IGVFDS4972ICEM

{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS4972ICEM/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS4972ICEM",
    "aliases": [
        "jesse-engreitz:auxiliary_sets-scRNAseq_2kG_2PMDox2_3"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS4972ICEM](/auxiliary-sets/IGVFDS4972ICEM/) has sequence file(s): [IGVFFI5615OENT](/sequence-files/IGVFFI5615OENT/), [IGVFFI8376NVAX](/sequence-files/IGVFFI8376NVAX/), [IGVFFI9779WRBT](/sequence-files/IGVFFI9779WRBT/), [IGVFFI9575YXQY](/sequence-files/IGVFFI9575YXQY/) 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/IGVFDS4972ICEM/"
            },
            {
                "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/"
            }
        ]
    },
    "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": "2024-02-06T19:29:44.484765+00:00",
    "donors": [
        {
            "@id": "/human-donors/IGVFDO3459DFTW/",
            "accession": "IGVFDO3459DFTW",
            "aliases": [
                "igvf:donor_of_teloHAEC"
            ],
            "sex": "female",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "file_set_type": "gRNA sequencing",
    "files": [
        {
            "@id": "/sequence-files/IGVFFI5615OENT/",
            "accession": "IGVFFI5615OENT",
            "aliases": [
                "jesse-engreitz:sequence_files-TeloHAEC_Perturb-seq_2kG-Dialout_2kg_2PMDox2_3_AACAATGG_L001_R1_001.fastq.gz"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-06T21:24:42.699901+00:00",
            "file_format": "fastq",
            "file_size": 323553219,
            "href": "/sequence-files/IGVFFI5615OENT/@@download/IGVFFI5615OENT.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/02/06/33f64ec4-030d-4932-8b90-909888ca5d3e/IGVFFI5615OENT.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0009173/",
            "status": "preview",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Users/gschnitz/dialout_files_for_helen/Dialout_2kg_2PMDox2_3_AACAATGG_L001_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8376NVAX/",
            "accession": "IGVFFI8376NVAX",
            "aliases": [
                "jesse-engreitz:sequence_files-TeloHAEC_Perturb-seq_2kG-Dialout_2kg_2PMDox2_3.2_AACAATGG_L001_R2_001.fastq.gz"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-06T21:25:01.105137+00:00",
            "file_format": "fastq",
            "file_size": 390795896,
            "href": "/sequence-files/IGVFFI8376NVAX/@@download/IGVFFI8376NVAX.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/02/06/adca8133-1f73-4ad5-854c-4021b0659732/IGVFFI8376NVAX.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0009173/",
            "status": "preview",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Users/gschnitz/dialout_files_for_helen/Dialout_2kg_2PMDox2_3.2_AACAATGG_L001_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9779WRBT/",
            "accession": "IGVFFI9779WRBT",
            "aliases": [
                "jesse-engreitz:sequence_files-TeloHAEC_Perturb-seq_2kG-Dialout_2kg_2PMDox2_3.2_AACAATGG_L001_R1_001.fastq.gz"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-06T21:24:54.743927+00:00",
            "file_format": "fastq",
            "file_size": 411596918,
            "href": "/sequence-files/IGVFFI9779WRBT/@@download/IGVFFI9779WRBT.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/02/06/0624d2c5-b4c1-43ac-a39c-04d4945414e2/IGVFFI9779WRBT.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0009173/",
            "status": "preview",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Users/gschnitz/dialout_files_for_helen/Dialout_2kg_2PMDox2_3.2_AACAATGG_L001_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9575YXQY/",
            "accession": "IGVFFI9575YXQY",
            "aliases": [
                "jesse-engreitz:sequence_files-TeloHAEC_Perturb-seq_2kG-Dialout_2kg_2PMDox2_3_AACAATGG_L001_R2_001.fastq.gz"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-06T21:24:48.490059+00:00",
            "file_format": "fastq",
            "file_size": 373571184,
            "href": "/sequence-files/IGVFFI9575YXQY/@@download/IGVFFI9575YXQY.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/02/06/6c55346b-86c9-4022-a29d-21567d7b48e9/IGVFFI9575YXQY.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0009173/",
            "status": "preview",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Users/gschnitz/dialout_files_for_helen/Dialout_2kg_2PMDox2_3_AACAATGG_L001_R2_001.fastq.gz",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS7943IIWZ/"
    ],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS4759EOBT/",
            "accession": "IGVFDS4759EOBT",
            "aliases": [
                "jesse-engreitz:measurement_set-scRNAseq_2kG_2PMDox2_3"
            ],
            "preferred_assay_title": "Perturb-seq",
            "status": "preview"
        }
    ],
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM0914ERRM/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM0914ERRM",
            "aliases": [
                "jesse-engreitz:in_vitro_systems-scRNAseq_2kG_2PMDox2_3"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS1298TUYG/"
            ],
            "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": "12",
    "status": "preview",
    "submitted_by": {
        "@id": "/users/4b2083b4-24c1-41d8-9daa-e79299f00d6e/",
        "title": "Ronghao Zhou"
    },
    "submitted_files_timestamp": "2024-02-06T21:24:42.699901+00:00",
    "summary": "gRNA sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting genes in many genomic loci",
    "uuid": "d9daf477-8c49-420d-adc3-2fdbb8ceb656"
}