IGVFFI9300PQFQ

preview
validated
{
    "@context": "/terms/",
    "@id": "/sequence-files/IGVFFI9300PQFQ/",
    "@type": [
        "SequenceFile",
        "File",
        "Item"
    ],
    "accession": "IGVFFI9300PQFQ",
    "aliases": [
        "igvf:corces_sequenceFile_RNA_X019_G6_P020_L004_R1"
    ],
    "assay_titles": [
        "10x multiome"
    ],
    "audit": {},
    "award": {
        "@id": "/awards/HG012076/",
        "component": "mapping"
    },
    "checkfiles_version": "v20",
    "content_md5sum": "06a61eb129d00819190ecfa89bfc887b",
    "content_type": "reads",
    "controlled_access": false,
    "creation_timestamp": "2025-03-20T01:22:14.518227+00:00",
    "externally_hosted": false,
    "file_format": "fastq",
    "file_set": {
        "@id": "/measurement-sets/IGVFDS0924SKZZ/",
        "@type": [
            "MeasurementSet",
            "FileSet",
            "Item"
        ],
        "accession": "IGVFDS0924SKZZ",
        "assay_term": {
            "@id": "/assay-terms/OBI_0003109/",
            "term_name": "single-nucleus RNA sequencing assay"
        },
        "file_set_type": "experimental data",
        "samples": [
            {
                "@id": "/multiplexed-samples/IGVFSM0150MSRW/",
                "@type": [
                    "MultiplexedSample",
                    "Sample",
                    "Item"
                ],
                "accession": "IGVFSM0150MSRW",
                "classifications": [
                    "tissue",
                    "multiplexed sample"
                ],
                "disease_terms": [
                    {
                        "@id": "/phenotype-terms/DOID_0080832/",
                        "@type": [
                            "PhenotypeTerm",
                            "OntologyTerm",
                            "Item"
                        ],
                        "status": "in progress",
                        "summary": "mild cognitive impairment",
                        "term_name": "mild cognitive impairment"
                    },
                    {
                        "@id": "/phenotype-terms/DOID_14330/",
                        "@type": [
                            "PhenotypeTerm",
                            "OntologyTerm",
                            "Item"
                        ],
                        "status": "in progress",
                        "summary": "Parkinson's disease",
                        "term_name": "Parkinson's disease"
                    },
                    {
                        "@id": "/phenotype-terms/DOID_9246/",
                        "@type": [
                            "PhenotypeTerm",
                            "OntologyTerm",
                            "Item"
                        ],
                        "status": "in progress",
                        "summary": "cerebral amyloid angiopathy",
                        "term_name": "cerebral amyloid angiopathy"
                    }
                ],
                "modifications": [],
                "sample_terms": [
                    {
                        "@id": "/sample-terms/UBERON_0001874/",
                        "status": "preview",
                        "term_name": "putamen"
                    },
                    {
                        "@id": "/sample-terms/UBERON_0002038/",
                        "status": "preview",
                        "term_name": "substantia nigra"
                    },
                    {
                        "@id": "/sample-terms/UBERON_0002129/",
                        "status": "preview",
                        "term_name": "cerebellar cortex"
                    },
                    {
                        "@id": "/sample-terms/UBERON_0002740/",
                        "status": "preview",
                        "term_name": "posterior cingulate gyrus"
                    },
                    {
                        "@id": "/sample-terms/UBERON_0002771/",
                        "status": "preview",
                        "term_name": "middle temporal gyrus"
                    }
                ],
                "status": "preview",
                "summary": "multiplexed sample: Homo sapiens (male, 78 years) substantia nigra tissue associated with Parkinson's disease, cerebral amyloid angiopathy, mild cognitive impairment; Homo sapiens (male, 87 years) substantia nigra tissue associated with Parkinson's disease, cerebral amyloid angiopathy; ... and 10 more samples",
                "taxa": "Homo sapiens",
                "treatments": []
            }
        ],
        "status": "preview",
        "summary": "single-nucleus RNA sequencing assay (10x multiome)"
    },
    "file_size": 11869193606,
    "flowcell_id": "HV7NNDSX5",
    "gene_list_for": [],
    "href": "/sequence-files/IGVFFI9300PQFQ/@@download/IGVFFI9300PQFQ.fastq.gz",
    "illumina_read_type": "R1",
    "input_file_for": [],
    "integrated_in": [],
    "lab": {
        "@id": "/labs/ryan-corces/",
        "title": "Ryan Corces, Gladstone Institute UCSF"
    },
    "lane": 4,
    "loci_list_for": [],
    "maximum_read_length": 101,
    "md5sum": "9b85bf00b6abbaab4764329b37debe81",
    "mean_read_length": 101,
    "minimum_read_length": 101,
    "quality_metrics": [],
    "read_count": 180349638,
    "read_names": [
        "Read 1"
    ],
    "s3_uri": "s3://igvf-files/2025/03/20/53baead5-b8ad-4ac9-8e9e-dc1678c087fa/IGVFFI9300PQFQ.fastq.gz",
    "schema_version": "15",
    "seqspecs": [],
    "sequencing_kit": "NovaSeq 6000 S4 Reagent Kit v1.5",
    "sequencing_platform": {
        "@id": "/platform-terms/EFO_0008637/",
        "status": "released",
        "term_name": "Illumina NovaSeq 6000"
    },
    "sequencing_run": 1,
    "status": "preview",
    "submitted_by": {
        "@id": "/users/c13db3ca-f844-4a69-9056-5fbc4a100f36/",
        "title": "Ryan Corces"
    },
    "submitted_file_name": "Multiome_RNA_X019_G6_L006_P020_S44_L004_R1_001.fastq.gz",
    "summary": "R1 reads from sequencing run 1",
    "upload_status": "validated",
    "uuid": "53baead5-b8ad-4ac9-8e9e-dc1678c087fa"
}