IGVFDS6454USPN

{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS6454USPN/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS6454USPN",
    "aliases": [
        "jesse-engreitz:auxiliary_sets-scRNAseq_2kG_11AMDox_2"
    ],
    "audit": {
        "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",
                "path": "/sample-terms/NTR_0000753/"
            },
            {
                "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",
                "name": "audit_missing_seqspec",
                "path": "/auxiliary-sets/IGVFDS6454USPN/"
            }
        ]
    },
    "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": "2024-02-06T19:29:31.239163+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/IGVFFI7088MWDI/",
            "accession": "IGVFFI7088MWDI",
            "aliases": [
                "jesse-engreitz:sequence_files-TeloHAEC_Perturb-seq_2kG-Dialout_2kg_11AMDox_2.2_CGTACTAG_L001_R1_001.fastq.gz"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-06T21:18:23.485077+00:00",
            "file_format": "fastq",
            "file_size": 360920721,
            "href": "/sequence-files/IGVFFI7088MWDI/@@download/IGVFFI7088MWDI.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/02/06/6de0d913-5cd9-494d-a6d0-03bf3a949241/IGVFFI7088MWDI.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_11AMDox_2.2_CGTACTAG_L001_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI2366TACA/",
            "accession": "IGVFFI2366TACA",
            "aliases": [
                "jesse-engreitz:sequence_files-TeloHAEC_Perturb-seq_2kG-Dialout_2kg_11AMDox_2.2_CGTACTAG_L001_R2_001.fastq.gz"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-06T21:18:29.510737+00:00",
            "file_format": "fastq",
            "file_size": 344120433,
            "href": "/sequence-files/IGVFFI2366TACA/@@download/IGVFFI2366TACA.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/02/06/f5a1eadc-e1e8-4f02-9494-e7330228763b/IGVFFI2366TACA.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_11AMDox_2.2_CGTACTAG_L001_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI2902MSBX/",
            "accession": "IGVFFI2902MSBX",
            "aliases": [
                "jesse-engreitz:sequence_files-TeloHAEC_Perturb-seq_2kG-Dialout_2kg_11AMDox_2_CGTACTAG_L001_R2_001.fastq.gz"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-06T21:18:16.766121+00:00",
            "file_format": "fastq",
            "file_size": 360865319,
            "href": "/sequence-files/IGVFFI2902MSBX/@@download/IGVFFI2902MSBX.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/02/06/d87d3bd2-6469-4fa3-953e-559d7710523d/IGVFFI2902MSBX.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_11AMDox_2_CGTACTAG_L001_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI7579ADQD/",
            "accession": "IGVFFI7579ADQD",
            "aliases": [
                "jesse-engreitz:sequence_files-TeloHAEC_Perturb-seq_2kG-Dialout_2kg_11AMDox_2_CGTACTAG_L001_R1_001.fastq.gz"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-06T21:18:11.091171+00:00",
            "file_format": "fastq",
            "file_size": 309609731,
            "href": "/sequence-files/IGVFFI7579ADQD/@@download/IGVFFI7579ADQD.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/02/06/937af98a-5b52-4f6e-a479-d5fe37efe226/IGVFFI7579ADQD.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_11AMDox_2_CGTACTAG_L001_R1_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/IGVFDS6988JXXY/",
            "accession": "IGVFDS6988JXXY",
            "aliases": [
                "jesse-engreitz:measurement_set-scRNAseq_2kG_11AMDox_2"
            ],
            "preferred_assay_title": "Perturb-seq",
            "status": "preview"
        }
    ],
    "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": [
                "/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": "2024-02-06T21:18:11.091171+00:00",
    "summary": "gRNA sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting genes in many genomic loci",
    "uuid": "015d269f-4be6-4e19-a26c-53a4e0c63df1"
}