IGVFDS2598INQR

released
{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS2598INQR/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS2598INQR",
    "aliases": [
        "charles-gersbach:measurement-set-crispra-region3-1umET1-ipsc-cm-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 [IGVFDS2598INQR](/measurement-sets/IGVFDS2598INQR/) has sequence file(s): [IGVFFI7928LBZM](/sequence-files/IGVFFI7928LBZM/), [IGVFFI3243VUUV](/sequence-files/IGVFFI3243VUUV/) 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/IGVFDS2598INQR/"
            }
        ]
    },
    "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": "2024-10-23T19:20:04.676160+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/IGVFFI7928LBZM/",
            "accession": "IGVFFI7928LBZM",
            "aliases": [
                "charles-gersbach:measurement-set-crispra-region3-1umET1-ipsc-cm-targeted-hicar-rep1-R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-10-23T19:29:40.450691+00:00",
            "file_format": "fastq",
            "file_size": 1125241163,
            "href": "/sequence-files/IGVFFI7928LBZM/@@download/IGVFFI7928LBZM.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/10/23/9595f9a2-d90f-4c2f-9450-9e4c039ba186/IGVFFI7928LBZM.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_1_1uMET1_ds.e858c0c6acc64a2ab755c9f2b042627c/H_vp64_r2_TA448_1_1uMET1_S8_L001_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3243VUUV/",
            "accession": "IGVFFI3243VUUV",
            "aliases": [
                "charles-gersbach:measurement-set-crispra-region3-1umET1-ipsc-cm-targeted-hicar-rep1-R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-10-23T19:29:39.394213+00:00",
            "file_format": "fastq",
            "file_size": 1009743541,
            "href": "/sequence-files/IGVFFI3243VUUV/@@download/IGVFFI3243VUUV.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/10/23/d0c5c992-279b-4a6c-a6f3-0a4524df5676/IGVFFI3243VUUV.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_1_1uMET1_ds.e858c0c6acc64a2ab755c9f2b042627c/H_vp64_r2_TA448_1_1uMET1_S8_L001_R1_001.fastq.gz",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS9608RUYZ/"
    ],
    "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": "2024-12-13T19:43:52.291246+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM6802DUZM/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM6802DUZM",
            "aliases": [
                "charles-gersbach:in-vitro-system-crispra-region3-1umET1-ipsc-cm-targeted-hicar-rep1"
            ],
            "classifications": [
                "differentiated cell specimen"
            ],
            "construct_library_sets": [
                {
                    "@id": "/construct-library-sets/IGVFDS5972DQKC/",
                    "accession": "IGVFDS5972DQKC",
                    "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 treated with 1 μM Endothelin-1 for 3 days, transfected with a guide library",
            "targeted_sample_term": {
                "@id": "/sample-terms/CL_0000746/",
                "status": "released",
                "term_name": "cardiac muscle cell"
            },
            "taxa": "Homo sapiens",
            "treatments": [
                {
                    "@id": "/treatments/bbe5df8d-a9e2-4a99-8942-9b3b7d12c605/",
                    "status": "released",
                    "treatment_term_name": "Endothelin-1"
                }
            ]
        }
    ],
    "schema_version": "23",
    "status": "released",
    "submitted_by": {
        "@id": "/users/3782ce69-0e9f-4b46-91f9-4578139785c7/",
        "title": "Ruhi Rai"
    },
    "submitted_files_timestamp": "2024-10-23T19:29:39.394213+00:00",
    "summary": "CRISPR HiCAR integrating a guide (sgRNA) library targeting accessible genome regions in a genomic locus",
    "uuid": "5f3938dd-7885-43af-a87e-a00af775b65c"
}