IGVFFI0939CCNQ

preview
validated
1{
2    "@context": "/terms/",
3    "@id": "/sequence-files/IGVFFI0939CCNQ/",
4    "@type": [
5        "SequenceFile",
6        "File",
7        "Item"
8    ],
9    "accession": "IGVFFI0939CCNQ",
10    "aliases": [
11        "igvf:corces_sequenceFile_ATAC_RP029_G8_P077_L005_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": "176a8705f38db75ae6eece04022f003a",
23    "content_type": "reads",
24    "controlled_access": false,
25    "creation_timestamp": "2025-03-21T03:09:32.444549+00:00",
26    "externally_hosted": false,
27    "file_format": "fastq",
28    "file_set": {
29        "@id": "/measurement-sets/IGVFDS0688NEEC/",
30        "@type": [
31            "MeasurementSet",
32            "FileSet",
33            "Item"
34        ],
35        "accession": "IGVFDS0688NEEC",
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/IGVFSM9143IXZW/",
44                "@type": [
45                    "MultiplexedSample",
46                    "Sample",
47                    "Item"
48                ],
49                "accession": "IGVFSM9143IXZW",
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                        "@id": "/phenotype-terms/MONDO_0004975/",
90                        "@type": [
91                            "PhenotypeTerm",
92                            "OntologyTerm",
93                            "Item"
94                        ],
95                        "status": "released",
96                        "summary": "Alzheimer disease",
97                        "term_name": "Alzheimer disease"
98                    }
99                ],
100                "modifications": [],
101                "sample_terms": [
102                    {
103                        "@id": "/sample-terms/UBERON_0001874/",
104                        "status": "preview",
105                        "term_name": "putamen"
106                    },
107                    {
108                        "@id": "/sample-terms/UBERON_0002038/",
109                        "status": "preview",
110                        "term_name": "substantia nigra"
111                    },
112                    {
113                        "@id": "/sample-terms/UBERON_0002740/",
114                        "status": "preview",
115                        "term_name": "posterior cingulate gyrus"
116                    }
117                ],
118                "status": "preview",
119                "summary": "multiplexed sample: Homo sapiens (male, 74 years) putamen tissue associated with Parkinson's disease; Homo sapiens (male, 89 years) posterior cingulate gyrus tissue; ... and 6 more samples",
120                "taxa": "Homo sapiens",
121                "treatments": []
122            }
123        ],
124        "status": "preview",
125        "summary": "single-nucleus ATAC-seq (10x multiome)"
126    },
127    "file_size": 2179330632,
128    "flowcell_id": "22F3GTLT3",
129    "gene_list_for": [],
130    "href": "/sequence-files/IGVFFI0939CCNQ/@@download/IGVFFI0939CCNQ.fastq.gz",
131    "illumina_read_type": "R3",
132    "input_file_for": [],
133    "integrated_in": [],
134    "lab": {
135        "@id": "/labs/ryan-corces/",
136        "title": "Ryan Corces, Gladstone Institute UCSF"
137    },
138    "lane": 5,
139    "loci_list_for": [],
140    "maximum_read_length": 50,
141    "md5sum": "826a604853c862f52686d1a759399ad9",
142    "mean_read_length": 50,
143    "minimum_read_length": 50,
144    "quality_metrics": [],
145    "read_count": 73658048,
146    "read_names": [
147        "Read 2"
148    ],
149    "s3_uri": "s3://igvf-files/2025/03/21/0f5f3d2a-54f0-4227-bdab-d6d592a9e81a/IGVFFI0939CCNQ.fastq.gz",
150    "schema_version": "15",
151    "seqspecs": [],
152    "sequencing_kit": "NovaSeq X Series 10B Reagent Kit",
153    "sequencing_platform": {
154        "@id": "/platform-terms/EFO_0022840/",
155        "status": "released",
156        "term_name": "Illumina NovaSeq X"
157    },
158    "sequencing_run": 1,
159    "status": "preview",
160    "submitted_by": {
161        "@id": "/users/c13db3ca-f844-4a69-9056-5fbc4a100f36/",
162        "title": "Ryan Corces"
163    },
164    "submitted_file_name": "Multiome_ATAC_RP029_G8_L008_P077_S34_L005_R3_001.fastq.gz",
165    "summary": "R3 reads from sequencing run 1",
166    "upload_status": "validated",
167    "uuid": "0f5f3d2a-54f0-4227-bdab-d6d592a9e81a"
168}