
    "summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting genes in many genomic loci",
    "uuid": "506f4995-5647-411b-8af6-6f196bd52da8"
}