IGVFFI4225SBCM

released
validated
1{
2    "@context": "/terms/",
3    "@id": "/sequence-files/IGVFFI4225SBCM/",
4    "@type": [
5        "SequenceFile",
6        "File",
7        "Item"
8    ],
9    "accession": "IGVFFI4225SBCM",
10    "aliases": [
11        "ansuman-satpathy:igvf_exp16_atac_10x3_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    "checkfiles_version": "v14",
22    "content_md5sum": "6b860012d19be31c40d6403fc8f78b36",
23    "content_type": "reads",
24    "controlled_access": true,
25    "creation_timestamp": "2025-02-03T22:33:15.455329+00:00",
26    "externally_hosted": false,
27    "file_format": "fastq",
28    "file_set": {
29        "@id": "/measurement-sets/IGVFDS4856BVTB/",
30        "@type": [
31            "MeasurementSet",
32            "FileSet",
33            "Item"
34        ],
35        "accession": "IGVFDS4856BVTB",
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/IGVFSM5332SKYG/",
44                "@type": [
45                    "MultiplexedSample",
46                    "Sample",
47                    "Item"
48                ],
49                "accession": "IGVFSM5332SKYG",
50                "classifications": [
51                    "differentiated cell specimen",
52                    "multiplexed sample"
53                ],
54                "disease_terms": [],
55                "modifications": [],
56                "sample_terms": [
57                    {
58                        "@id": "/sample-terms/EFO_0004905/",
59                        "status": "released",
60                        "term_name": "induced pluripotent stem cell"
61                    }
62                ],
63                "status": "released",
64                "summary": "multiplexed sample: Homo sapiens (mixed sex) induced pluripotent stem differentiated cell specimen induced to islet of Langerhans for 11 days; Homo sapiens (mixed sex) induced pluripotent stem differentiated cell specimen induced to islet of Langerhans for 3 days; ... and 6 more samples",
65                "taxa": "Homo sapiens",
66                "treatments": []
67            }
68        ],
69        "status": "released",
70        "summary": "single-nucleus ATAC-seq (10x multiome with MULTI-seq)"
71    },
72    "file_size": 7942118337,
73    "flowcell_id": "22NC7YLT3",
74    "gene_list_for": [],
75    "href": "/sequence-files/IGVFFI4225SBCM/@@download/IGVFFI4225SBCM.fastq.gz",
76    "illumina_read_type": "R3",
77    "input_file_for": [
78        "/tabular-files/IGVFFI9091HPCI/"
79    ],
80    "integrated_in": [],
81    "lab": {
82        "@id": "/labs/ansuman-satpathy/",
83        "title": "Ansuman Satpathy, Stanford"
84    },
85    "lane": 6,
86    "loci_list_for": [],
87    "maximum_read_length": 50,
88    "md5sum": "79a9f36d49caba0992d47bd10f946d5c",
89    "mean_read_length": 50,
90    "minimum_read_length": 50,
91    "quality_metrics": [],
92    "read_count": 256469015,
93    "read_names": [
94        "Read 2"
95    ],
96    "release_timestamp": "2025-03-22T00:41:22.662376+00:00",
97    "s3_uri": "s3://igvf-restricted-files/2025/02/03/a0d84ce5-ee53-45b0-8954-01dfb750fe24/IGVFFI4225SBCM.fastq.gz",
98    "schema_version": "15",
99    "seqspecs": [
100        "/configuration-files/IGVFFI7187OYZU/"
101    ],
102    "sequencing_kit": "NovaSeq X Series 10B Reagent Kit",
103    "sequencing_platform": {
104        "@id": "/platform-terms/EFO_0022840/",
105        "status": "released",
106        "term_name": "Illumina NovaSeq X"
107    },
108    "sequencing_run": 1,
109    "status": "released",
110    "submitted_by": {
111        "@id": "/users/353655bc-31a1-4cd9-bac3-c7d34faf722f/",
112        "title": "Christopher Mcginnis"
113    },
114    "submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/igvf16/ATAC/CMAS18_ATAC3_S60_L006_R3_001.fastq.gz",
115    "summary": "R3 reads from sequencing run 1",
116    "upload_status": "validated",
117    "uuid": "a0d84ce5-ee53-45b0-8954-01dfb750fe24"
118}