IGVFFI2106SEWY

released
validated
1{
2    "@context": "/terms/",
3    "@id": "/sequence-files/IGVFFI2106SEWY/",
4    "@type": [
5        "SequenceFile",
6        "File",
7        "Item"
8    ],
9    "accession": "IGVFFI2106SEWY",
10    "aliases": [
11        "ansuman-satpathy:igvf_exp13_atac_10x2_NGS2_r3"
12    ],
13    "assay_titles": [
14        "10x multiome with MULTI-seq"
15    ],
16    "audit": {},
17    "award": {
18        "@id": "/awards/HG012076/",
19        "component": "mapping"
20    },
21    "content_md5sum": "bcb57de55c2f417f9cac4fc050d5d9bc",
22    "content_type": "reads",
23    "controlled_access": true,
24    "creation_timestamp": "2024-07-23T21:30:35.329520+00:00",
25    "externally_hosted": false,
26    "file_format": "fastq",
27    "file_set": {
28        "@id": "/measurement-sets/IGVFDS4493CHDR/",
29        "@type": [
30            "MeasurementSet",
31            "FileSet",
32            "Item"
33        ],
34        "accession": "IGVFDS4493CHDR",
35        "assay_term": {
36            "@id": "/assay-terms/OBI_0002762/",
37            "term_name": "single-nucleus ATAC-seq"
38        },
39        "file_set_type": "experimental data",
40        "samples": [
41            {
42                "@id": "/multiplexed-samples/IGVFSM7106DAZZ/",
43                "@type": [
44                    "MultiplexedSample",
45                    "Sample",
46                    "Item"
47                ],
48                "accession": "IGVFSM7106DAZZ",
49                "classifications": [
50                    "tissue",
51                    "multiplexed sample"
52                ],
53                "disease_terms": [
54                    {
55                        "@id": "/phenotype-terms/MONDO_0005010/",
56                        "@type": [
57                            "PhenotypeTerm",
58                            "OntologyTerm",
59                            "Item"
60                        ],
61                        "status": "released",
62                        "summary": "coronary artery disorder",
63                        "term_name": "coronary artery disorder"
64                    }
65                ],
66                "modifications": [],
67                "sample_terms": [
68                    {
69                        "@id": "/sample-terms/UBERON_0001626/",
70                        "status": "released",
71                        "term_name": "left coronary artery"
72                    }
73                ],
74                "status": "released",
75                "summary": "multiplexed sample: Homo sapiens (female, 48 years) left coronary artery tissue associated with coronary artery disorder; Homo sapiens (female, 73 years) left coronary artery tissue associated with coronary artery disorder; ... and 2 more samples",
76                "taxa": "Homo sapiens",
77                "treatments": []
78            }
79        ],
80        "status": "released",
81        "summary": "single-nucleus ATAC-seq (10x multiome with MULTI-seq)"
82    },
83    "file_size": 9212857529,
84    "flowcell_id": "22JL3GLT3",
85    "gene_list_for": [],
86    "href": "/sequence-files/IGVFFI2106SEWY/@@download/IGVFFI2106SEWY.fastq.gz",
87    "illumina_read_type": "R3",
88    "input_file_for": [
89        "/tabular-files/IGVFFI9484EEZH/"
90    ],
91    "integrated_in": [],
92    "lab": {
93        "@id": "/labs/ansuman-satpathy/",
94        "title": "Ansuman Satpathy, Stanford"
95    },
96    "lane": 2,
97    "loci_list_for": [],
98    "maximum_read_length": 50,
99    "md5sum": "d3db4f3b75f0add41af52c1ee083a1b3",
100    "mean_read_length": 50,
101    "minimum_read_length": 50,
102    "quality_metrics": [],
103    "read_count": 310628034,
104    "read_names": [
105        "Read 2"
106    ],
107    "release_timestamp": "2025-03-22T00:40:31.193771+00:00",
108    "s3_uri": "s3://igvf-restricted-files/2024/07/23/3a95601c-3a67-449d-ba9e-b0ab139aeb60/IGVFFI2106SEWY.fastq.gz",
109    "schema_version": "15",
110    "seqspecs": [
111        "/configuration-files/IGVFFI6725RIWP/"
112    ],
113    "sequencing_kit": "NovaSeq X Series 10B Reagent Kit",
114    "sequencing_platform": {
115        "@id": "/platform-terms/EFO_0022840/",
116        "status": "released",
117        "term_name": "Illumina NovaSeq X"
118    },
119    "sequencing_run": 1,
120    "status": "released",
121    "submitted_by": {
122        "@id": "/users/353655bc-31a1-4cd9-bac3-c7d34faf722f/",
123        "title": "Christopher Mcginnis"
124    },
125    "submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/tq_fastqs/ATAC/igvf13_s2_atac_S2_L002_R3_001.fastq.gz",
126    "summary": "R3 reads from sequencing run 1",
127    "upload_status": "validated",
128    "uuid": "3a95601c-3a67-449d-ba9e-b0ab139aeb60"
129}