IGVFFI2836GXUE

{
    "@context": "/terms/",
    "@id": "/sequence-files/IGVFFI2836GXUE/",
    "@type": [
        "SequenceFile",
        "File",
        "Item"
    ],
    "accession": "IGVFFI2836GXUE",
    "aliases": [
        "jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF2-BinF-PCR3_S162"
    ],
    "assay_titles": [
        "CRISPR FlowFISH screen"
    ],
    "audit": {},
    "award": {
        "@id": "/awards/HG011972/",
        "component": "functional characterization"
    },
    "content_md5sum": "7833ea61563c44ad853051f70b4f164f",
    "content_type": "reads",
    "controlled_access": false,
    "creation_timestamp": "2024-06-03T15:26:24.459928+00:00",
    "externally_hosted": false,
    "file_format": "fastq",
    "file_set": {
        "@id": "/auxiliary-sets/IGVFDS0078EAAP/",
        "accession": "IGVFDS0078EAAP",
        "file_set_type": "gRNA sequencing",
        "samples": [
            {
                "@id": "/in-vitro-systems/IGVFSM4713PHAB/",
                "accession": "IGVFSM4713PHAB",
                "classifications": [
                    "cell line"
                ],
                "modifications": [
                    {
                        "@id": "/degron-modifications/95081d1b-08b4-49ed-b324-e53fc43d8456/",
                        "modality": "degradation",
                        "summary": "AID system targeting RAD21"
                    },
                    {
                        "@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
                        "modality": "interference",
                        "summary": "CRISPRi Sp-dCas9-KOX1-KRAB"
                    }
                ],
                "sample_terms": [
                    {
                        "@id": "/sample-terms/EFO_0002824/",
                        "term_name": "HCT116"
                    }
                ],
                "summary": "HCT116 cell line, male, Homo sapiens (sorting details: FACS bin F for 80-100% expression of KITLG) treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours, modified with AID system targeting RAD21, CRISPRi Sp-dCas9-KOX1-KRAB, transfected with a guide library",
                "taxa": "Homo sapiens",
                "treatments": [
                    {
                        "@id": "/treatments/d35868d1-c45b-49ae-8ff3-a9c0c22551c2/",
                        "purpose": "activation",
                        "summary": "Treatment of 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours",
                        "treatment_term_name": "5-Phenyl-1H-indole-3-acetic acid"
                    }
                ]
            }
        ],
        "summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci"
    },
    "file_size": 16180873,
    "gene_list_for": [],
    "href": "/sequence-files/IGVFFI2836GXUE/@@download/IGVFFI2836GXUE.fastq.gz",
    "index": "CTAACTCG:ATTG",
    "input_file_for": [
        "/tabular-files/IGVFFI5319EGKY/"
    ],
    "integrated_in": [],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "loci_list_for": [],
    "maximum_read_length": 21,
    "md5sum": "371a17c895b84cd279578c2512e8609e",
    "mean_read_length": 21,
    "minimum_read_length": 21,
    "read_count": 673714,
    "release_timestamp": "2024-07-10T20:17:40.951994+00:00",
    "s3_uri": "s3://igvf-files/2024/06/03/1937eec8-b3fd-44af-b9fd-d802981edb56/IGVFFI2836GXUE.fastq.gz",
    "schema_version": "14",
    "seqspecs": [
        "/configuration-files/IGVFFI8909CZJU/"
    ],
    "sequencing_platform": {
        "@id": "/platform-terms/EFO_0008565/",
        "term_name": "Illumina HiSeq 2500"
    },
    "sequencing_run": 1,
    "status": "released",
    "submitted_by": {
        "@id": "/users/100f06c6-83a7-4b4d-9dfd-053a1829773b/",
        "title": "Benjamin Doughty"
    },
    "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF2-BinF-PCR3_S162_R1_001.fastq.gz",
    "summary": "reads from sequencing run 1",
    "upload_status": "validated",
    "uuid": "1937eec8-b3fd-44af-b9fd-d802981edb56"
}