IGVFFI8031MMGX

preview
validated
1{
2    "@context": "/terms/",
3    "@id": "/sequence-files/IGVFFI8031MMGX/",
4    "@type": [
5        "SequenceFile",
6        "File",
7        "Item"
8    ],
9    "accession": "IGVFFI8031MMGX",
10    "aliases": [
11        "igvf:corces_sequenceFile_ATAC_X004_G1_P003_L004_I1"
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": "3e9fa969b6c10fe8746c789da5832fe8",
23    "content_type": "reads",
24    "controlled_access": false,
25    "creation_timestamp": "2025-03-20T00:39:34.894559+00:00",
26    "externally_hosted": false,
27    "file_format": "fastq",
28    "file_set": {
29        "@id": "/measurement-sets/IGVFDS9661AXWU/",
30        "@type": [
31            "MeasurementSet",
32            "FileSet",
33            "Item"
34        ],
35        "accession": "IGVFDS9661AXWU",
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": "/tissues/IGVFSM7491SDBL/",
44                "@type": [
45                    "Tissue",
46                    "Biosample",
47                    "Sample",
48                    "Item"
49                ],
50                "accession": "IGVFSM7491SDBL",
51                "classifications": [
52                    "tissue"
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                        "@id": "/phenotype-terms/DOID_0080832/",
79                        "@type": [
80                            "PhenotypeTerm",
81                            "OntologyTerm",
82                            "Item"
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84                        "status": "in progress",
85                        "summary": "mild cognitive impairment",
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87                    }
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89                "sample_terms": [
90                    {
91                        "@id": "/sample-terms/UBERON_0002740/",
92                        "status": "preview",
93                        "term_name": "posterior cingulate gyrus"
94                    }
95                ],
96                "status": "preview",
97                "summary": "Homo sapiens (male, 80 years) posterior cingulate gyrus tissue associated with Parkinson's disease, cerebral amyloid angiopathy, mild cognitive impairment",
98                "taxa": "Homo sapiens"
99            }
100        ],
101        "status": "preview",
102        "summary": "single-nucleus ATAC-seq (10x multiome)"
103    },
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105    "flowcell_id": "H5TH7DSX5",
106    "gene_list_for": [],
107    "href": "/sequence-files/IGVFFI8031MMGX/@@download/IGVFFI8031MMGX.fastq.gz",
108    "illumina_read_type": "I1",
109    "input_file_for": [],
110    "integrated_in": [],
111    "lab": {
112        "@id": "/labs/ryan-corces/",
113        "title": "Ryan Corces, Gladstone Institute UCSF"
114    },
115    "lane": 4,
116    "loci_list_for": [],
117    "maximum_read_length": 8,
118    "md5sum": "feffbc010d07b7841224dcb7f5671eff",
119    "mean_read_length": 8,
120    "minimum_read_length": 8,
121    "quality_metrics": [],
122    "read_count": 195993543,
123    "s3_uri": "s3://igvf-files/2025/03/20/ae3a09b9-c713-432c-a18d-8911a82a3709/IGVFFI8031MMGX.fastq.gz",
124    "schema_version": "15",
125    "seqspecs": [],
126    "sequencing_kit": "NovaSeq 6000 S4 Reagent Kit v1.5",
127    "sequencing_platform": {
128        "@id": "/platform-terms/EFO_0008637/",
129        "status": "released",
130        "term_name": "Illumina NovaSeq 6000"
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132    "sequencing_run": 1,
133    "status": "preview",
134    "submitted_by": {
135        "@id": "/users/c13db3ca-f844-4a69-9056-5fbc4a100f36/",
136        "title": "Ryan Corces"
137    },
138    "submitted_file_name": "Multiome_ATAC_PD_16-14_CING_X004_S01_L001_B1_T1_P003_S15_L004_I1_001.fastq.gz",
139    "summary": "I1 reads from sequencing run 1",
140    "upload_status": "validated",
141    "uuid": "ae3a09b9-c713-432c-a18d-8911a82a3709"
142}