IGVFDS9869EMNE

released
{
    "@context": "/terms/",
    "@id": "/construct-library-sets/IGVFDS9869EMNE/",
    "@type": [
        "ConstructLibrarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS9869EMNE",
    "aliases": [
        "jesse-engreitz:construct_library_CRUDO_TAPseq"
    ],
    "applied_to_samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM9983LVUX/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM9983LVUX",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_TAPseq-Auxin6hrs-Rep1"
            ],
            "classifications": [
                "cell line"
            ],
            "donors": [
                {
                    "@id": "/human-donors/IGVFDO0384OZRW/",
                    "taxa": "Homo sapiens"
                }
            ],
            "sample_terms": [
                {
                    "@id": "/sample-terms/EFO_0002824/",
                    "term_name": "HCT116"
                }
            ],
            "status": "released",
            "summary": "HCT116 cell line, male, Homo sapiens treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours, modified with a guide library"
        },
        {
            "@id": "/in-vitro-systems/IGVFSM2061VHMZ/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM2061VHMZ",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_TAPseq-Rep2"
            ],
            "classifications": [
                "cell line"
            ],
            "donors": [
                {
                    "@id": "/human-donors/IGVFDO0384OZRW/",
                    "taxa": "Homo sapiens"
                }
            ],
            "sample_terms": [
                {
                    "@id": "/sample-terms/EFO_0002824/",
                    "term_name": "HCT116"
                }
            ],
            "status": "released",
            "summary": "HCT116 cell line, male, Homo sapiens modified with a guide library"
        },
        {
            "@id": "/in-vitro-systems/IGVFSM5799ZEJH/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM5799ZEJH",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_TAPseq-Auxin0hrs-Rep1"
            ],
            "classifications": [
                "cell line"
            ],
            "donors": [
                {
                    "@id": "/human-donors/IGVFDO0384OZRW/",
                    "taxa": "Homo sapiens"
                }
            ],
            "sample_terms": [
                {
                    "@id": "/sample-terms/EFO_0002824/",
                    "term_name": "HCT116"
                }
            ],
            "status": "released",
            "summary": "HCT116 cell line, male, Homo sapiens modified with a guide library"
        },
        {
            "@id": "/in-vitro-systems/IGVFSM0767GJUV/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM0767GJUV",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_TAPseq-Auxin0hrs-Rep2"
            ],
            "classifications": [
                "cell line"
            ],
            "donors": [
                {
                    "@id": "/human-donors/IGVFDO0384OZRW/",
                    "taxa": "Homo sapiens"
                }
            ],
            "sample_terms": [
                {
                    "@id": "/sample-terms/EFO_0002824/",
                    "term_name": "HCT116"
                }
            ],
            "status": "released",
            "summary": "HCT116 cell line, male, Homo sapiens modified with a guide library"
        },
        {
            "@id": "/in-vitro-systems/IGVFSM8511JOMW/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM8511JOMW",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_TAPseq-Auxin6hrs-Rep2"
            ],
            "classifications": [
                "cell line"
            ],
            "donors": [
                {
                    "@id": "/human-donors/IGVFDO0384OZRW/",
                    "taxa": "Homo sapiens"
                }
            ],
            "sample_terms": [
                {
                    "@id": "/sample-terms/EFO_0002824/",
                    "term_name": "HCT116"
                }
            ],
            "status": "released",
            "summary": "HCT116 cell line, male, Homo sapiens treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours, modified with a guide library"
        },
        {
            "@id": "/in-vitro-systems/IGVFSM5760JFFX/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM5760JFFX",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_TAPseq-Rep1"
            ],
            "classifications": [
                "cell line"
            ],
            "donors": [
                {
                    "@id": "/human-donors/IGVFDO0384OZRW/",
                    "taxa": "Homo sapiens"
                }
            ],
            "sample_terms": [
                {
                    "@id": "/sample-terms/EFO_0002824/",
                    "term_name": "HCT116"
                }
            ],
            "status": "released",
            "summary": "HCT116 cell line, male, Homo sapiens modified with a guide library"
        }
    ],
    "audit": {
        "WARNING": [
            {
                "category": "missing sequencing kit",
                "detail": "Construct library set [IGVFDS9869EMNE](/construct-library-sets/IGVFDS9869EMNE/) has sequence file(s) [IGVFFI7017ICQL](/sequence-files/IGVFFI7017ICQL/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
                "level": 40,
                "level_name": "WARNING",
                "name": "audit_inconsistent_sequencing_kit",
                "path": "/construct-library-sets/IGVFDS9869EMNE/"
            },
            {
                "category": "missing analysis",
                "detail": "Construct library set [IGVFDS9869EMNE](/construct-library-sets/IGVFDS9869EMNE/) 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": 40,
                "level_name": "WARNING",
                "name": "audit_input_file_set_for",
                "path": "/construct-library-sets/IGVFDS9869EMNE/"
            }
        ]
    },
    "award": {
        "@id": "/awards/HG011972/",
        "component": "functional characterization"
    },
    "control_for": [],
    "creation_timestamp": "2024-06-06T17:55:14.122190+00:00",
    "documents": [
        "/documents/6f05cff9-a97a-45f7-9503-ebd5c44873b0/"
    ],
    "file_set_type": "guide library",
    "files": [
        {
            "@id": "/sequence-files/IGVFFI7017ICQL/",
            "accession": "IGVFFI7017ICQL",
            "aliases": [
                "jesse-engreitz:gRNAlibrary_file_CRUDO_TAPseq"
            ],
            "content_type": "reads",
            "file_format": "fastq",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI0944DQUA/",
            "accession": "IGVFFI0944DQUA",
            "aliases": [
                "jesse-engreitz:seqspecfile_testguideseq_CRUDO_TAPseq"
            ],
            "content_type": "seqspec",
            "file_format": "yaml",
            "upload_status": "validated"
        }
    ],
    "guide_type": "sgRNA",
    "input_file_set_for": [],
    "integrated_content_files": [
        {
            "@id": "/tabular-files/IGVFFI5298NREB/",
            "accession": "IGVFFI5298NREB",
            "aliases": [
                "jesse-engreitz:guidedesign_file_CRUDO_TAPseq"
            ],
            "content_type": "guide RNA sequences",
            "file_format": "tsv",
            "upload_status": "validated"
        }
    ],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "release_timestamp": "2024-07-10T19:53:27.817316+00:00",
    "schema_version": "9",
    "scope": "loci",
    "selection_criteria": [
        "accessible genome regions"
    ],
    "small_scale_loci_list": [
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    ],
    "sources": [
        "/labs/jesse-engreitz/"
    ],
    "status": "released",
    "submitted_by": {
        "@id": "/users/100f06c6-83a7-4b4d-9dfd-053a1829773b/",
        "title": "Benjamin Doughty"
    },
    "submitted_files_timestamp": "2024-06-06T17:55:54.696319+00:00",
    "summary": "Guide (sgRNA) library targeting accessible genome regions in 29 genomic loci",
    "tiling_modality": "sparse peaks",
    "uuid": "64a6d5d9-f026-4aab-ba29-dea1672a0065"
}