IGVFFI4698BRVW

preview
validated
{
    "@context": "/terms/",
    "@id": "/sequence-files/IGVFFI4698BRVW/",
    "@type": [
        "SequenceFile",
        "File",
        "Item"
    ],
    "accession": "IGVFFI4698BRVW",
    "aliases": [
        "igvf:corces_sequenceFile_RNA_X041_G1_P042_L001_R2"
    ],
    "assay_titles": [
        "10x multiome"
    ],
    "audit": {},
    "award": {
        "@id": "/awards/HG012076/",
        "component": "mapping"
    },
    "checkfiles_version": "v20",
    "content_md5sum": "2ed350a6454f664a02f1355117f28f60",
    "content_type": "reads",
    "controlled_access": false,
    "creation_timestamp": "2025-03-20T12:59:59.816219+00:00",
    "externally_hosted": false,
    "file_format": "fastq",
    "file_set": {
        "@id": "/measurement-sets/IGVFDS1691KPWU/",
        "@type": [
            "MeasurementSet",
            "FileSet",
            "Item"
        ],
        "accession": "IGVFDS1691KPWU",
        "assay_term": {
            "@id": "/assay-terms/OBI_0003109/",
            "term_name": "single-nucleus RNA sequencing assay"
        },
        "file_set_type": "experimental data",
        "samples": [
            {
                "@id": "/multiplexed-samples/IGVFSM1990PUGQ/",
                "@type": [
                    "MultiplexedSample",
                    "Sample",
                    "Item"
                ],
                "accession": "IGVFSM1990PUGQ",
                "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_2377/",
                        "@type": [
                            "PhenotypeTerm",
                            "OntologyTerm",
                            "Item"
                        ],
                        "status": "in progress",
                        "summary": "multiple sclerosis",
                        "term_name": "multiple sclerosis"
                    },
                    {
                        "@id": "/phenotype-terms/DOID_9246/",
                        "@type": [
                            "PhenotypeTerm",
                            "OntologyTerm",
                            "Item"
                        ],
                        "status": "in progress",
                        "summary": "cerebral amyloid angiopathy",
                        "term_name": "cerebral amyloid angiopathy"
                    },
                    {
                        "@id": "/phenotype-terms/MONDO_0004975/",
                        "@type": [
                            "PhenotypeTerm",
                            "OntologyTerm",
                            "Item"
                        ],
                        "status": "released",
                        "summary": "Alzheimer disease",
                        "term_name": "Alzheimer disease"
                    }
                ],
                "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, 72 years) middle temporal gyrus tissue associated with cerebral amyloid angiopathy; Homo sapiens (female, 82 years) substantia nigra tissue associated with Alzheimer disease, Parkinson's disease, cerebral amyloid angiopathy, multiple sclerosis; ... and 10 more samples",
                "taxa": "Homo sapiens",
                "treatments": []
            }
        ],
        "status": "preview",
        "summary": "single-nucleus RNA sequencing assay (10x multiome)"
    },
    "file_size": 3138640976,
    "flowcell_id": "222YMLLT3",
    "gene_list_for": [],
    "href": "/sequence-files/IGVFFI4698BRVW/@@download/IGVFFI4698BRVW.fastq.gz",
    "illumina_read_type": "R2",
    "input_file_for": [],
    "integrated_in": [],
    "lab": {
        "@id": "/labs/ryan-corces/",
        "title": "Ryan Corces, Gladstone Institute UCSF"
    },
    "lane": 1,
    "loci_list_for": [],
    "maximum_read_length": 90,
    "md5sum": "62caac07ca5ec7b0af18c66c861ea365",
    "mean_read_length": 90,
    "minimum_read_length": 90,
    "quality_metrics": [],
    "read_count": 74293198,
    "read_names": [
        "Read 2"
    ],
    "s3_uri": "s3://igvf-files/2025/03/20/d6b3905d-01e8-482a-9e30-4b14b262f3d3/IGVFFI4698BRVW.fastq.gz",
    "schema_version": "15",
    "seqspecs": [],
    "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": "preview",
    "submitted_by": {
        "@id": "/users/c13db3ca-f844-4a69-9056-5fbc4a100f36/",
        "title": "Ryan Corces"
    },
    "submitted_file_name": "Multiome_RNA_X041_G1_L001_P042_S11_L001_R2_001.fastq.gz",
    "summary": "R2 reads from sequencing run 1",
    "upload_status": "validated",
    "uuid": "d6b3905d-01e8-482a-9e30-4b14b262f3d3"
}