Jurkat — IGVFSM7399BQSM

released
{
    "@context": "/terms/",
    "@id": "/in-vitro-systems/IGVFSM7399BQSM/",
    "@type": [
        "InVitroSystem",
        "Biosample",
        "Sample",
        "Item"
    ],
    "accession": "IGVFSM7399BQSM",
    "age": "unknown",
    "aliases": [
        "jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep1-FFrep1"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequencing kit",
                "detail": "Construct library set [IGVFDS2385DHZO](/construct-library-sets/IGVFDS2385DHZO/) has sequence file(s) [IGVFFI0147UKIB](/sequence-files/IGVFFI0147UKIB/), [IGVFFI4510NYOZ](/sequence-files/IGVFFI4510NYOZ/), [IGVFFI9768NZXQ](/sequence-files/IGVFFI9768NZXQ/), [IGVFFI2088KESL](/sequence-files/IGVFFI2088KESL/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_inconsistent_sequencing_kit",
                "path": "/construct-library-sets/IGVFDS2385DHZO/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Construct library set [IGVFDS2385DHZO](/construct-library-sets/IGVFDS2385DHZO/) has sequence file(s): [IGVFFI0147UKIB](/sequence-files/IGVFFI0147UKIB/), [IGVFFI4510NYOZ](/sequence-files/IGVFFI4510NYOZ/), [IGVFFI9768NZXQ](/sequence-files/IGVFFI9768NZXQ/), [IGVFFI2088KESL](/sequence-files/IGVFFI2088KESL/) 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": "/construct-library-sets/IGVFDS2385DHZO/"
            },
            {
                "category": "mismatched status",
                "detail": "Released in vitro system [IGVFSM7399BQSM](/in-vitro-systems/IGVFSM7399BQSM/) has in progress subobject construct library set [IGVFDS2385DHZO](/construct-library-sets/IGVFDS2385DHZO/).",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_item_status",
                "path": "/in-vitro-systems/IGVFSM7399BQSM/"
            },
            {
                "category": "missing sample",
                "detail": "In vitro system [IGVFSM7399BQSM](/in-vitro-systems/IGVFSM7399BQSM/) has only 1 child sample [IGVFSM9783LUAL](/in-vitro-systems/IGVFSM9783LUAL/) in `parts`. Parent samples are expected to have multiple child samples.",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_parent_sample_with_singular_child",
                "path": "/in-vitro-systems/IGVFSM7399BQSM/"
            }
        ],
        "NOT_COMPLIANT": [
            {
                "category": "missing plasmid map",
                "detail": "Construct library set [IGVFDS2385DHZO](/construct-library-sets/IGVFDS2385DHZO/) does not have a plasmid map attached in `documents`. Construct library sets are expected to be associated with a plasmid map document.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_construct_library_set_plasmid_map",
                "path": "/construct-library-sets/IGVFDS2385DHZO/"
            },
            {
                "category": "missing guide RNA sequences",
                "detail": "Construct library set [IGVFDS2385DHZO](/construct-library-sets/IGVFDS2385DHZO/) has no `integrated_content_files`. Guide libraries are expected to link to an integrated content file of guide RNA sequences.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_integrated_content_files",
                "path": "/construct-library-sets/IGVFDS2385DHZO/"
            },
            {
                "category": "missing analysis",
                "detail": "Construct library set [IGVFDS2385DHZO](/construct-library-sets/IGVFDS2385DHZO/) is a raw data set with files, but is not listed in any `input_file_sets` for any analysis sets. Raw data sets with files are expected to be associated with at least one analysis set.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_input_for",
                "path": "/construct-library-sets/IGVFDS2385DHZO/"
            }
        ]
    },
    "award": {
        "@id": "/awards/HG011972/",
        "component": "functional characterization"
    },
    "classifications": [
        "cell line"
    ],
    "construct_library_sets": [
        {
            "@id": "/construct-library-sets/IGVFDS2385DHZO/",
            "accession": "IGVFDS2385DHZO",
            "file_set_type": "guide library",
            "status": "in progress"
        }
    ],
    "creation_timestamp": "2023-12-13T08:36:56.489850+00:00",
    "demultiplexed_to": [],
    "donors": [
        "/human-donors/IGVFDO1080XFGV/"
    ],
    "file_sets": [],
    "institutional_certificates": [],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "modifications": [
        {
            "@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
            "cas": "nCas9",
            "cas_species": "Streptococcus pyogenes (Sp)",
            "fused_domain": "M-MLV RT (PE2)",
            "modality": "prime editing",
            "status": "released",
            "summary": "CRISPR prime editing Sp-nCas9-M-MLV RT (PE2)"
        }
    ],
    "multiplexed_in": [],
    "notes": "The \"classification\" of this in vitro system was moved into the array property \"classifications.\" This sample's modifications originally included Modification /modifications/e8d549e6-cef0-482a-9deb-76d3b7ecaac3/ which was deleted and replaced with a Crispr Modification igvf:replacement_of_e8d549e6-cef0-482a-9deb-76d3b7ecaac3.",
    "origin_of": [],
    "part_of": "/in-vitro-systems/IGVFSM0085CVRD/",
    "parts": [
        "/in-vitro-systems/IGVFSM9783LUAL/"
    ],
    "pooled_in": [],
    "release_timestamp": "2023-12-20T22:55:40.543935+00:00",
    "sample_terms": [
        {
            "@id": "/sample-terms/EFO_0002796/",
            "status": "released",
            "term_name": "Jurkat"
        }
    ],
    "schema_version": "23",
    "sex": "male",
    "sorted_fractions": [
        "/in-vitro-systems/IGVFSM0519CRES/",
        "/in-vitro-systems/IGVFSM0211VADB/",
        "/in-vitro-systems/IGVFSM6493PXNX/",
        "/in-vitro-systems/IGVFSM9226UZTE/"
    ],
    "sources": [
        {
            "@id": "/sources/atcc/",
            "status": "released",
            "title": "ATCC"
        }
    ],
    "status": "released",
    "submitted_by": {
        "@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
        "title": "Michael Montgomery"
    },
    "summary": "Jurkat cell line, male, Homo sapiens modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transfected with a guide library",
    "taxa": "Homo sapiens",
    "uuid": "09cc140f-7cd7-4b08-a202-ff0e3a6f66ac",
    "virtual": false
}