IGVFDS7037REPR

{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS7037REPR/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS7037REPR",
    "aliases": [
        "charles-gersbach:measurement-set-crispra-region3-mouse-hl1-targeted-hicar-rep1"
    ],
    "assay_term": {
        "@id": "/assay-terms/OBI_0002440/",
        "status": "released",
        "term_name": "Hi-C assay"
    },
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS7037REPR](/measurement-sets/IGVFDS7037REPR/) has sequence file(s): [IGVFFI8764YHFM](/sequence-files/IGVFFI8764YHFM/), [IGVFFI2546KBWD](/sequence-files/IGVFFI2546KBWD/) 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/IGVFDS7037REPR/"
            }
        ]
    },
    "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": "2024-10-23T19:20:10.512429+00:00",
    "donors": [
        {
            "@id": "/rodent-donors/IGVFDO1434JYIN/",
            "accession": "IGVFDO1434JYIN",
            "aliases": [
                "charles-gersbach:mouse-donor-HL-1"
            ],
            "sex": "female",
            "status": "released",
            "taxa": "Mus musculus"
        }
    ],
    "externally_hosted": false,
    "file_set_type": "experimental data",
    "files": [
        {
            "@id": "/sequence-files/IGVFFI8764YHFM/",
            "accession": "IGVFFI8764YHFM",
            "aliases": [
                "charles-gersbach:measurement-set-crispra-region3-mouse-hl1-targeted-hicar-rep1-R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-10-23T19:29:52.987015+00:00",
            "file_format": "fastq",
            "file_size": 1094712255,
            "href": "/sequence-files/IGVFFI8764YHFM/@@download/IGVFFI8764YHFM.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/10/23/119e0f43-078b-4567-8f5b-549e5049fe8c/IGVFFI8764YHFM.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_mouse/crispra_hicar_mouse_fastq/HL_1_TA446_1_noET1_ds.62ae2232c0cc4744bd32ce6a0473f891/HL_1_TA446_1_noET1_S14_L001_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI2546KBWD/",
            "accession": "IGVFFI2546KBWD",
            "aliases": [
                "charles-gersbach:measurement-set-crispra-region3-mouse-hl1-targeted-hicar-rep1-R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-10-23T19:29:54.301898+00:00",
            "file_format": "fastq",
            "file_size": 1222467796,
            "href": "/sequence-files/IGVFFI2546KBWD/@@download/IGVFFI2546KBWD.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/10/23/43a4e601-2469-4854-9d94-9d1d10a47e00/IGVFFI2546KBWD.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_mouse/crispra_hicar_mouse_fastq/HL_1_TA446_1_noET1_ds.62ae2232c0cc4744bd32ce6a0473f891/HL_1_TA446_1_noET1_S14_L001_R2_001.fastq.gz",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS3159CKGQ/"
    ],
    "lab": {
        "@id": "/labs/charles-gersbach/",
        "title": "Charles Gersbach, Duke"
    },
    "preferred_assay_title": "HiCAR",
    "protocols": [
        "https://www.protocols.io/view/hicar-for-mouse-hl-1-cells-following-enhancer-pert-36wgqn2yygk5"
    ],
    "release_timestamp": "2024-12-13T19:43:28.527692+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM3147FFHB/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM3147FFHB",
            "aliases": [
                "charles-gersbach:in-vitro-system-crispra-region3-mouse-hl1-targeted-hicar-rep1"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                {
                    "@id": "/construct-library-sets/IGVFDS8122GWMC/",
                    "accession": "IGVFDS8122GWMC",
                    "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_0022835/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
                        "Item"
                    ],
                    "status": "released",
                    "summary": "HL-1",
                    "term_name": "HL-1"
                }
            ],
            "status": "released",
            "summary": "HL-1 cell line, female, Mus musculus C57BL/6J transfected with a guide library",
            "taxa": "Mus musculus"
        }
    ],
    "schema_version": "23",
    "status": "released",
    "submitted_by": {
        "@id": "/users/3782ce69-0e9f-4b46-91f9-4578139785c7/",
        "title": "Ruhi Rai"
    },
    "submitted_files_timestamp": "2024-10-23T19:29:52.987015+00:00",
    "summary": "CRISPR HiCAR integrating a guide (sgRNA) library targeting accessible genome regions in a genomic locus",
    "uuid": "a5970146-02a0-4cb6-96c9-8ff26bc867eb"
}