IGVFFI0305RRIM

released
validated
1{
2    "@context": "/terms/",
3    "@id": "/sequence-files/IGVFFI0305RRIM/",
4    "@type": [
5        "SequenceFile",
6        "File",
7        "Item"
8    ],
9    "accession": "IGVFFI0305RRIM",
10    "aliases": [
11        "ansuman-satpathy:igvf_mouse_bridge_101_atac_r1"
12    ],
13    "assay_titles": [
14        "10x multiome"
15    ],
16    "audit": {},
17    "award": {
18        "@id": "/awards/HG012076/",
19        "component": "mapping"
20    },
21    "content_md5sum": "84b43e94f57b1c1baed0f16114513a13",
22    "content_type": "reads",
23    "controlled_access": false,
24    "creation_timestamp": "2024-07-23T02:08:39.313094+00:00",
25    "externally_hosted": false,
26    "file_format": "fastq",
27    "file_set": {
28        "@id": "/measurement-sets/IGVFDS6819TPGN/",
29        "@type": [
30            "MeasurementSet",
31            "FileSet",
32            "Item"
33        ],
34        "accession": "IGVFDS6819TPGN",
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": "/tissues/IGVFSM2776DDRF/",
43                "@type": [
44                    "Tissue",
45                    "Biosample",
46                    "Sample",
47                    "Item"
48                ],
49                "accession": "IGVFSM2776DDRF",
50                "classifications": [
51                    "tissue"
52                ],
53                "sample_terms": [
54                    {
55                        "@id": "/sample-terms/NTR_0000646/",
56                        "status": "released",
57                        "term_name": "left cerebral cortex"
58                    }
59                ],
60                "status": "released",
61                "summary": "Mus musculus CAST/EiJ (male, 10 weeks) left cerebral cortex tissue",
62                "taxa": "Mus musculus"
63            }
64        ],
65        "status": "released",
66        "summary": "single-nucleus ATAC-seq (10x multiome)"
67    },
68    "file_size": 18149966934,
69    "flowcell_id": "HV7LKDSX5",
70    "gene_list_for": [],
71    "href": "/sequence-files/IGVFFI0305RRIM/@@download/IGVFFI0305RRIM.fastq.gz",
72    "illumina_read_type": "R1",
73    "input_file_for": [
74        "/tabular-files/IGVFFI4670FGKO/"
75    ],
76    "integrated_in": [],
77    "lab": {
78        "@id": "/labs/ansuman-satpathy/",
79        "title": "Ansuman Satpathy, Stanford"
80    },
81    "lane": 1,
82    "loci_list_for": [],
83    "maximum_read_length": 100,
84    "md5sum": "fd3cbd773f9b3f3e6f99b17fa7755d1a",
85    "mean_read_length": 100,
86    "minimum_read_length": 100,
87    "quality_metrics": [],
88    "read_count": 340495388,
89    "read_names": [
90        "Read 1"
91    ],
92    "release_timestamp": "2025-03-07T01:18:30.097067+00:00",
93    "s3_uri": "s3://igvf-files/2024/07/23/1e0e0c7c-6bba-4461-91e0-de580fcc9500/IGVFFI0305RRIM.fastq.gz",
94    "schema_version": "15",
95    "seqspecs": [
96        "/configuration-files/IGVFFI6533YMOZ/"
97    ],
98    "sequencing_kit": "NovaSeq 6000 S4 Reagent Kit v1.5",
99    "sequencing_platform": {
100        "@id": "/platform-terms/EFO_0008637/",
101        "status": "released",
102        "term_name": "Illumina NovaSeq 6000"
103    },
104    "sequencing_run": 1,
105    "status": "released",
106    "submitted_by": {
107        "@id": "/users/353655bc-31a1-4cd9-bac3-c7d34faf722f/",
108        "title": "Christopher Mcginnis"
109    },
110    "submitted_file_name": "/oak/stanford/projects/igvf/Projects/230622_IGVF_Bridge_McGinnis/ATAC/ATAC_101_S1_L001_R1_001.fastq.gz",
111    "summary": "R1 reads from sequencing run 1",
112    "upload_status": "validated",
113    "uuid": "1e0e0c7c-6bba-4461-91e0-de580fcc9500"
114}