IGVFFI4375DYIS

preview
validated
1{
2    "@context": "/terms/",
3    "@id": "/sequence-files/IGVFFI4375DYIS/",
4    "@type": [
5        "SequenceFile",
6        "File",
7        "Item"
8    ],
9    "accession": "IGVFFI4375DYIS",
10    "aliases": [
11        "igvf:corces_sequenceFile_ATAC_X006_G3_P003_L004_R2"
12    ],
13    "assay_titles": [
14        "10x multiome"
15    ],
16    "audit": {},
17    "award": {
18        "@id": "/awards/HG012076/",
19        "component": "mapping"
20    },
21    "checkfiles_version": "v20",
22    "content_md5sum": "c0c39d17cf1ce00e7386bf8bc4e6f216",
23    "content_type": "reads",
24    "controlled_access": false,
25    "creation_timestamp": "2025-03-20T00:39:32.161139+00:00",
26    "externally_hosted": false,
27    "file_format": "fastq",
28    "file_set": {
29        "@id": "/measurement-sets/IGVFDS1795MXXR/",
30        "@type": [
31            "MeasurementSet",
32            "FileSet",
33            "Item"
34        ],
35        "accession": "IGVFDS1795MXXR",
36        "assay_term": {
37            "@id": "/assay-terms/OBI_0002762/",
38            "term_name": "single-nucleus ATAC-seq"
39        },
40        "file_set_type": "experimental data",
41        "samples": [
42            {
43                "@id": "/tissues/IGVFSM9093ETCZ/",
44                "@type": [
45                    "Tissue",
46                    "Biosample",
47                    "Sample",
48                    "Item"
49                ],
50                "accession": "IGVFSM9093ETCZ",
51                "classifications": [
52                    "tissue"
53                ],
54                "disease_terms": [
55                    {
56                        "@id": "/phenotype-terms/DOID_14330/",
57                        "@type": [
58                            "PhenotypeTerm",
59                            "OntologyTerm",
60                            "Item"
61                        ],
62                        "status": "in progress",
63                        "summary": "Parkinson's disease",
64                        "term_name": "Parkinson's disease"
65                    },
66                    {
67                        "@id": "/phenotype-terms/DOID_9246/",
68                        "@type": [
69                            "PhenotypeTerm",
70                            "OntologyTerm",
71                            "Item"
72                        ],
73                        "status": "in progress",
74                        "summary": "cerebral amyloid angiopathy",
75                        "term_name": "cerebral amyloid angiopathy"
76                    },
77                    {
78                        "@id": "/phenotype-terms/DOID_0080832/",
79                        "@type": [
80                            "PhenotypeTerm",
81                            "OntologyTerm",
82                            "Item"
83                        ],
84                        "status": "in progress",
85                        "summary": "mild cognitive impairment",
86                        "term_name": "mild cognitive impairment"
87                    }
88                ],
89                "sample_terms": [
90                    {
91                        "@id": "/sample-terms/UBERON_0002038/",
92                        "status": "preview",
93                        "term_name": "substantia nigra"
94                    }
95                ],
96                "status": "preview",
97                "summary": "Homo sapiens (male, 73 years) substantia nigra tissue associated with Parkinson's disease, cerebral amyloid angiopathy, mild cognitive impairment",
98                "taxa": "Homo sapiens"
99            }
100        ],
101        "status": "preview",
102        "summary": "single-nucleus ATAC-seq (10x multiome)"
103    },
104    "file_size": 3084094450,
105    "flowcell_id": "H5TH7DSX5",
106    "gene_list_for": [],
107    "href": "/sequence-files/IGVFFI4375DYIS/@@download/IGVFFI4375DYIS.fastq.gz",
108    "illumina_read_type": "R2",
109    "input_file_for": [],
110    "integrated_in": [],
111    "lab": {
112        "@id": "/labs/ryan-corces/",
113        "title": "Ryan Corces, Gladstone Institute UCSF"
114    },
115    "lane": 4,
116    "loci_list_for": [],
117    "maximum_read_length": 24,
118    "md5sum": "fe221d577044f0334671911c54a01f55",
119    "mean_read_length": 24,
120    "minimum_read_length": 24,
121    "quality_metrics": [],
122    "read_count": 178487232,
123    "read_names": [
124        "Barcode index"
125    ],
126    "s3_uri": "s3://igvf-files/2025/03/20/44277c47-084c-4711-96a0-a0b69aefd0a2/IGVFFI4375DYIS.fastq.gz",
127    "schema_version": "15",
128    "seqspecs": [],
129    "sequencing_kit": "NovaSeq 6000 S4 Reagent Kit v1.5",
130    "sequencing_platform": {
131        "@id": "/platform-terms/EFO_0008637/",
132        "status": "released",
133        "term_name": "Illumina NovaSeq 6000"
134    },
135    "sequencing_run": 1,
136    "status": "preview",
137    "submitted_by": {
138        "@id": "/users/c13db3ca-f844-4a69-9056-5fbc4a100f36/",
139        "title": "Ryan Corces"
140    },
141    "submitted_file_name": "Multiome_ATAC_PD_15-70_SN_X006_S03_L003_B1_T1_P003_S29_L004_R2_001.fastq.gz",
142    "summary": "R2 reads from sequencing run 1",
143    "upload_status": "validated",
144    "uuid": "44277c47-084c-4711-96a0-a0b69aefd0a2"
145}