IGVFFI1215XWXM

{
    "@context": "/terms/",
    "@id": "/sequence-files/IGVFFI1215XWXM/",
    "@type": [
        "SequenceFile",
        "File",
        "Item"
    ],
    "accession": "IGVFFI1215XWXM",
    "aliases": [
        "jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep4-BinC-PCRrep8_R1"
    ],
    "assay_titles": [
        "Variant FlowFISH"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "mismatched status",
                "detail": "Released sequence file [IGVFFI1215XWXM](/sequence-files/IGVFFI1215XWXM/) has in progress subobject auxiliary set [IGVFDS8308NVXH](/auxiliary-sets/IGVFDS8308NVXH/).",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_item_status",
                "path": "/sequence-files/IGVFFI1215XWXM/"
            }
        ]
    },
    "award": {
        "@id": "/awards/HG011972/",
        "component": "functional characterization"
    },
    "content_md5sum": "c7aac5a5d6aabc940e177e9d1c6f72c9",
    "content_type": "reads",
    "controlled_access": false,
    "creation_timestamp": "2023-12-13T09:21:06.553633+00:00",
    "externally_hosted": false,
    "file_format": "fastq",
    "file_set": {
        "@id": "/auxiliary-sets/IGVFDS8308NVXH/",
        "accession": "IGVFDS8308NVXH",
        "file_set_type": "variant sequencing",
        "samples": [
            {
                "@id": "/in-vitro-systems/IGVFSM1406ICND/",
                "accession": "IGVFSM1406ICND",
                "classifications": [
                    "cell line"
                ],
                "modifications": [
                    {
                        "@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
                        "modality": "prime editing",
                        "summary": "CRISPR prime editing Sp-nCas9-M-MLV RT (PE2)"
                    }
                ],
                "sample_terms": [
                    {
                        "@id": "/sample-terms/EFO_0001253/",
                        "term_name": "THP-1"
                    }
                ],
                "summary": "THP-1 cell line, male, Homo sapiens (sorting details: FACS bin for 51-75% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transfected with a guide library",
                "taxa": "Homo sapiens"
            }
        ],
        "summary": "variant sequencing for prime editing Variant FlowFISH integrating a guide (sgRNA) library targeting sequence variants in a genomic locus"
    },
    "file_size": 9178385,
    "gene_list_for": [],
    "href": "/sequence-files/IGVFFI1215XWXM/@@download/IGVFFI1215XWXM.fastq.gz",
    "illumina_read_type": "R1",
    "index": "GCCTAGCC:TGAC",
    "input_file_for": [],
    "integrated_in": [],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "loci_list_for": [],
    "maximum_read_length": 150,
    "md5sum": "79cda0c318d6f099dbb100fa5528db54",
    "mean_read_length": 150,
    "minimum_read_length": 150,
    "read_count": 245358,
    "release_timestamp": "2023-12-21T00:38:15.743716+00:00",
    "s3_uri": "s3://igvf-files/2023/12/13/ff594040-8ecf-4b69-bee1-2a4dc9d22024/IGVFFI1215XWXM.fastq.gz",
    "schema_version": "14",
    "seqspecs": [],
    "sequencing_platform": {
        "@id": "/platform-terms/EFO_0008566/",
        "term_name": "Illumina NextSeq 550"
    },
    "sequencing_run": 1,
    "status": "released",
    "submitted_by": {
        "@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
        "title": "Michael Montgomery"
    },
    "submitted_file_name": "230523pPPIFEnformerTHP1-THP1-PE-pPPIF_Enformer-Amp-pPPIF-BioRep2-FFRep4_BinC-PCRrep8_S368_R1_001.fastq.gz",
    "summary": "R1 reads from sequencing run 1",
    "upload_status": "validated",
    "uuid": "ff594040-8ecf-4b69-bee1-2a4dc9d22024"
}