{
"@context": "/terms/",
"@id": "/sequence-files/IGVFFI8659RGAG/",
"@type": [
"SequenceFile",
"File",
"Item"
],
"accession": "IGVFFI8659RGAG",
"aliases": [
"igvf:corces_sequenceFile_RNA_X019_G6_P020_L004_I2"
],
"assay_titles": [
"10x multiome"
],
"audit": {},
"award": {
"@id": "/awards/HG012076/",
"component": "mapping"
},
"checkfiles_version": "v20",
"content_md5sum": "0f345229451e9a1370c518e7f389ba64",
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-20T01:22:11.767120+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)"
},
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"flowcell_id": "HV7NNDSX5",
"gene_list_for": [],
"href": "/sequence-files/IGVFFI8659RGAG/@@download/IGVFFI8659RGAG.fastq.gz",
"illumina_read_type": "I2",
"input_file_for": [],
"integrated_in": [],
"lab": {
"@id": "/labs/ryan-corces/",
"title": "Ryan Corces, Gladstone Institute UCSF"
},
"lane": 4,
"loci_list_for": [],
"maximum_read_length": 10,
"md5sum": "0c48a9f9e3ac765e31f0c9fcfb9d8486",
"mean_read_length": 10,
"minimum_read_length": 10,
"quality_metrics": [],
"read_count": 180349638,
"s3_uri": "s3://igvf-files/2025/03/20/bbea2438-a7e0-48d9-931b-4604ff12d596/IGVFFI8659RGAG.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_I2_001.fastq.gz",
"summary": "I2 reads from sequencing run 1",
"upload_status": "validated",
"uuid": "bbea2438-a7e0-48d9-931b-4604ff12d596"
}