IGVFFI9427ESFD

{
    "@context": "/terms/",
    "@id": "/sequence-files/IGVFFI9427ESFD/",
    "@type": [
        "SequenceFile",
        "File",
        "Item"
    ],
    "accession": "IGVFFI9427ESFD",
    "aliases": [
        "jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep1-BinD-PCRrep1_R2"
    ],
    "assay_titles": [
        "Variant-EFFECTS"
    ],
    "audit": {},
    "award": {
        "@id": "/awards/HG011972/",
        "component": "functional characterization"
    },
    "content_md5sum": "da3c4619c00068ea03a33e47c345b796",
    "content_type": "reads",
    "controlled_access": false,
    "creation_timestamp": "2023-12-05T19:45:56.453342+00:00",
    "externally_hosted": false,
    "file_format": "fastq",
    "file_set": {
        "@id": "/measurement-sets/IGVFDS0506RSOE/",
        "accession": "IGVFDS0506RSOE",
        "file_set_type": "experimental data",
        "samples": [
            {
                "@id": "/in-vitro-systems/IGVFSM9615VPZF/",
                "accession": "IGVFSM9615VPZF",
                "classifications": [
                    "cell line"
                ],
                "modifications": [
                    {
                        "@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
                        "modality": "prime editing",
                        "status": "released",
                        "summary": "CRISPR prime editing Sp-nCas9-M-MLV RT (PE2)"
                    }
                ],
                "sample_terms": [
                    {
                        "@id": "/sample-terms/EFO_0002796/",
                        "status": "released",
                        "term_name": "Jurkat"
                    }
                ],
                "status": "released",
                "summary": "Jurkat cell line, male, Homo sapiens (sorting details: FACS bin for 55-65% expression of PPIF) treated with 100 ng/mL phorbol 13-acetate 12-myristate for 4 hours, 5 μg/mL T-cell surface glycoprotein CD3 gamma chain for 4 hours, modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transfected with a guide library",
                "taxa": "Homo sapiens",
                "treatments": [
                    {
                        "@id": "/treatments/df02c0d4-f796-4f77-bfbc-388cdbfcc615/",
                        "purpose": "stimulation",
                        "status": "released",
                        "summary": "Treatment of 5 μg/mL T-cell surface glycoprotein CD3 gamma chain for 4 hours",
                        "treatment_term_name": "T-cell surface glycoprotein CD3 gamma chain"
                    },
                    {
                        "@id": "/treatments/42b3c61d-38de-4bd2-bb39-33c125a417cb/",
                        "purpose": "stimulation",
                        "status": "released",
                        "summary": "Treatment of 100 ng/mL phorbol 13-acetate 12-myristate for 4 hours",
                        "treatment_term_name": "phorbol 13-acetate 12-myristate"
                    }
                ]
            }
        ],
        "status": "released",
        "summary": "CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus"
    },
    "file_size": 13195474,
    "gene_list_for": [],
    "href": "/sequence-files/IGVFFI9427ESFD/@@download/IGVFFI9427ESFD.fastq.gz",
    "illumina_read_type": "R2",
    "index": "CAATAGTC:GTCA",
    "input_file_for": [
        "/tabular-files/IGVFFI7903UEWZ/"
    ],
    "integrated_in": [],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "loci_list_for": [],
    "maximum_read_length": 150,
    "md5sum": "89aaa8ed7cb995bd8e0b429983648f65",
    "mean_read_length": 150,
    "minimum_read_length": 150,
    "read_count": 383992,
    "release_timestamp": "2023-12-20T23:22:20.217971+00:00",
    "s3_uri": "s3://igvf-files/2023/12/05/0be6af20-396c-42ce-b347-64b18ce5b940/IGVFFI9427ESFD.fastq.gz",
    "schema_version": "14",
    "seqspecs": [],
    "sequencing_platform": {
        "@id": "/platform-terms/EFO_0008566/",
        "status": "released",
        "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": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S19-BioRep4-FFRep1-BinD-PCRrep1_S158_R2_001.fastq.gz",
    "summary": "R2 reads from sequencing run 1",
    "upload_status": "validated",
    "uuid": "0be6af20-396c-42ce-b347-64b18ce5b940"
}