IGVFFI5847LLGI

released
validated
1{
2    "@context": "/terms/",
3    "@id": "/sequence-files/IGVFFI5847LLGI/",
4    "@type": [
5        "SequenceFile",
6        "File",
7        "Item"
8    ],
9    "accession": "IGVFFI5847LLGI",
10    "aliases": [
11        "ansuman-satpathy:igvf_exp9_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": "c716852bb04e93c3ab93282fd8578ae2",
22    "content_type": "reads",
23    "controlled_access": true,
24    "creation_timestamp": "2024-07-23T22:07:29.506092+00:00",
25    "externally_hosted": false,
26    "file_format": "fastq",
27    "file_set": {
28        "@id": "/measurement-sets/IGVFDS2108XESQ/",
29        "@type": [
30            "MeasurementSet",
31            "FileSet",
32            "Item"
33        ],
34        "accession": "IGVFDS2108XESQ",
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/IGVFSM2512OHNK/",
43                "@type": [
44                    "MultiplexedSample",
45                    "Sample",
46                    "Item"
47                ],
48                "accession": "IGVFSM2512OHNK",
49                "classifications": [
50                    "differentiated cell specimen",
51                    "multiplexed sample"
52                ],
53                "disease_terms": [],
54                "modifications": [],
55                "sample_terms": [
56                    {
57                        "@id": "/sample-terms/CL_0000236/",
58                        "status": "released",
59                        "term_name": "B cell"
60                    }
61                ],
62                "status": "released",
63                "summary": "multiplexed sample: Homo sapiens (male) B differentiated cell specimen induced to plasmablast for 1 day; Homo sapiens (male) B differentiated cell specimen induced to plasmablast for 5 days; ... and 5 more samples",
64                "taxa": "Homo sapiens",
65                "treatments": []
66            }
67        ],
68        "status": "released",
69        "summary": "single-nucleus ATAC-seq (10x multiome with MULTI-seq)"
70    },
71    "file_size": 12161704576,
72    "flowcell_id": "223JGVLT3",
73    "gene_list_for": [],
74    "href": "/sequence-files/IGVFFI5847LLGI/@@download/IGVFFI5847LLGI.fastq.gz",
75    "illumina_read_type": "R3",
76    "input_file_for": [
77        "/tabular-files/IGVFFI4907GYFZ/"
78    ],
79    "integrated_in": [],
80    "lab": {
81        "@id": "/labs/ansuman-satpathy/",
82        "title": "Ansuman Satpathy, Stanford"
83    },
84    "lane": 6,
85    "loci_list_for": [],
86    "maximum_read_length": 50,
87    "md5sum": "fc1f4daa8f4cde60f5df0ab4635e5b72",
88    "mean_read_length": 50,
89    "minimum_read_length": 50,
90    "quality_metrics": [],
91    "read_count": 411263055,
92    "read_names": [
93        "Read 2"
94    ],
95    "release_timestamp": "2025-03-22T00:38:22.597692+00:00",
96    "s3_uri": "s3://igvf-restricted-files/2024/07/23/4055b128-b008-4d2a-93bb-1cb92f791a90/IGVFFI5847LLGI.fastq.gz",
97    "schema_version": "15",
98    "seqspecs": [
99        "/configuration-files/IGVFFI2789XFWJ/"
100    ],
101    "sequencing_kit": "NovaSeq X Series 10B Reagent Kit",
102    "sequencing_platform": {
103        "@id": "/platform-terms/EFO_0022840/",
104        "status": "released",
105        "term_name": "Illumina NovaSeq X"
106    },
107    "sequencing_run": 1,
108    "status": "released",
109    "submitted_by": {
110        "@id": "/users/353655bc-31a1-4cd9-bac3-c7d34faf722f/",
111        "title": "Christopher Mcginnis"
112    },
113    "submitted_file_name": "/oak/stanford/projects/igvf/Projects/230707_IGVF9_McGinnis/ATAC/FASTQ/ATAC_2CMAS_IGVF9_A_S22_L006_R3_001.fastq.gz",
114    "summary": "R3 reads from sequencing run 1",
115    "upload_status": "validated",
116    "uuid": "4055b128-b008-4d2a-93bb-1cb92f791a90"
117}