IGVFFI2390EJVQ

preview
validated
1{
2    "@context": "/terms/",
3    "@id": "/sequence-files/IGVFFI2390EJVQ/",
4    "@type": [
5        "SequenceFile",
6        "File",
7        "Item"
8    ],
9    "accession": "IGVFFI2390EJVQ",
10    "aliases": [
11        "igvf:corces_sequenceFile_ATAC_RP010_G8_P059_L008_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": "1f1c55fdbed877b63fa0aa74f473e213",
23    "content_type": "reads",
24    "controlled_access": false,
25    "creation_timestamp": "2025-03-20T17:50:52.577262+00:00",
26    "externally_hosted": false,
27    "file_format": "fastq",
28    "file_set": {
29        "@id": "/measurement-sets/IGVFDS6707ABHS/",
30        "@type": [
31            "MeasurementSet",
32            "FileSet",
33            "Item"
34        ],
35        "accession": "IGVFDS6707ABHS",
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/IGVFSM6509YCTF/",
44                "@type": [
45                    "MultiplexedSample",
46                    "Sample",
47                    "Item"
48                ],
49                "accession": "IGVFSM6509YCTF",
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_0002129/",
103                        "status": "preview",
104                        "term_name": "cerebellar cortex"
105                    },
106                    {
107                        "@id": "/sample-terms/UBERON_0002740/",
108                        "status": "preview",
109                        "term_name": "posterior cingulate gyrus"
110                    },
111                    {
112                        "@id": "/sample-terms/UBERON_0002771/",
113                        "status": "preview",
114                        "term_name": "middle temporal gyrus"
115                    }
116                ],
117                "status": "preview",
118                "summary": "multiplexed sample: Homo sapiens (male, 70 years) substantia nigra tissue associated with Parkinson's disease; Homo sapiens (male, 78 years) putamen tissue associated with Parkinson's disease, mild cognitive impairment; ... and 12 more samples",
119                "taxa": "Homo sapiens",
120                "treatments": []
121            }
122        ],
123        "status": "preview",
124        "summary": "single-nucleus ATAC-seq (10x multiome)"
125    },
126    "file_size": 1609846977,
127    "flowcell_id": "225CCCLT3",
128    "gene_list_for": [],
129    "href": "/sequence-files/IGVFFI2390EJVQ/@@download/IGVFFI2390EJVQ.fastq.gz",
130    "illumina_read_type": "R1",
131    "input_file_for": [],
132    "integrated_in": [],
133    "lab": {
134        "@id": "/labs/ryan-corces/",
135        "title": "Ryan Corces, Gladstone Institute UCSF"
136    },
137    "lane": 8,
138    "loci_list_for": [],
139    "maximum_read_length": 50,
140    "md5sum": "8b1f78faaf2129166347b206b7ada24a",
141    "mean_read_length": 50,
142    "minimum_read_length": 50,
143    "quality_metrics": [],
144    "read_count": 54298950,
145    "read_names": [
146        "Read 1"
147    ],
148    "s3_uri": "s3://igvf-files/2025/03/20/350c4950-a941-423e-b970-e822cf757fae/IGVFFI2390EJVQ.fastq.gz",
149    "schema_version": "15",
150    "seqspecs": [],
151    "sequencing_kit": "NovaSeq X Series 10B Reagent Kit",
152    "sequencing_platform": {
153        "@id": "/platform-terms/EFO_0022840/",
154        "status": "released",
155        "term_name": "Illumina NovaSeq X"
156    },
157    "sequencing_run": 1,
158    "status": "preview",
159    "submitted_by": {
160        "@id": "/users/c13db3ca-f844-4a69-9056-5fbc4a100f36/",
161        "title": "Ryan Corces"
162    },
163    "submitted_file_name": "Multiome_ATAC_RP010_G8_L008_P059_S72_L008_R1_001.fastq.gz",
164    "summary": "R1 reads from sequencing run 1",
165    "upload_status": "validated",
166    "uuid": "350c4950-a941-423e-b970-e822cf757fae"
167}