HCT116 — IGVFSM0671URTU

released
{
    "@context": "/terms/",
    "@id": "/in-vitro-systems/IGVFSM0671URTU/",
    "@type": [
        "InVitroSystem",
        "Biosample",
        "Sample",
        "Item"
    ],
    "accession": "IGVFSM0671URTU",
    "age": "unknown",
    "aliases": [
        "jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF2-BinE-PCR1-Rep1_S233",
        "jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF2-BinE-PCR2-Rep1_S239",
        "jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF2-BinE-PCR3-Rep1_S275",
        "jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF2-BinE-PCR4-Rep1_S281"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequencing kit",
                "detail": "Construct library set [IGVFDS6351FGNG](/construct-library-sets/IGVFDS6351FGNG/) has sequence file(s) [IGVFFI1612RZTD](/sequence-files/IGVFFI1612RZTD/) 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/IGVFDS6351FGNG/"
            }
        ],
        "NOT_COMPLIANT": [
            {
                "category": "missing analysis",
                "detail": "Construct library set [IGVFDS6351FGNG](/construct-library-sets/IGVFDS6351FGNG/) 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/IGVFDS6351FGNG/"
            }
        ]
    },
    "award": {
        "@id": "/awards/HG011972/",
        "component": "functional characterization"
    },
    "classifications": [
        "cell line"
    ],
    "construct_library_sets": [
        {
            "@id": "/construct-library-sets/IGVFDS6351FGNG/",
            "accession": "IGVFDS6351FGNG",
            "file_set_type": "guide library",
            "status": "released"
        }
    ],
    "creation_timestamp": "2024-05-09T21:48:54.651111+00:00",
    "demultiplexed_to": [],
    "documents": [
        "/documents/a1a19741-90cc-46ea-b90c-96c4a4b70d8e/",
        "/documents/b0663905-6249-42ea-9937-9b2f645c787d/"
    ],
    "donors": [
        "/human-donors/IGVFDO0384OZRW/"
    ],
    "file_sets": [
        {
            "@id": "/measurement-sets/IGVFDS5565SKCZ/",
            "accession": "IGVFDS5565SKCZ",
            "aliases": [
                "jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF2-BinE-PCR1-Rep1_S233",
                "jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF2-BinE-PCR2-Rep1_S239",
                "jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF2-BinE-PCR3-Rep1_S275",
                "jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF2-BinE-PCR4-Rep1_S281"
            ],
            "file_set_type": "experimental data",
            "lab": {
                "title": "Jesse Engreitz, Stanford"
            },
            "preferred_assay_title": "CRISPR FlowFISH screen",
            "status": "released",
            "summary": "mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci"
        },
        {
            "@id": "/auxiliary-sets/IGVFDS6282WCIA/",
            "accession": "IGVFDS6282WCIA",
            "aliases": [
                "jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF2-BinE-PCR1-Rep1_S233",
                "jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF2-BinE-PCR2-Rep1_S239",
                "jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF2-BinE-PCR3-Rep1_S275",
                "jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF2-BinE-PCR4-Rep1_S281"
            ],
            "file_set_type": "gRNA sequencing",
            "lab": {
                "title": "Jesse Engreitz, Stanford"
            },
            "status": "released",
            "summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci"
        },
        {
            "@id": "/auxiliary-sets/IGVFDS1549RKIJ/",
            "accession": "IGVFDS1549RKIJ",
            "aliases": [
                "jesse-engreitz:auxiliary_sortparams_CRUDO_CCND1_Auxin0hrs-FF2"
            ],
            "file_set_type": "cell sorting",
            "lab": {
                "title": "Jesse Engreitz, Stanford"
            },
            "status": "released",
            "summary": "cell sorting for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci, mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci, ... and 4 more measurement sets"
        },
        {
            "@id": "/analysis-sets/IGVFDS1569RNPD/",
            "accession": "IGVFDS1569RNPD",
            "aliases": [
                "jesse-engreitz:analysis_set_CRUDO_CCND1"
            ],
            "file_set_type": "principal analysis",
            "lab": {
                "title": "Jesse Engreitz, Stanford"
            },
            "status": "in progress",
            "summary": "CRISPR degradation, interference FlowFISH screen targeting CCND1: differential element quantifications"
        }
    ],
    "institutional_certificates": [],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "modifications": [
        {
            "@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
            "cas": "dCas9",
            "cas_species": "Streptococcus pyogenes (Sp)",
            "fused_domain": "KOX1-KRAB",
            "modality": "interference",
            "status": "released",
            "summary": "CRISPRi Sp-dCas9-KOX1-KRAB"
        },
        {
            "@id": "/degron-modifications/2e8d10cc-fc98-44d5-a7d9-e2892e16c98a/",
            "degron_system": "AID",
            "modality": "degradation",
            "status": "released",
            "summary": "inactive AID system targeting RAD21",
            "tagged_proteins": [
                {
                    "@id": "/genes/ENSG00000164754/",
                    "status": "released",
                    "summary": "RAD21 - ENSG00000164754 (Homo sapiens)",
                    "symbol": "RAD21"
                }
            ]
        }
    ],
    "multiplexed_in": [],
    "notes": "This sample's modifications originally included Modification /modifications/56d6a4f4-5fa4-4989-890e-aafb032f1e7d/ which was deleted and replaced with a Crispr Modification igvf:replacement_of_56d6a4f4-5fa4-4989-890e-aafb032f1e7d. The original alias jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF2-BinE-PCR4-Rep1_S2817 was changed to jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF2-BinE-PCR4-Rep1_S281",
    "origin_of": [],
    "parts": [],
    "pooled_in": [],
    "release_timestamp": "2024-07-10T19:38:59.357547+00:00",
    "sample_terms": [
        {
            "@id": "/sample-terms/EFO_0002824/",
            "status": "released",
            "term_name": "HCT116"
        }
    ],
    "schema_version": "23",
    "sex": "male",
    "sorted_fractions": [],
    "sorted_from": {
        "@id": "/in-vitro-systems/IGVFSM7006DNJX/",
        "accession": "IGVFSM7006DNJX",
        "status": "released"
    },
    "sorted_from_detail": "FACS bin E for 80-90% expression of CCND1",
    "sources": [
        {
            "@id": "/sources/atcc/",
            "status": "released",
            "title": "ATCC"
        }
    ],
    "status": "released",
    "submitted_by": {
        "@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
        "title": "Chongyon Park"
    },
    "summary": "HCT116 cell line, male, Homo sapiens (sorting details: FACS bin E for 80-90% expression of CCND1) modified with CRISPRi Sp-dCas9-KOX1-KRAB, inactive AID system targeting RAD21, transfected with a guide library",
    "taxa": "Homo sapiens",
    "uuid": "934eafb0-5142-44ca-84a4-d655d092e139",
    "virtual": false
}