IGVFFI9026YNOD

{
    "@context": "/terms/",
    "@id": "/sequence-files/IGVFFI9026YNOD/",
    "@type": [
        "SequenceFile",
        "File",
        "Item"
    ],
    "accession": "IGVFFI9026YNOD",
    "aliases": [
        "jesse-engreitz:measurement_files_CRUDO_TAPseq-Auxin6hrs-Rep1_S4_R2"
    ],
    "assay_titles": [
        "TAP-seq"
    ],
    "audit": {},
    "award": {
        "@id": "/awards/HG011972/",
        "component": "functional characterization"
    },
    "content_md5sum": "08f0e9ba1ae7fe85da5cb22773b16fe6",
    "content_type": "reads",
    "controlled_access": false,
    "creation_timestamp": "2024-06-03T19:11:17.545002+00:00",
    "externally_hosted": false,
    "file_format": "fastq",
    "file_set": {
        "@id": "/measurement-sets/IGVFDS6896VSKX/",
        "accession": "IGVFDS6896VSKX",
        "file_set_type": "experimental data",
        "samples": [
            {
                "@id": "/in-vitro-systems/IGVFSM9983LVUX/",
                "accession": "IGVFSM9983LVUX",
                "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 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": "mixed TAP-seq integrating a guide (sgRNA) library targeting accessible genome regions in 29 genomic loci"
    },
    "file_size": 2689520897,
    "gene_list_for": [],
    "href": "/sequence-files/IGVFFI9026YNOD/@@download/IGVFFI9026YNOD.fastq.gz",
    "illumina_read_type": "R2",
    "input_file_for": [
        "/tabular-files/IGVFFI1012PVIG/",
        "/tabular-files/IGVFFI4629HCQH/"
    ],
    "integrated_in": [],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "lane": 4,
    "loci_list_for": [],
    "maximum_read_length": 90,
    "md5sum": "b2cd1af50a1c07476f214865335587fb",
    "mean_read_length": 90,
    "minimum_read_length": 90,
    "read_count": 50652888,
    "release_timestamp": "2024-07-10T19:53:41.522592+00:00",
    "s3_uri": "s3://igvf-files/2024/06/03/f36eb85b-6968-4d2b-8374-910b86e0f081/IGVFFI9026YNOD.fastq.gz",
    "schema_version": "14",
    "seqspecs": [
        "/configuration-files/IGVFFI1426OVDM/"
    ],
    "sequencing_platform": {
        "@id": "/platform-terms/EFO_0008566/",
        "term_name": "Illumina NextSeq 550"
    },
    "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/221125_Cohesin_TAPseq_v1/221125_Cohesin_TAPseq_v1/outs/fastq_path/L362_S3_L004_R2_001.fastq.gz",
    "summary": "R2 reads from sequencing run 1",
    "upload_status": "validated",
    "uuid": "f36eb85b-6968-4d2b-8374-910b86e0f081"
}