{
"@context": "/terms/",
"@id": "/sequence-files/IGVFFI1153VROB/",
"@type": [
"SequenceFile",
"File",
"Item"
],
"accession": "IGVFFI1153VROB",
"aliases": [
"igvf:corces_sequenceFile_ATAC_RP016_G4_P063_L006_I1"
],
"assay_titles": [
"10x multiome"
],
"audit": {},
"award": {
"@id": "/awards/HG012076/",
"component": "mapping"
},
"checkfiles_version": "v20",
"content_md5sum": "cb9f42f17af0ae5e0fb10a7419dff680",
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-21T00:06:29.540108+00:00",
"externally_hosted": false,
"file_format": "fastq",
"file_set": {
"@id": "/measurement-sets/IGVFDS4019QZRA/",
"@type": [
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"FileSet",
"Item"
],
"accession": "IGVFDS4019QZRA",
"assay_term": {
"@id": "/assay-terms/OBI_0002762/",
"term_name": "single-nucleus ATAC-seq"
},
"file_set_type": "experimental data",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM6715EBSB/",
"@type": [
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"Sample",
"Item"
],
"accession": "IGVFSM6715EBSB",
"classifications": [
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"multiplexed sample"
],
"disease_terms": [
{
"@id": "/phenotype-terms/DOID_0080832/",
"@type": [
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"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": [
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],
"status": "in progress",
"summary": "cerebral amyloid angiopathy",
"term_name": "cerebral amyloid angiopathy"
}
],
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"sample_terms": [
{
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"status": "preview",
"term_name": "putamen"
},
{
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"status": "preview",
"term_name": "substantia nigra"
},
{
"@id": "/sample-terms/UBERON_0002740/",
"status": "preview",
"term_name": "posterior cingulate gyrus"
},
{
"@id": "/sample-terms/UBERON_0002771/",
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"term_name": "middle temporal gyrus"
}
],
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"summary": "multiplexed sample: Homo sapiens (female, 83 years) substantia nigra tissue associated with Parkinson's disease, cerebral amyloid angiopathy, mild cognitive impairment; Homo sapiens (male, 70 years) substantia nigra tissue associated with Parkinson's disease, mild cognitive impairment; ... and 10 more samples",
"taxa": "Homo sapiens",
"treatments": []
}
],
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"summary": "single-nucleus ATAC-seq (10x multiome)"
},
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"href": "/sequence-files/IGVFFI1153VROB/@@download/IGVFFI1153VROB.fastq.gz",
"illumina_read_type": "I1",
"input_file_for": [],
"integrated_in": [],
"lab": {
"@id": "/labs/ryan-corces/",
"title": "Ryan Corces, Gladstone Institute UCSF"
},
"lane": 6,
"loci_list_for": [],
"maximum_read_length": 8,
"md5sum": "df2f60f9ced80625b9c7005410a15b95",
"mean_read_length": 8,
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"schema_version": "15",
"seqspecs": [],
"sequencing_kit": "NovaSeq X Series 10B Reagent Kit",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
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"status": "preview",
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"title": "Ryan Corces"
},
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"summary": "I1 reads from sequencing run 1",
"upload_status": "validated",
"uuid": "f50a2fbb-e18f-45cc-89a2-45d4e86d899a"
}