{
"@context": "/terms/",
"@id": "/sequence-files/IGVFFI4312KGTK/",
"@type": [
"SequenceFile",
"File",
"Item"
],
"accession": "IGVFFI4312KGTK",
"aliases": [
"igvf:corces_sequenceFile_ATAC_X043_G8_P043_L008_I1"
],
"assay_titles": [
"10x multiome"
],
"audit": {},
"award": {
"@id": "/awards/HG012076/",
"component": "mapping"
},
"checkfiles_version": "v20",
"content_md5sum": "fa2c473131d7d5ab189b78125d39e32f",
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-20T04:09:40.249623+00:00",
"externally_hosted": false,
"file_format": "fastq",
"file_set": {
"@id": "/measurement-sets/IGVFDS0624REZE/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0624REZE",
"assay_term": {
"@id": "/assay-terms/OBI_0002762/",
"term_name": "single-nucleus ATAC-seq"
},
"file_set_type": "experimental data",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM9265WOCK/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM9265WOCK",
"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"
},
{
"@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 (female, 79 years) substantia nigra tissue associated with Parkinson's disease, cerebral amyloid angiopathy; Homo sapiens (male, 79 years) cerebellar cortex tissue associated with Alzheimer disease, Parkinson's disease; ... and 10 more samples",
"taxa": "Homo sapiens",
"treatments": []
}
],
"status": "preview",
"summary": "single-nucleus ATAC-seq (10x multiome)"
},
"file_size": 383547431,
"flowcell_id": "223JJTLT3",
"gene_list_for": [],
"href": "/sequence-files/IGVFFI4312KGTK/@@download/IGVFFI4312KGTK.fastq.gz",
"illumina_read_type": "I1",
"input_file_for": [],
"integrated_in": [],
"lab": {
"@id": "/labs/ryan-corces/",
"title": "Ryan Corces, Gladstone Institute UCSF"
},
"lane": 8,
"loci_list_for": [],
"maximum_read_length": 8,
"md5sum": "2162386b028ffc015f19000b06086d90",
"mean_read_length": 8,
"minimum_read_length": 8,
"quality_metrics": [],
"read_count": 53521837,
"s3_uri": "s3://igvf-files/2025/03/20/fce1a4eb-e82e-4da5-a2f6-c16bedb2703f/IGVFFI4312KGTK.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_ATAC_X043_G8_L008_P043_S34_L008_I1_001.fastq.gz",
"summary": "I1 reads from sequencing run 1",
"upload_status": "validated",
"uuid": "fce1a4eb-e82e-4da5-a2f6-c16bedb2703f"
}