IGVFFI7970OVSK

1{
2    "@context": "/terms/",
3    "@id": "/sequence-files/IGVFFI7970OVSK/",
4    "@type": [
5        "SequenceFile",
6        "File",
7        "Item"
8    ],
9    "accession": "IGVFFI7970OVSK",
10    "aliases": [
11        "igvf:corces_sequenceFile_ATAC_X048_G2_P049_L001_R1"
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": "bc0b879cf2c6a5f41fc1c5975ea6f07b",
23    "content_type": "reads",
24    "controlled_access": false,
25    "creation_timestamp": "2025-03-20T13:47:00.799068+00:00",
26    "externally_hosted": false,
27    "file_format": "fastq",
28    "file_set": {
29        "@id": "/measurement-sets/IGVFDS3125EBYU/",
30        "@type": [
31            "MeasurementSet",
32            "FileSet",
33            "Item"
34        ],
35        "accession": "IGVFDS3125EBYU",
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": "/multiplexed-samples/IGVFSM4666GHWA/",
44                "@type": [
45                    "MultiplexedSample",
46                    "Sample",
47                    "Item"
48                ],
49                "accession": "IGVFSM4666GHWA",
50                "classifications": [
51                    "tissue",
52                    "multiplexed sample"
53                ],
54                "disease_terms": [
55                    {
56                        "@id": "/phenotype-terms/DOID_0080832/",
57                        "@type": [
58                            "PhenotypeTerm",
59                            "OntologyTerm",
60                            "Item"
61                        ],
62                        "status": "in progress",
63                        "summary": "mild cognitive impairment",
64                        "term_name": "mild cognitive impairment"
65                    },
66                    {
67                        "@id": "/phenotype-terms/DOID_14330/",
68                        "@type": [
69                            "PhenotypeTerm",
70                            "OntologyTerm",
71                            "Item"
72                        ],
73                        "status": "in progress",
74                        "summary": "Parkinson's disease",
75                        "term_name": "Parkinson's disease"
76                    },
77                    {
78                        "@id": "/phenotype-terms/DOID_9246/",
79                        "@type": [
80                            "PhenotypeTerm",
81                            "OntologyTerm",
82                            "Item"
83                        ],
84                        "status": "in progress",
85                        "summary": "cerebral amyloid angiopathy",
86                        "term_name": "cerebral amyloid angiopathy"
87                    }
88                ],
89                "modifications": [],
90                "sample_terms": [
91                    {
92                        "@id": "/sample-terms/UBERON_0002038/",
93                        "status": "preview",
94                        "term_name": "substantia nigra"
95                    },
96                    {
97                        "@id": "/sample-terms/UBERON_0002740/",
98                        "status": "preview",
99                        "term_name": "posterior cingulate gyrus"
100                    }
101                ],
102                "status": "preview",
103                "summary": "multiplexed sample: Homo sapiens (male, 93 years) substantia nigra tissue; Homo sapiens (male, 75 years) substantia nigra tissue associated with Parkinson's disease, mild cognitive impairment; ... and 10 more samples",
104                "taxa": "Homo sapiens",
105                "treatments": []
106            }
107        ],
108        "status": "preview",
109        "summary": "single-nucleus ATAC-seq (10x multiome)"
110    },
111    "file_size": 6966228715,
112    "flowcell_id": "H7VW3DSX7",
113    "gene_list_for": [],
114    "href": "/sequence-files/IGVFFI7970OVSK/@@download/IGVFFI7970OVSK.fastq.gz",
115    "illumina_read_type": "R1",
116    "input_file_for": [],
117    "integrated_in": [],
118    "lab": {
119        "@id": "/labs/ryan-corces/",
120        "title": "Ryan Corces, Gladstone Institute UCSF"
121    },
122    "lane": 1,
123    "loci_list_for": [],
124    "maximum_read_length": 50,
125    "md5sum": "7ed0c0ebc9f24c6d665cbb41d3729f7d",
126    "mean_read_length": 50,
127    "minimum_read_length": 50,
128    "quality_metrics": [],
129    "read_count": 214427601,
130    "read_names": [
131        "Read 1"
132    ],
133    "s3_uri": "s3://igvf-files/2025/03/20/8e3dd684-f74b-4c0b-89ac-f47df901c241/IGVFFI7970OVSK.fastq.gz",
134    "schema_version": "15",
135    "seqspecs": [],
136    "sequencing_kit": "NovaSeq 6000 S4 Reagent Kit v1.5",
137    "sequencing_platform": {
138        "@id": "/platform-terms/EFO_0008637/",
139        "status": "released",
140        "term_name": "Illumina NovaSeq 6000"
141    },
142    "sequencing_run": 1,
143    "status": "preview",
144    "submitted_by": {
145        "@id": "/users/c13db3ca-f844-4a69-9056-5fbc4a100f36/",
146        "title": "Ryan Corces"
147    },
148    "submitted_file_name": "Multiome_ATAC_X048_G2_L002_P049_S6_L001_R1_001.fastq.gz",
149    "summary": "R1 reads from sequencing run 1",
150    "upload_status": "validated",
151    "uuid": "8e3dd684-f74b-4c0b-89ac-f47df901c241"
152}