IGVFFI2881CQMD

{
    "@context": "/terms/",
    "@id": "/sequence-files/IGVFFI2881CQMD/",
    "@type": [
        "SequenceFile",
        "File",
        "Item"
    ],
    "accession": "IGVFFI2881CQMD",
    "aliases": [
        "ansuman-satpathy:igvf_exp5_multi_10x2_NGS3_r2"
    ],
    "assay_titles": [
        "10x multiome with MULTI-seq"
    ],
    "audit": {},
    "award": {
        "@id": "/awards/HG012076/",
        "component": "mapping"
    },
    "content_md5sum": "284607ce42531221836d66d8ab2a0004",
    "content_type": "reads",
    "controlled_access": false,
    "creation_timestamp": "2024-07-22T00:32:28.091306+00:00",
    "externally_hosted": false,
    "file_format": "fastq",
    "file_set": {
        "@id": "/auxiliary-sets/IGVFDS5515DQMD/",
        "accession": "IGVFDS5515DQMD",
        "file_set_type": "lipid-conjugated oligo sequencing",
        "samples": [
            {
                "@id": "/multiplexed-samples/IGVFSM3202SKCS/",
                "accession": "IGVFSM3202SKCS",
                "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": "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": 2262598521,
    "flowcell_id": "223JJCLT3",
    "gene_list_for": [],
    "href": "/sequence-files/IGVFFI2881CQMD/@@download/IGVFFI2881CQMD.fastq.gz",
    "illumina_read_type": "R2",
    "input_file_for": [
        "/tabular-files/IGVFFI2172JZIP/"
    ],
    "integrated_in": [],
    "lab": {
        "@id": "/labs/ansuman-satpathy/",
        "title": "Ansuman Satpathy, Stanford"
    },
    "lane": 7,
    "loci_list_for": [],
    "maximum_read_length": 90,
    "md5sum": "464c33576dd52bd7f2a8d6d65d11e80e",
    "mean_read_length": 90,
    "minimum_read_length": 90,
    "quality_metrics": [],
    "read_count": 50126248,
    "release_timestamp": "2025-03-07T01:11:54.527571+00:00",
    "s3_uri": "s3://igvf-files/2024/07/22/13698639-67ae-4426-a5e4-2798fd560961/IGVFFI2881CQMD.fastq.gz",
    "schema_version": "15",
    "seqspecs": [
        "/configuration-files/IGVFFI6268OCGQ/"
    ],
    "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/MULTI/FASTQ/MULTI_2_S22_L007_R2_001.fastq.gz",
    "summary": "R2 reads from sequencing run 1",
    "upload_status": "validated",
    "uuid": "13698639-67ae-4426-a5e4-2798fd560961"
}