IGVFFI7045FILJ

preview
validated
1{
2    "@context": "/terms/",
3    "@id": "/sequence-files/IGVFFI7045FILJ/",
4    "@type": [
5        "SequenceFile",
6        "File",
7        "Item"
8    ],
9    "accession": "IGVFFI7045FILJ",
10    "aliases": [
11        "igvf:corces_sequenceFile_ATAC_RP030_G8_P077_L004_I1"
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": "c6efcf99290c9e0d4c7a8026054503be",
23    "content_type": "reads",
24    "controlled_access": false,
25    "creation_timestamp": "2025-03-21T03:16:49.148561+00:00",
26    "externally_hosted": false,
27    "file_format": "fastq",
28    "file_set": {
29        "@id": "/measurement-sets/IGVFDS8187GTTC/",
30        "@type": [
31            "MeasurementSet",
32            "FileSet",
33            "Item"
34        ],
35        "accession": "IGVFDS8187GTTC",
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/IGVFSM3517DKCV/",
44                "@type": [
45                    "MultiplexedSample",
46                    "Sample",
47                    "Item"
48                ],
49                "accession": "IGVFSM3517DKCV",
50                "classifications": [
51                    "tissue",
52                    "multiplexed sample"
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                "modifications": [],
79                "sample_terms": [
80                    {
81                        "@id": "/sample-terms/UBERON_0001874/",
82                        "status": "preview",
83                        "term_name": "putamen"
84                    },
85                    {
86                        "@id": "/sample-terms/UBERON_0002038/",
87                        "status": "preview",
88                        "term_name": "substantia nigra"
89                    },
90                    {
91                        "@id": "/sample-terms/UBERON_0002740/",
92                        "status": "preview",
93                        "term_name": "posterior cingulate gyrus"
94                    },
95                    {
96                        "@id": "/sample-terms/UBERON_0002771/",
97                        "status": "preview",
98                        "term_name": "middle temporal gyrus"
99                    }
100                ],
101                "status": "preview",
102                "summary": "multiplexed sample: Homo sapiens (female, 79 years) substantia nigra tissue associated with Parkinson's disease; Homo sapiens (male, 78 years) posterior cingulate gyrus tissue associated with Parkinson's disease; ... and 6 more samples",
103                "taxa": "Homo sapiens",
104                "treatments": []
105            }
106        ],
107        "status": "preview",
108        "summary": "single-nucleus ATAC-seq (10x multiome)"
109    },
110    "file_size": 555783682,
111    "flowcell_id": "22F3GTLT3",
112    "gene_list_for": [],
113    "href": "/sequence-files/IGVFFI7045FILJ/@@download/IGVFFI7045FILJ.fastq.gz",
114    "illumina_read_type": "I1",
115    "input_file_for": [],
116    "integrated_in": [],
117    "lab": {
118        "@id": "/labs/ryan-corces/",
119        "title": "Ryan Corces, Gladstone Institute UCSF"
120    },
121    "lane": 4,
122    "loci_list_for": [],
123    "maximum_read_length": 8,
124    "md5sum": "b4f890c2969f6ca5829e10e475de41b1",
125    "mean_read_length": 8,
126    "minimum_read_length": 8,
127    "quality_metrics": [],
128    "read_count": 76996779,
129    "s3_uri": "s3://igvf-files/2025/03/21/18456101-9842-4885-811b-318c4f671c71/IGVFFI7045FILJ.fastq.gz",
130    "schema_version": "15",
131    "seqspecs": [],
132    "sequencing_kit": "NovaSeq X Series 10B Reagent Kit",
133    "sequencing_platform": {
134        "@id": "/platform-terms/EFO_0022840/",
135        "status": "released",
136        "term_name": "Illumina NovaSeq X"
137    },
138    "sequencing_run": 1,
139    "status": "preview",
140    "submitted_by": {
141        "@id": "/users/c13db3ca-f844-4a69-9056-5fbc4a100f36/",
142        "title": "Ryan Corces"
143    },
144    "submitted_file_name": "Multiome_ATAC_RP030_G8_L008_P077_S42_L004_I1_001.fastq.gz",
145    "summary": "I1 reads from sequencing run 1",
146    "upload_status": "validated",
147    "uuid": "18456101-9842-4885-811b-318c4f671c71"
148}