IGVFFI3642OVXE

{
    "@context": "/terms/",
    "@id": "/sequence-files/IGVFFI3642OVXE/",
    "@type": [
        "SequenceFile",
        "File",
        "Item"
    ],
    "accession": "IGVFFI3642OVXE",
    "aliases": [
        "ansuman-satpathy:igvf_exp18_multi_10x4_NGS1_r1"
    ],
    "assay_titles": [
        "10x multiome with MULTI-seq"
    ],
    "audit": {},
    "award": {
        "@id": "/awards/HG012076/",
        "component": "mapping"
    },
    "checkfiles_version": "v14",
    "content_md5sum": "fd156f85939cb4a7e664af161ef64873",
    "content_type": "reads",
    "controlled_access": false,
    "creation_timestamp": "2025-01-28T04:17:15.149437+00:00",
    "externally_hosted": false,
    "file_format": "fastq",
    "file_set": {
        "@id": "/auxiliary-sets/IGVFDS6039YTCL/",
        "accession": "IGVFDS6039YTCL",
        "file_set_type": "lipid-conjugated oligo sequencing",
        "samples": [
            {
                "@id": "/multiplexed-samples/IGVFSM3125MLLP/",
                "accession": "IGVFSM3125MLLP",
                "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": "lipid-conjugated oligo sequencing for single-nucleus RNA sequencing assay (10x multiome with MULTI-seq), single-nucleus ATAC-seq (10x multiome with MULTI-seq)"
    },
    "file_size": 70098741,
    "flowcell_id": "22JL3JLT4",
    "gene_list_for": [],
    "href": "/sequence-files/IGVFFI3642OVXE/@@download/IGVFFI3642OVXE.fastq.gz",
    "illumina_read_type": "R1",
    "input_file_for": [
        "/tabular-files/IGVFFI3422CZRF/"
    ],
    "integrated_in": [],
    "lab": {
        "@id": "/labs/ansuman-satpathy/",
        "title": "Ansuman Satpathy, Stanford"
    },
    "lane": 1,
    "loci_list_for": [],
    "maximum_read_length": 28,
    "md5sum": "4fe8cac1290710bfee747b708ae2538f",
    "mean_read_length": 28,
    "minimum_read_length": 28,
    "quality_metrics": [],
    "read_count": 3146722,
    "release_timestamp": "2025-03-07T01:18:09.155271+00:00",
    "s3_uri": "s3://igvf-files/2025/01/28/90f9ef40-a8cc-4253-b83a-d7da3818371b/IGVFFI3642OVXE.fastq.gz",
    "schema_version": "15",
    "seqspecs": [
        "/configuration-files/IGVFFI2796VZZW/"
    ],
    "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/MULTI/IGVF18_MULTI4-CMAS24_S59_L004_R1_001.fastq.gz",
    "summary": "R1 reads from sequencing run 1",
    "upload_status": "validated",
    "uuid": "90f9ef40-a8cc-4253-b83a-d7da3818371b"
}