IGVFDS4288VPSU

{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS4288VPSU/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS4288VPSU",
    "aliases": [
        "jesse-engreitz:auxiliary_sets-scRNAseq_2kG_2PMDox1_3"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS4288VPSU](/auxiliary-sets/IGVFDS4288VPSU/) has sequence file(s): [IGVFFI0292YEIE](/sequence-files/IGVFFI0292YEIE/), [IGVFFI9133PDUV](/sequence-files/IGVFFI9133PDUV/), [IGVFFI9889IEMK](/sequence-files/IGVFFI9889IEMK/), [IGVFFI6242AIOG](/sequence-files/IGVFFI6242AIOG/) 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/IGVFDS4288VPSU/"
            },
            {
                "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": "2024-02-06T19:29:37.951711+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/IGVFFI0292YEIE/",
            "accession": "IGVFFI0292YEIE",
            "aliases": [
                "jesse-engreitz:sequence_files-TeloHAEC_Perturb-seq_2kG-Dialout_2kg_2PMDox1_3_redo_GCACACGA_L001_R1_001.fastq.gz"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-06T21:21:02.070443+00:00",
            "file_format": "fastq",
            "file_size": 299883207,
            "href": "/sequence-files/IGVFFI0292YEIE/@@download/IGVFFI0292YEIE.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/02/06/0bc08d6e-13ff-4964-b758-5b3b54e861d2/IGVFFI0292YEIE.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_2PMDox1_3_redo_GCACACGA_L001_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9133PDUV/",
            "accession": "IGVFFI9133PDUV",
            "aliases": [
                "jesse-engreitz:sequence_files-TeloHAEC_Perturb-seq_2kG-Dialout_2kg_2PMDox1_3.2_GCACACGA_L001_R2_001.fastq.gz"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-06T21:21:20.172159+00:00",
            "file_format": "fastq",
            "file_size": 394397874,
            "href": "/sequence-files/IGVFFI9133PDUV/@@download/IGVFFI9133PDUV.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/02/06/371f2e0c-4479-4d90-ab0c-720749cc1d06/IGVFFI9133PDUV.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_2PMDox1_3.2_GCACACGA_L001_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9889IEMK/",
            "accession": "IGVFFI9889IEMK",
            "aliases": [
                "jesse-engreitz:sequence_files-TeloHAEC_Perturb-seq_2kG-Dialout_2kg_2PMDox1_3_redo_GCACACGA_L001_R2_001.fastq.gz"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-06T21:21:07.389396+00:00",
            "file_format": "fastq",
            "file_size": 355785955,
            "href": "/sequence-files/IGVFFI9889IEMK/@@download/IGVFFI9889IEMK.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/02/06/d21b702c-ae02-4d53-a63e-269befe66aa8/IGVFFI9889IEMK.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_2PMDox1_3_redo_GCACACGA_L001_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI6242AIOG/",
            "accession": "IGVFFI6242AIOG",
            "aliases": [
                "jesse-engreitz:sequence_files-TeloHAEC_Perturb-seq_2kG-Dialout_2kg_2PMDox1_3.2_GCACACGA_L001_R1_001.fastq.gz"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-06T21:21:13.651399+00:00",
            "file_format": "fastq",
            "file_size": 415987470,
            "href": "/sequence-files/IGVFFI6242AIOG/@@download/IGVFFI6242AIOG.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/02/06/d64fa569-025d-438b-846d-690a793af960/IGVFFI6242AIOG.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_2PMDox1_3.2_GCACACGA_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/IGVFDS1330GUQX/",
            "accession": "IGVFDS1330GUQX",
            "aliases": [
                "jesse-engreitz:measurement_set-scRNAseq_2kG_2PMDox1_3"
            ],
            "preferred_assay_title": "Perturb-seq",
            "status": "preview"
        }
    ],
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM9151FQCE/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM9151FQCE",
            "aliases": [
                "jesse-engreitz:in_vitro_systems-scRNAseq_2kG_2PMDox1_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": "2024-02-06T21:21:02.070443+00:00",
    "summary": "gRNA sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting genes in many genomic loci",
    "uuid": "17af7c98-3dd7-4adc-9cf6-8bdedbbde911"
}