IGVFFI2957JCDB

preview
validated
1{
2    "@context": "/terms/",
3    "@id": "/sequence-files/IGVFFI2957JCDB/",
4    "@type": [
5        "SequenceFile",
6        "File",
7        "Item"
8    ],
9    "accession": "IGVFFI2957JCDB",
10    "aliases": [
11        "igvf:corces_sequenceFile_ATAC_RP033_G1_P079_L006_R3"
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": "03763099481efad5fea2641f87c278ee",
23    "content_type": "reads",
24    "controlled_access": false,
25    "creation_timestamp": "2025-03-21T03:28:44.968610+00:00",
26    "externally_hosted": false,
27    "file_format": "fastq",
28    "file_set": {
29        "@id": "/measurement-sets/IGVFDS2443ZQHK/",
30        "@type": [
31            "MeasurementSet",
32            "FileSet",
33            "Item"
34        ],
35        "accession": "IGVFDS2443ZQHK",
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/IGVFSM6670KYMT/",
44                "@type": [
45                    "MultiplexedSample",
46                    "Sample",
47                    "Item"
48                ],
49                "accession": "IGVFSM6670KYMT",
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                "status": "preview",
97                "summary": "multiplexed sample: Homo sapiens (male, 70 years) substantia nigra tissue associated with Parkinson's disease; Homo sapiens (female, 70 years) substantia nigra tissue associated with Parkinson's disease; ... and 6 more samples",
98                "taxa": "Homo sapiens",
99                "treatments": []
100            }
101        ],
102        "status": "preview",
103        "summary": "single-nucleus ATAC-seq (10x multiome)"
104    },
105    "file_size": 9336045676,
106    "flowcell_id": "19U7CA4LE",
107    "gene_list_for": [],
108    "href": "/sequence-files/IGVFFI2957JCDB/@@download/IGVFFI2957JCDB.fastq.gz",
109    "illumina_read_type": "R3",
110    "input_file_for": [],
111    "integrated_in": [],
112    "lab": {
113        "@id": "/labs/ryan-corces/",
114        "title": "Ryan Corces, Gladstone Institute UCSF"
115    },
116    "lane": 6,
117    "loci_list_for": [],
118    "maximum_read_length": 150,
119    "md5sum": "79e03ccdb7c2319df31cc7ec9f6c49b5",
120    "mean_read_length": 150,
121    "minimum_read_length": 150,
122    "quality_metrics": [],
123    "read_count": 136458531,
124    "read_names": [
125        "Read 2"
126    ],
127    "s3_uri": "s3://igvf-files/2025/03/21/53e3e776-9a3a-41a0-8d8e-b735faf9e514/IGVFFI2957JCDB.fastq.gz",
128    "schema_version": "15",
129    "seqspecs": [],
130    "sequencing_kit": "NovaSeq X Series 10B Reagent Kit",
131    "sequencing_platform": {
132        "@id": "/platform-terms/EFO_0022840/",
133        "status": "released",
134        "term_name": "Illumina NovaSeq X"
135    },
136    "sequencing_run": 1,
137    "status": "preview",
138    "submitted_by": {
139        "@id": "/users/c13db3ca-f844-4a69-9056-5fbc4a100f36/",
140        "title": "Ryan Corces"
141    },
142    "submitted_file_name": "Multiome_ATAC_RP033_G1_L001_P079_S25_L006_R3_001.fastq.gz",
143    "summary": "R3 reads from sequencing run 1",
144    "upload_status": "validated",
145    "uuid": "53e3e776-9a3a-41a0-8d8e-b735faf9e514"
146}