IGVFDS2818XKLS

released
{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS2818XKLS/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS2818XKLS",
    "aliases": [
        "charles-gersbach:measurement-set-crispra-region3-0umET1-ipsc-cm-targeted-hicar-rep2"
    ],
    "assay_term": {
        "@id": "/assay-terms/OBI_0002440/",
        "status": "released",
        "term_name": "Hi-C assay"
    },
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS2818XKLS](/measurement-sets/IGVFDS2818XKLS/) has sequence file(s): [IGVFFI5220OJEV](/sequence-files/IGVFFI5220OJEV/), [IGVFFI6458FXIE](/sequence-files/IGVFFI6458FXIE/) 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": "/measurement-sets/IGVFDS2818XKLS/"
            }
        ]
    },
    "award": {
        "@id": "/awards/HG012053/",
        "component": "functional characterization",
        "contact_pi": {
            "@id": "/users/5d329c0e-3ea9-49bf-9bb9-844a53a882c0/",
            "title": "Charles Gersbach"
        },
        "title": "High-Throughput Functional Annotation of Gene Regulatory Elements and Variants Critical to Complex Cellular Phenotypes"
    },
    "control_for": [],
    "creation_timestamp": "2024-10-23T19:20:00.420481+00:00",
    "donors": [
        {
            "@id": "/human-donors/IGVFDO3212TBUN/",
            "accession": "IGVFDO3212TBUN",
            "aliases": [
                "charles-gersbach:human-donor-WTC11"
            ],
            "sex": "male",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "externally_hosted": false,
    "file_set_type": "experimental data",
    "files": [
        {
            "@id": "/sequence-files/IGVFFI5220OJEV/",
            "accession": "IGVFFI5220OJEV",
            "aliases": [
                "charles-gersbach:measurement-set-crispra-region3-0umET1-ipsc-cm-targeted-hicar-rep2-R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-10-23T19:29:29.667310+00:00",
            "file_format": "fastq",
            "file_size": 1347859755,
            "href": "/sequence-files/IGVFFI5220OJEV/@@download/IGVFFI5220OJEV.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/10/23/85038bbf-8d15-41ad-8b75-0071f2f726f1/IGVFFI5220OJEV.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0010963/",
                "status": "released",
                "term_name": "Illumina NextSeq 2000"
            },
            "status": "released",
            "submitted_file_name": "/hpc/group/gersbachlab/tda17/IGVF_data_files/HiCAR/fastq/crispra_human/crispra_hicar_human_fastq/H_vp64_r2_TA448_2_noET1_ds.a943dbc7f7394acd9ce08acc722b0b90/H_vp64_r2_TA448_2_noET1_S4_L001_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI6458FXIE/",
            "accession": "IGVFFI6458FXIE",
            "aliases": [
                "charles-gersbach:measurement-set-crispra-region3-0umET1-ipsc-cm-targeted-hicar-rep2-R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-10-23T19:29:30.713012+00:00",
            "file_format": "fastq",
            "file_size": 1508405014,
            "href": "/sequence-files/IGVFFI6458FXIE/@@download/IGVFFI6458FXIE.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/10/23/90750fe2-e9fa-4237-b960-9af4ed524915/IGVFFI6458FXIE.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0010963/",
                "status": "released",
                "term_name": "Illumina NextSeq 2000"
            },
            "status": "released",
            "submitted_file_name": "/hpc/group/gersbachlab/tda17/IGVF_data_files/HiCAR/fastq/crispra_human/crispra_hicar_human_fastq/H_vp64_r2_TA448_2_noET1_ds.a943dbc7f7394acd9ce08acc722b0b90/H_vp64_r2_TA448_2_noET1_S4_L001_R2_001.fastq.gz",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS4789MLTX/"
    ],
    "lab": {
        "@id": "/labs/charles-gersbach/",
        "title": "Charles Gersbach, Duke"
    },
    "preferred_assay_title": "HiCAR",
    "protocols": [
        "https://www.protocols.io/view/hicar-for-human-ipsc-cm-following-enhancer-perturb-3byl49mdrgo5"
    ],
    "release_timestamp": "2024-12-13T19:43:46.251738+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM3768JSRU/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM3768JSRU",
            "aliases": [
                "charles-gersbach:in-vitro-system-crispra-region3-0umET1-ipsc-cm-targeted-hicar-rep2"
            ],
            "classifications": [
                "differentiated cell specimen"
            ],
            "construct_library_sets": [
                {
                    "@id": "/construct-library-sets/IGVFDS8010GDNS/",
                    "accession": "IGVFDS8010GDNS",
                    "file_set_type": "guide library",
                    "status": "released",
                    "summary": "guide (sgRNA) library targeting accessible genome regions in a genomic locus"
                }
            ],
            "sample_terms": [
                {
                    "@id": "/sample-terms/EFO_0009747/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
                        "Item"
                    ],
                    "aliases": [
                        "igvf:WTC11"
                    ],
                    "status": "released",
                    "summary": "GM25256 (WTC-11)",
                    "term_name": "GM25256 (WTC-11)"
                }
            ],
            "status": "released",
            "summary": "GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 42 days, male, Homo sapiens transfected with a guide library",
            "targeted_sample_term": {
                "@id": "/sample-terms/CL_0000746/",
                "status": "released",
                "term_name": "cardiac muscle cell"
            },
            "taxa": "Homo sapiens"
        }
    ],
    "schema_version": "23",
    "status": "released",
    "submitted_by": {
        "@id": "/users/3782ce69-0e9f-4b46-91f9-4578139785c7/",
        "title": "Ruhi Rai"
    },
    "submitted_files_timestamp": "2024-10-23T19:29:29.667310+00:00",
    "summary": "CRISPR HiCAR integrating a guide (sgRNA) library targeting accessible genome regions in a genomic locus",
    "uuid": "7a68c270-0071-46a5-9556-7a549ddecffc"
}