IGVFFI0799SCDB

{
    "@context": "/terms/",
    "@id": "/sequence-files/IGVFFI0799SCDB/",
    "@type": [
        "SequenceFile",
        "File",
        "Item"
    ],
    "accession": "IGVFFI0799SCDB",
    "aliases": [
        "ansuman-satpathy:igvf_exp5_atac_10x1_NGS2_r3"
    ],
    "assay_titles": [
        "10x multiome with MULTI-seq"
    ],
    "audit": {},
    "award": {
        "@id": "/awards/HG012076/",
        "component": "mapping"
    },
    "content_md5sum": "f05222fd664029407985e6f34474ce61",
    "content_type": "reads",
    "controlled_access": false,
    "creation_timestamp": "2024-07-22T16:22:40.005299+00:00",
    "externally_hosted": false,
    "file_format": "fastq",
    "file_set": {
        "@id": "/measurement-sets/IGVFDS9743PIFM/",
        "accession": "IGVFDS9743PIFM",
        "file_set_type": "experimental data",
        "samples": [
            {
                "@id": "/multiplexed-samples/IGVFSM1143WWLK/",
                "accession": "IGVFSM1143WWLK",
                "classifications": [
                    "cell line",
                    "differentiated cell specimen",
                    "gastruloid",
                    "multiplexed sample"
                ],
                "disease_terms": [],
                "modifications": [],
                "sample_terms": [
                    {
                        "@id": "/sample-terms/EFO_0001184/",
                        "status": "released",
                        "term_name": "HEK293T"
                    },
                    {
                        "@id": "/sample-terms/EFO_0003042/",
                        "status": "released",
                        "term_name": "H1-hESC"
                    },
                    {
                        "@id": "/sample-terms/EFO_0003045/",
                        "status": "released",
                        "term_name": "H9"
                    },
                    {
                        "@id": "/sample-terms/EFO_0009747/",
                        "status": "released",
                        "term_name": "GM25256 (WTC-11)"
                    }
                ],
                "status": "released",
                "summary": "multiplexed sample: H9 differentiated cell specimen induced to neuron for 6 days, female, Homo sapiens; H9 differentiated cell specimen induced to neuron for 6 days, female, Homo sapiens; ... and 6 more samples",
                "taxa": "Homo sapiens",
                "treatments": []
            }
        ],
        "status": "released",
        "summary": "single-nucleus ATAC-seq (10x multiome with MULTI-seq)"
    },
    "file_size": 8399282250,
    "flowcell_id": "222YV7LT3",
    "gene_list_for": [],
    "href": "/sequence-files/IGVFFI0799SCDB/@@download/IGVFFI0799SCDB.fastq.gz",
    "illumina_read_type": "R3",
    "input_file_for": [
        "/tabular-files/IGVFFI3412IJQJ/"
    ],
    "integrated_in": [],
    "lab": {
        "@id": "/labs/ansuman-satpathy/",
        "title": "Ansuman Satpathy, Stanford"
    },
    "lane": 6,
    "loci_list_for": [],
    "maximum_read_length": 51,
    "md5sum": "8fd7ef01fdfe7a8903eeb764e36bb691",
    "mean_read_length": 51,
    "minimum_read_length": 51,
    "quality_metrics": [],
    "read_count": 272745798,
    "read_names": [
        "Read 2"
    ],
    "release_timestamp": "2025-03-07T01:11:47.624422+00:00",
    "s3_uri": "s3://igvf-files/2024/07/22/0f3117d6-0dfc-4f0c-ab41-353c893ec117/IGVFFI0799SCDB.fastq.gz",
    "schema_version": "15",
    "seqspecs": [
        "/configuration-files/IGVFFI6846ZLPE/"
    ],
    "sequencing_kit": "NovaSeq X Series 10B Reagent Kit",
    "sequencing_platform": {
        "@id": "/platform-terms/EFO_0022840/",
        "status": "released",
        "term_name": "Illumina NovaSeq X"
    },
    "sequencing_run": 1,
    "status": "released",
    "submitted_by": {
        "@id": "/users/353655bc-31a1-4cd9-bac3-c7d34faf722f/",
        "title": "Christopher Mcginnis"
    },
    "submitted_file_name": "/oak/stanford/projects/igvf/Projects/230522_IGVF5_McGinnis/ATAC/FASTQ/ATAC_1_S7_L006_R3_001.fastq.gz",
    "summary": "R3 reads from sequencing run 1",
    "upload_status": "validated",
    "uuid": "0f3117d6-0dfc-4f0c-ab41-353c893ec117"
}