IGVFDS0385ESBQ

{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS0385ESBQ/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS0385ESBQ",
    "aliases": [
        "jesse-engreitz:measurement_set-scRNAseq_2kG_2PMDox1_6"
    ],
    "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 [IGVFDS0385ESBQ](/measurement-sets/IGVFDS0385ESBQ/) has sequence file(s): [IGVFFI9790VMAE](/sequence-files/IGVFFI9790VMAE/), [IGVFFI0226LNBE](/sequence-files/IGVFFI0226LNBE/), [IGVFFI4899TNXF](/sequence-files/IGVFFI4899TNXF/) 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/IGVFDS0385ESBQ/"
            },
            {
                "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": "Auxiliary set [IGVFDS2031LFEN](/auxiliary-sets/IGVFDS2031LFEN/) has sequence file(s): [IGVFFI8535CSXL](/sequence-files/IGVFFI8535CSXL/), [IGVFFI4014XSAK](/sequence-files/IGVFFI4014XSAK/), [IGVFFI3955WSPN](/sequence-files/IGVFFI3955WSPN/), [IGVFFI6132PXBN](/sequence-files/IGVFFI6132PXBN/), [IGVFFI5712MZTB](/sequence-files/IGVFFI5712MZTB/), [IGVFFI6559SZAD](/sequence-files/IGVFFI6559SZAD/), [IGVFFI8066GKDM](/sequence-files/IGVFFI8066GKDM/), [IGVFFI0864MICP](/sequence-files/IGVFFI0864MICP/) 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/IGVFDS2031LFEN/"
            }
        ]
    },
    "auxiliary_sets": [
        {
            "@id": "/auxiliary-sets/IGVFDS2031LFEN/",
            "accession": "IGVFDS2031LFEN",
            "aliases": [
                "jesse-engreitz:auxiliary_sets-scRNAseq_2kG_2PMDox1_6"
            ],
            "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"
    },
    "control_for": [],
    "creation_timestamp": "2024-01-18T03:10:04.363202+00:00",
    "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/IGVFFI9790VMAE/",
            "accession": "IGVFFI9790VMAE",
            "aliases": [
                "jesse-engreitz:sequence_file-teloHAEC_2kG_library-NovaSeq1-scRNAseq_2kG_2PMDox1_6_S1_L001_I1_001.fastq.gz"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2023-12-20T23:32:50.626102+00:00",
            "file_format": "fastq",
            "file_size": 3044834888,
            "href": "/sequence-files/IGVFFI9790VMAE/@@download/IGVFFI9790VMAE.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/20/4582b17d-c9aa-453a-b8e1-fc13d1a99b57/IGVFFI9790VMAE.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_2PMDox1_6_S1_L001_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI0226LNBE/",
            "accession": "IGVFFI0226LNBE",
            "aliases": [
                "jesse-engreitz:sequence_file-teloHAEC_2kG_library-NovaSeq1-scRNAseq_2kG_2PMDox1_6_S1_L001_R1_001.fastq.gz"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2023-12-20T23:33:24.982322+00:00",
            "file_format": "fastq",
            "file_size": 10638894903,
            "href": "/sequence-files/IGVFFI0226LNBE/@@download/IGVFFI0226LNBE.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/20/715b701f-cac7-4445-aacd-00b8c71778d0/IGVFFI0226LNBE.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_2PMDox1_6_S1_L001_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI4899TNXF/",
            "accession": "IGVFFI4899TNXF",
            "aliases": [
                "jesse-engreitz:sequence_file-teloHAEC_2kG_library-NovaSeq1-scRNAseq_2kG_2PMDox1_6_S1_L001_R2_001.fastq.gz"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2023-12-20T23:34:58.911520+00:00",
            "file_format": "fastq",
            "file_size": 14285208928,
            "href": "/sequence-files/IGVFFI4899TNXF/@@download/IGVFFI4899TNXF.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/20/2eaa3093-d945-42e9-bbd4-3b683bc3f0b2/IGVFFI4899TNXF.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0008637/",
                "status": "released",
                "term_name": "Illumina NovaSeq 6000"
            },
            "status": "preview",
            "submitted_file_name": "/seq/landerlabCE/Users/Helen/TeloHAEC_Perturb-seq_2kG/240210_IGVF_recombined_fastqs/scRNAseq_2kG_2PMDox1_6_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/IGVFSM9019CRXH/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM9019CRXH",
            "aliases": [
                "jesse-engreitz:in_vitro_systems-scRNAseq_2kG_2PMDox1_6"
            ],
            "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": "2023-12-20T23:32:50.626102+00:00",
    "summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting genes in many genomic loci",
    "uuid": "ed99fd09-9ae3-48b3-8eeb-84908cf5f1e1"
}