IGVFFI6277MCHG

preview
validated
1{
2    "@context": "/terms/",
3    "@id": "/sequence-files/IGVFFI6277MCHG/",
4    "@type": [
5        "SequenceFile",
6        "File",
7        "Item"
8    ],
9    "accession": "IGVFFI6277MCHG",
10    "aliases": [
11        "igvf:corces_sequenceFile_ATAC_X031_G3_P031_L001_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": "be2ccbeae65162282d06facb2a868f79",
23    "content_type": "reads",
24    "controlled_access": false,
25    "creation_timestamp": "2025-03-20T02:00:09.649840+00:00",
26    "externally_hosted": false,
27    "file_format": "fastq",
28    "file_set": {
29        "@id": "/measurement-sets/IGVFDS1916OYNE/",
30        "@type": [
31            "MeasurementSet",
32            "FileSet",
33            "Item"
34        ],
35        "accession": "IGVFDS1916OYNE",
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/IGVFSM8532DSVV/",
44                "@type": [
45                    "MultiplexedSample",
46                    "Sample",
47                    "Item"
48                ],
49                "accession": "IGVFSM8532DSVV",
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 (female, 80 years) middle temporal gyrus tissue associated with Parkinson's disease; Homo sapiens (male, 80 years) posterior cingulate gyrus tissue associated with Parkinson's disease; ... and 10 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": 1165356021,
127    "flowcell_id": "HV7VHDSX5",
128    "gene_list_for": [],
129    "href": "/sequence-files/IGVFFI6277MCHG/@@download/IGVFFI6277MCHG.fastq.gz",
130    "illumina_read_type": "I1",
131    "input_file_for": [],
132    "integrated_in": [],
133    "lab": {
134        "@id": "/labs/ryan-corces/",
135        "title": "Ryan Corces, Gladstone Institute UCSF"
136    },
137    "lane": 1,
138    "loci_list_for": [],
139    "maximum_read_length": 8,
140    "md5sum": "46384faaf170d4aa7710ab3f9938cdec",
141    "mean_read_length": 8,
142    "minimum_read_length": 8,
143    "quality_metrics": [],
144    "read_count": 161873958,
145    "s3_uri": "s3://igvf-files/2025/03/20/72ebd404-c1c7-459f-a0b5-b3d33b9f66d1/IGVFFI6277MCHG.fastq.gz",
146    "schema_version": "15",
147    "seqspecs": [],
148    "sequencing_kit": "NovaSeq 6000 S4 Reagent Kit v1.5",
149    "sequencing_platform": {
150        "@id": "/platform-terms/EFO_0008637/",
151        "status": "released",
152        "term_name": "Illumina NovaSeq 6000"
153    },
154    "sequencing_run": 1,
155    "status": "preview",
156    "submitted_by": {
157        "@id": "/users/c13db3ca-f844-4a69-9056-5fbc4a100f36/",
158        "title": "Ryan Corces"
159    },
160    "submitted_file_name": "Multiome_ATAC_X031_G3_L003_P031_S9_L001_I1_001.fastq.gz",
161    "summary": "I1 reads from sequencing run 1",
162    "upload_status": "validated",
163    "uuid": "72ebd404-c1c7-459f-a0b5-b3d33b9f66d1"
164}