IGVFFI5491CDBF

preview
validated
1{
2    "@context": "/terms/",
3    "@id": "/sequence-files/IGVFFI5491CDBF/",
4    "@type": [
5        "SequenceFile",
6        "File",
7        "Item"
8    ],
9    "accession": "IGVFFI5491CDBF",
10    "aliases": [
11        "igvf:corces_sequenceFile_ATAC_X036_G6_P037_L001_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": "2523e66e3c71700a6527074939f0aaf5",
23    "content_type": "reads",
24    "controlled_access": false,
25    "creation_timestamp": "2025-03-20T02:55:51.564695+00:00",
26    "externally_hosted": false,
27    "file_format": "fastq",
28    "file_set": {
29        "@id": "/measurement-sets/IGVFDS0749RBHU/",
30        "@type": [
31            "MeasurementSet",
32            "FileSet",
33            "Item"
34        ],
35        "accession": "IGVFDS0749RBHU",
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/IGVFSM0887BJSQ/",
44                "@type": [
45                    "MultiplexedSample",
46                    "Sample",
47                    "Item"
48                ],
49                "accession": "IGVFSM0887BJSQ",
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_0002129/",
92                        "status": "preview",
93                        "term_name": "cerebellar cortex"
94                    },
95                    {
96                        "@id": "/sample-terms/UBERON_0002740/",
97                        "status": "preview",
98                        "term_name": "posterior cingulate gyrus"
99                    },
100                    {
101                        "@id": "/sample-terms/UBERON_0002771/",
102                        "status": "preview",
103                        "term_name": "middle temporal gyrus"
104                    }
105                ],
106                "status": "preview",
107                "summary": "multiplexed sample: Homo sapiens (female, 83 years) putamen tissue associated with Parkinson's disease, cerebral amyloid angiopathy; Homo sapiens (male, 81 years) posterior cingulate gyrus tissue associated with Parkinson's disease, cerebral amyloid angiopathy; ... and 10 more samples",
108                "taxa": "Homo sapiens",
109                "treatments": []
110            }
111        ],
112        "status": "preview",
113        "summary": "single-nucleus ATAC-seq (10x multiome)"
114    },
115    "file_size": 4302428811,
116    "flowcell_id": "H5VM5DSX7",
117    "gene_list_for": [],
118    "href": "/sequence-files/IGVFFI5491CDBF/@@download/IGVFFI5491CDBF.fastq.gz",
119    "illumina_read_type": "R2",
120    "input_file_for": [],
121    "integrated_in": [],
122    "lab": {
123        "@id": "/labs/ryan-corces/",
124        "title": "Ryan Corces, Gladstone Institute UCSF"
125    },
126    "lane": 1,
127    "loci_list_for": [],
128    "maximum_read_length": 24,
129    "md5sum": "bffc8334e5e54efbba8b2ce218ba34bb",
130    "mean_read_length": 24,
131    "minimum_read_length": 24,
132    "quality_metrics": [],
133    "read_count": 244517080,
134    "read_names": [
135        "Barcode index"
136    ],
137    "s3_uri": "s3://igvf-files/2025/03/20/b8f732d7-d5fa-40a9-a150-01cdaab5e296/IGVFFI5491CDBF.fastq.gz",
138    "schema_version": "15",
139    "seqspecs": [],
140    "sequencing_kit": "NovaSeq 6000 S4 Reagent Kit v1.5",
141    "sequencing_platform": {
142        "@id": "/platform-terms/EFO_0008637/",
143        "status": "released",
144        "term_name": "Illumina NovaSeq 6000"
145    },
146    "sequencing_run": 1,
147    "status": "preview",
148    "submitted_by": {
149        "@id": "/users/c13db3ca-f844-4a69-9056-5fbc4a100f36/",
150        "title": "Ryan Corces"
151    },
152    "submitted_file_name": "Multiome_ATAC_X036_G6_L006_P037_S4_L001_R2_001.fastq.gz",
153    "summary": "R2 reads from sequencing run 1",
154    "upload_status": "validated",
155    "uuid": "b8f732d7-d5fa-40a9-a150-01cdaab5e296"
156}