IGVFFI3947RDEN

preview
validated
1{
2    "@context": "/terms/",
3    "@id": "/sequence-files/IGVFFI3947RDEN/",
4    "@type": [
5        "SequenceFile",
6        "File",
7        "Item"
8    ],
9    "accession": "IGVFFI3947RDEN",
10    "aliases": [
11        "igvf:corces_sequenceFile_ATAC_RP023_G2_P067_L004_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": "7f274cf829c15d1b6560a41cd2e64844",
23    "content_type": "reads",
24    "controlled_access": false,
25    "creation_timestamp": "2025-03-20T22:22:21.539869+00:00",
26    "externally_hosted": false,
27    "file_format": "fastq",
28    "file_set": {
29        "@id": "/measurement-sets/IGVFDS1426FMMN/",
30        "@type": [
31            "MeasurementSet",
32            "FileSet",
33            "Item"
34        ],
35        "accession": "IGVFDS1426FMMN",
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/IGVFSM7198XDQQ/",
44                "@type": [
45                    "MultiplexedSample",
46                    "Sample",
47                    "Item"
48                ],
49                "accession": "IGVFSM7198XDQQ",
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_0001874/",
93                        "status": "preview",
94                        "term_name": "putamen"
95                    },
96                    {
97                        "@id": "/sample-terms/UBERON_0002038/",
98                        "status": "preview",
99                        "term_name": "substantia nigra"
100                    },
101                    {
102                        "@id": "/sample-terms/UBERON_0002740/",
103                        "status": "preview",
104                        "term_name": "posterior cingulate gyrus"
105                    },
106                    {
107                        "@id": "/sample-terms/UBERON_0002771/",
108                        "status": "preview",
109                        "term_name": "middle temporal gyrus"
110                    }
111                ],
112                "status": "preview",
113                "summary": "multiplexed sample: Homo sapiens (female, 52 years) posterior cingulate gyrus tissue; Homo sapiens (male, 87 years) putamen tissue associated with Parkinson's disease, cerebral amyloid angiopathy; ... and 10 more samples",
114                "taxa": "Homo sapiens",
115                "treatments": []
116            }
117        ],
118        "status": "preview",
119        "summary": "single-nucleus ATAC-seq (10x multiome)"
120    },
121    "file_size": 1585313186,
122    "flowcell_id": "223HC3LT3",
123    "gene_list_for": [],
124    "href": "/sequence-files/IGVFFI3947RDEN/@@download/IGVFFI3947RDEN.fastq.gz",
125    "illumina_read_type": "R1",
126    "input_file_for": [],
127    "integrated_in": [],
128    "lab": {
129        "@id": "/labs/ryan-corces/",
130        "title": "Ryan Corces, Gladstone Institute UCSF"
131    },
132    "lane": 4,
133    "loci_list_for": [],
134    "maximum_read_length": 50,
135    "md5sum": "46fd83af4296792acf28a26502d8fa5c",
136    "mean_read_length": 50,
137    "minimum_read_length": 50,
138    "quality_metrics": [],
139    "read_count": 51106445,
140    "read_names": [
141        "Read 1"
142    ],
143    "s3_uri": "s3://igvf-files/2025/03/20/1754280e-87b4-4f3e-a0ad-1e4456e01d32/IGVFFI3947RDEN.fastq.gz",
144    "schema_version": "15",
145    "seqspecs": [],
146    "sequencing_kit": "NovaSeq X Series 10B Reagent Kit",
147    "sequencing_platform": {
148        "@id": "/platform-terms/EFO_0022840/",
149        "status": "released",
150        "term_name": "Illumina NovaSeq X"
151    },
152    "sequencing_run": 1,
153    "status": "preview",
154    "submitted_by": {
155        "@id": "/users/c13db3ca-f844-4a69-9056-5fbc4a100f36/",
156        "title": "Ryan Corces"
157    },
158    "submitted_file_name": "Multiome_ATAC_RP023_G2_L002_P067_S14_L004_R1_001.fastq.gz",
159    "summary": "R1 reads from sequencing run 1",
160    "upload_status": "validated",
161    "uuid": "1754280e-87b4-4f3e-a0ad-1e4456e01d32"
162}