IGVFFI1876KVCT

{
    "@context": "/terms/",
    "@id": "/sequence-files/IGVFFI1876KVCT/",
    "@type": [
        "SequenceFile",
        "File",
        "Item"
    ],
    "accession": "IGVFFI1876KVCT",
    "aliases": [
        "richard-sherwood:18loci_uptake_Rep3_top40_read2"
    ],
    "assay_titles": [
        "CRISPR FACS screen"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "mismatched status",
                "detail": "Released sequence file [IGVFFI1876KVCT](/sequence-files/IGVFFI1876KVCT/) has in progress subobject platform term [NTR_0000785](/platform-terms/NTR_0000785/).",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_item_status",
                "path": "/sequence-files/IGVFFI1876KVCT/"
            }
        ]
    },
    "award": {
        "@id": "/awards/HG012010/",
        "component": "functional characterization"
    },
    "checkfiles_version": "v17",
    "content_md5sum": "5a8a8d23f7273545096c2ce9e31dcfd5",
    "content_type": "reads",
    "controlled_access": false,
    "creation_timestamp": "2024-11-20T20:04:52.544636+00:00",
    "externally_hosted": false,
    "file_format": "fastq",
    "file_set": {
        "@id": "/measurement-sets/IGVFDS9030KZWL/",
        "accession": "IGVFDS9030KZWL",
        "file_set_type": "experimental data",
        "samples": [
            {
                "@id": "/in-vitro-systems/IGVFSM4480HBZE/",
                "accession": "IGVFSM4480HBZE",
                "classifications": [
                    "cell line"
                ],
                "modifications": [
                    {
                        "@id": "/crispr-modifications/464b468a-3a69-4880-96b1-3a5efa246118/",
                        "modality": "base editing",
                        "status": "in progress",
                        "summary": "CRISPR base editing SpRY-ABE8e"
                    }
                ],
                "sample_terms": [
                    {
                        "@id": "/sample-terms/EFO_0001187/",
                        "status": "released",
                        "term_name": "HepG2"
                    }
                ],
                "status": "released",
                "summary": "HepG2 cell line, male, Homo sapiens (sorting details: Sorted for Top 20-40% LDL-C uptake) modified with CRISPR base editing SpRY-ABE8e, transduced (lentivirus) with a guide library (MOI of 0.5)",
                "taxa": "Homo sapiens"
            }
        ],
        "status": "released",
        "summary": "CRISPR base editing FACS screen integrating a guide (sgRNA) library targeting phenotype-associated variants genome-wide"
    },
    "file_size": 17267984,
    "gene_list_for": [],
    "href": "/sequence-files/IGVFFI1876KVCT/@@download/IGVFFI1876KVCT.fastq.gz",
    "illumina_read_type": "R2",
    "input_file_for": [
        "/tabular-files/IGVFFI5972QBNS/"
    ],
    "integrated_in": [],
    "lab": {
        "@id": "/labs/richard-sherwood/",
        "title": "Richard Sherwood, Brigham and Women's Hospital"
    },
    "loci_list_for": [],
    "maximum_read_length": 60,
    "md5sum": "e258ba770ce10ce428d93c84ced1b4cd",
    "mean_read_length": 60,
    "minimum_read_length": 60,
    "quality_metrics": [],
    "read_count": 516408,
    "release_timestamp": "2025-03-07T23:05:54.968053+00:00",
    "s3_uri": "s3://igvf-files/2024/11/20/9ee771a8-b0ac-413a-b5d0-be422269796b/IGVFFI1876KVCT.fastq.gz",
    "schema_version": "15",
    "seqspecs": [],
    "sequencing_platform": {
        "@id": "/platform-terms/NTR_0000785/",
        "status": "in progress",
        "term_name": "Element Biosciences AVITI"
    },
    "sequencing_run": 1,
    "status": "released",
    "submitted_by": {
        "@id": "/users/892d6eba-c6de-4b35-89ff-639c5c5390c9/",
        "title": "Quang Vinh Phan"
    },
    "submitted_file_name": "/net/bgm/sherwood/Tian_demult_data/nextseq_051523_Tian/fixed/18loci_uptake_Rep3_top40_R2.fastq.gz",
    "summary": "R2 reads from sequencing run 1",
    "upload_status": "validated",
    "uuid": "9ee771a8-b0ac-413a-b5d0-be422269796b"
}