IGVFFI2590TULH

{
    "@context": "/terms/",
    "@id": "/sequence-files/IGVFFI2590TULH/",
    "@type": [
        "SequenceFile",
        "File",
        "Item"
    ],
    "accession": "IGVFFI2590TULH",
    "aliases": [
        "ansuman-satpathy:igvf_exp18_atac_10x1_NGS1_r2"
    ],
    "assay_titles": [
        "10x multiome with MULTI-seq"
    ],
    "audit": {},
    "award": {
        "@id": "/awards/HG012076/",
        "component": "mapping"
    },
    "checkfiles_version": "v14",
    "content_md5sum": "4300bfef5383c84a7f86a110def89297",
    "content_type": "reads",
    "controlled_access": false,
    "creation_timestamp": "2025-01-28T03:46:02.041245+00:00",
    "externally_hosted": false,
    "file_format": "fastq",
    "file_set": {
        "@id": "/measurement-sets/IGVFDS1427CODJ/",
        "accession": "IGVFDS1427CODJ",
        "file_set_type": "experimental data",
        "samples": [
            {
                "@id": "/multiplexed-samples/IGVFSM4392KEFB/",
                "accession": "IGVFSM4392KEFB",
                "classifications": [
                    "cell line",
                    "differentiated cell specimen",
                    "multiplexed sample"
                ],
                "disease_terms": [],
                "modifications": [],
                "sample_terms": [
                    {
                        "@id": "/sample-terms/EFO_0001196/",
                        "status": "released",
                        "term_name": "IMR-90"
                    },
                    {
                        "@id": "/sample-terms/EFO_0001203/",
                        "status": "released",
                        "term_name": "MCF-7"
                    },
                    {
                        "@id": "/sample-terms/EFO_0002824/",
                        "status": "released",
                        "term_name": "HCT116"
                    },
                    {
                        "@id": "/sample-terms/EFO_0003072/",
                        "status": "released",
                        "term_name": "SK-N-SH"
                    },
                    {
                        "@id": "/sample-terms/EFO_0022838/",
                        "status": "released",
                        "term_name": "HUDEP-2"
                    },
                    {
                        "@id": "/sample-terms/NTR_0000753/",
                        "status": "released",
                        "term_name": "TeloHAEC"
                    }
                ],
                "status": "released",
                "summary": "multiplexed sample: IMR-90 cell line, female, Homo sapiens; MCF-7 cell line, female, Homo sapiens; ... and 17 more samples",
                "taxa": "Homo sapiens",
                "treatments": [
                    {
                        "@id": "/treatments/ff03c6ff-c1f5-4b47-bd9d-62f22d5794c5/",
                        "purpose": "perturbation",
                        "status": "in progress",
                        "summary": "Treatment of 3 μM Yoda1 for 4 hours",
                        "treatment_term_name": "Yoda1"
                    }
                ]
            }
        ],
        "status": "released",
        "summary": "single-nucleus ATAC-seq (10x multiome with MULTI-seq)"
    },
    "file_size": 12591442778,
    "flowcell_id": "22FL7YLT4",
    "gene_list_for": [],
    "href": "/sequence-files/IGVFFI2590TULH/@@download/IGVFFI2590TULH.fastq.gz",
    "illumina_read_type": "R2",
    "input_file_for": [
        "/tabular-files/IGVFFI6686KVZP/"
    ],
    "integrated_in": [],
    "lab": {
        "@id": "/labs/ansuman-satpathy/",
        "title": "Ansuman Satpathy, Stanford"
    },
    "lane": 1,
    "loci_list_for": [],
    "maximum_read_length": 24,
    "md5sum": "6b60ad5c9295d31ee28d820a6a05b2ae",
    "mean_read_length": 24,
    "minimum_read_length": 24,
    "quality_metrics": [],
    "read_count": 724414038,
    "read_names": [
        "Barcode index"
    ],
    "release_timestamp": "2025-03-07T01:17:56.809523+00:00",
    "s3_uri": "s3://igvf-files/2025/01/28/8de408ec-13ad-44e8-bf45-086ddfbd7188/IGVFFI2590TULH.fastq.gz",
    "schema_version": "15",
    "seqspecs": [
        "/configuration-files/IGVFFI7509TWYF/"
    ],
    "sequencing_kit": "NovaSeq X Series 25B 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/groups/satpathy/users/backup/cmcg/igvf18/ATAC/ATAC1-CMAS23A_S33_L006_R2_001.fastq.gz",
    "summary": "R2 reads from sequencing run 1",
    "upload_status": "validated",
    "uuid": "8de408ec-13ad-44e8-bf45-086ddfbd7188"
}