H9 — IGVFSM5657YKPN

{
    "@context": "/terms/",
    "@id": "/in-vitro-systems/IGVFSM5657YKPN/",
    "@type": [
        "InVitroSystem",
        "Biosample",
        "Sample",
        "Item"
    ],
    "accession": "IGVFSM5657YKPN",
    "age": "unknown",
    "aliases": [
        "gary-hon:differentiated_H9_shen_construct_sgRNA_Lenti_LW271"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "mismatched status",
                "detail": "Preview construct library set [IGVFDS9629YZLO](/construct-library-sets/IGVFDS9629YZLO/) has in progress subobject tabular file [IGVFFI4543YHDW](/tabular-files/IGVFFI4543YHDW/).",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_item_status",
                "path": "/construct-library-sets/IGVFDS9629YZLO/"
            }
        ],
        "NOT_COMPLIANT": [
            {
                "category": "missing plasmid map",
                "detail": "Construct library set [IGVFDS9629YZLO](/construct-library-sets/IGVFDS9629YZLO/) 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/IGVFDS9629YZLO/"
            }
        ],
        "WARNING": [
            {
                "category": "missing files",
                "detail": "Construct library set [IGVFDS9629YZLO](/construct-library-sets/IGVFDS9629YZLO/) has no `files`. File sets are expected to have files.",
                "level": 40,
                "level_name": "WARNING",
                "name": "audit_no_files",
                "path": "/construct-library-sets/IGVFDS9629YZLO/"
            }
        ]
    },
    "award": {
        "@id": "/awards/HG011996/",
        "component": "functional characterization"
    },
    "cell_fate_change_protocol": "/documents/3959d1b4-07fd-4841-864a-c2e7b4381edb/",
    "cellular_sub_pool": "subpool_LW271",
    "classifications": [
        "differentiated cell specimen"
    ],
    "construct_library_sets": [
        {
            "@id": "/construct-library-sets/IGVFDS9629YZLO/",
            "accession": "IGVFDS9629YZLO",
            "file_set_type": "guide library",
            "status": "preview"
        }
    ],
    "creation_timestamp": "2024-04-25T21:26:48.900805+00:00",
    "demultiplexed_to": [],
    "documents": [
        "/documents/3959d1b4-07fd-4841-864a-c2e7b4381edb/"
    ],
    "donors": [
        "/human-donors/IGVFDO2718IDDQ/"
    ],
    "file_sets": [
        {
            "@id": "/auxiliary-sets/IGVFDS1004SBHR/",
            "accession": "IGVFDS1004SBHR",
            "aliases": [
                "gary-hon:CM_Pilot_2_Mini_sgRNA_Lenti_LW271"
            ],
            "file_set_type": "gRNA sequencing",
            "lab": {
                "title": "Gary Hon, UT"
            },
            "status": "preview",
            "summary": "gRNA sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci"
        },
        {
            "@id": "/auxiliary-sets/IGVFDS2739QDQI/",
            "accession": "IGVFDS2739QDQI",
            "aliases": [
                "gary-hon:CM_Pilot_2_Mini_HTO_Lenti_LW271"
            ],
            "file_set_type": "cell hashing barcode sequencing",
            "lab": {
                "title": "Gary Hon, UT"
            },
            "status": "preview",
            "summary": "cell hashing barcode sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci"
        },
        {
            "@id": "/measurement-sets/IGVFDS8449CDOE/",
            "accession": "IGVFDS8449CDOE",
            "aliases": [
                "gary-hon:CM_Pilot_2_Mini_Lenti_LW271"
            ],
            "file_set_type": "experimental data",
            "lab": {
                "title": "Gary Hon, UT"
            },
            "preferred_assay_title": "Perturb-seq",
            "status": "preview",
            "summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci"
        },
        {
            "@id": "/analysis-sets/IGVFDS2873EPIU/",
            "accession": "IGVFDS2873EPIU",
            "aliases": [
                "gary-hon:H9_shen_construct_sgRNA_Lenti_PrimaryAnalysis"
            ],
            "file_set_type": "principal analysis",
            "lab": {
                "title": "Gary Hon, UT"
            },
            "status": "preview",
            "summary": "interference Perturb-seq: filtered feature barcode matrix, raw feature barcode matrix, sparse gene count matrix, unfiltered global differential expression, unfiltered local differential expression"
        }
    ],
    "institutional_certificates": [],
    "lab": {
        "@id": "/labs/gary-hon/",
        "title": "Gary Hon, UT"
    },
    "modifications": [
        {
            "@id": "/crispr-modifications/0a63b754-eca4-44aa-bbc2-fccdc6c44fb5/",
            "cas": "dCas9",
            "cas_species": "Streptococcus pyogenes (Sp)",
            "modality": "interference",
            "status": "preview",
            "summary": "CRISPRi Sp-dCas9"
        }
    ],
    "multiplexed_in": [],
    "notes": "This sample's modifications originally included Modification /modifications/5f12e117-5d61-464b-a1e5-c826c83d6b10/ which was deleted and replaced with a Crispr Modification igvf:replacement_of_5f12e117-5d61-464b-a1e5-c826c83d6b10.",
    "nucleic_acid_delivery": "lentiviral transduction",
    "origin_of": [],
    "originated_from": {
        "@id": "/in-vitro-systems/IGVFSM7411AQVC/",
        "accession": "IGVFSM7411AQVC",
        "status": "preview"
    },
    "part_of": "/in-vitro-systems/IGVFSM8305VDSK/",
    "parts": [],
    "pooled_in": [],
    "sample_terms": [
        {
            "@id": "/sample-terms/EFO_0003045/",
            "status": "released",
            "term_name": "H9"
        }
    ],
    "schema_version": "23",
    "sex": "female",
    "sorted_fractions": [],
    "sources": [
        {
            "@id": "/labs/gary-hon/",
            "status": "current",
            "title": "Gary Hon, UT"
        }
    ],
    "status": "preview",
    "submitted_by": {
        "@id": "/users/b05645f1-2d56-4a5e-b272-4601e555a3fa/",
        "title": "Mpathi Nzima"
    },
    "summary": "H9 differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW271), female, Homo sapiens modified with CRISPRi Sp-dCas9, transduced (lentivirus) with a guide library",
    "targeted_sample_term": {
        "@id": "/sample-terms/CL_0000746/",
        "status": "released",
        "term_name": "cardiac muscle cell"
    },
    "taxa": "Homo sapiens",
    "time_post_change": 12,
    "time_post_change_units": "day",
    "time_post_library_delivery": 3,
    "time_post_library_delivery_units": "week",
    "uuid": "bef1de91-d559-4788-a681-fe5996949b3e",
    "virtual": false
}