IGVFFI3412LYTO

{
    "@context": "/terms/",
    "@id": "/sequence-files/IGVFFI3412LYTO/",
    "@type": [
        "SequenceFile",
        "File",
        "Item"
    ],
    "accession": "IGVFFI3412LYTO",
    "aliases": [
        "richard-sherwood:18loci_uptake_Rep1_bottom20_read2"
    ],
    "assay_titles": [
        "CRISPR FACS screen"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "mismatched status",
                "detail": "Released sequence file [IGVFFI3412LYTO](/sequence-files/IGVFFI3412LYTO/) 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/IGVFFI3412LYTO/"
            }
        ]
    },
    "award": {
        "@id": "/awards/HG012010/",
        "component": "functional characterization"
    },
    "checkfiles_version": "v17",
    "content_md5sum": "8a7205b3d5fe9986effc7eae030a78d3",
    "content_type": "reads",
    "controlled_access": false,
    "creation_timestamp": "2024-11-20T20:02:59.430569+00:00",
    "externally_hosted": false,
    "file_format": "fastq",
    "file_set": {
        "@id": "/measurement-sets/IGVFDS6464SOVZ/",
        "accession": "IGVFDS6464SOVZ",
        "file_set_type": "experimental data",
        "samples": [
            {
                "@id": "/in-vitro-systems/IGVFSM0239RDRJ/",
                "accession": "IGVFSM0239RDRJ",
                "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 Bottom 20% 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": 12627182,
    "gene_list_for": [],
    "href": "/sequence-files/IGVFFI3412LYTO/@@download/IGVFFI3412LYTO.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": "973efba714150e5b46f7f08e7affa84e",
    "mean_read_length": 60,
    "minimum_read_length": 60,
    "quality_metrics": [],
    "read_count": 375966,
    "release_timestamp": "2025-03-07T23:06:40.143492+00:00",
    "s3_uri": "s3://igvf-files/2024/11/20/5c906866-25a9-48a3-8ee5-b7a25aa0f114/IGVFFI3412LYTO.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_Rep1_bottom20_R2.fastq.gz",
    "summary": "R2 reads from sequencing run 1",
    "upload_status": "validated",
    "uuid": "5c906866-25a9-48a3-8ee5-b7a25aa0f114"
}