IGVFFI3960XUKA

preview
validated
1{
2    "@context": "/terms/",
3    "@id": "/sequence-files/IGVFFI3960XUKA/",
4    "@type": [
5        "SequenceFile",
6        "File",
7        "Item"
8    ],
9    "accession": "IGVFFI3960XUKA",
10    "aliases": [
11        "maya-kasowski:Scale_scATAC_lane2_I2"
12    ],
13    "assay_titles": [
14        "scATAC-seq"
15    ],
16    "audit": {},
17    "award": {
18        "@id": "/awards/HG012076/",
19        "component": "mapping"
20    },
21    "checkfiles_version": "v17",
22    "content_md5sum": "1873b54820e64e07ec3c72132778b814",
23    "content_type": "reads",
24    "controlled_access": true,
25    "creation_timestamp": "2025-03-07T21:35:21.458976+00:00",
26    "externally_hosted": false,
27    "file_format": "fastq",
28    "file_set": {
29        "@id": "/measurement-sets/IGVFDS1790XLZR/",
30        "@type": [
31            "MeasurementSet",
32            "FileSet",
33            "Item"
34        ],
35        "accession": "IGVFDS1790XLZR",
36        "assay_term": {
37            "@id": "/assay-terms/OBI_0002764/",
38            "term_name": "single-cell ATAC-seq"
39        },
40        "file_set_type": "experimental data",
41        "samples": [
42            {
43                "@id": "/multiplexed-samples/IGVFSM1625LLXE/",
44                "@type": [
45                    "MultiplexedSample",
46                    "Sample",
47                    "Item"
48                ],
49                "accession": "IGVFSM1625LLXE",
50                "classifications": [
51                    "primary cell",
52                    "multiplexed sample"
53                ],
54                "disease_terms": [],
55                "modifications": [],
56                "sample_terms": [
57                    {
58                        "@id": "/sample-terms/UBERON_0002371/",
59                        "status": "released",
60                        "term_name": "bone marrow"
61                    }
62                ],
63                "status": "preview",
64                "summary": "multiplexed sample: Homo sapiens bone marrow cell; Homo sapiens (female) bone marrow cell; ... and 21 more samples",
65                "taxa": "Homo sapiens",
66                "treatments": []
67            }
68        ],
69        "status": "preview",
70        "summary": "scATAC-seq"
71    },
72    "file_size": 12134045445,
73    "gene_list_for": [],
74    "href": "/sequence-files/IGVFFI3960XUKA/@@download/IGVFFI3960XUKA.fastq.gz",
75    "illumina_read_type": "I2",
76    "input_file_for": [],
77    "integrated_in": [],
78    "lab": {
79        "@id": "/labs/maya-kasowski/",
80        "title": "Maya Kasowski, Stanford"
81    },
82    "lane": 2,
83    "loci_list_for": [],
84    "maximum_read_length": 24,
85    "md5sum": "aca07011616df75c85a686acd5f33041",
86    "mean_read_length": 24,
87    "minimum_read_length": 24,
88    "quality_metrics": [],
89    "read_count": 489595290,
90    "read_names": [
91        "Barcode index"
92    ],
93    "s3_uri": "s3://igvf-restricted-files/2025/03/07/54d97e26-49aa-4719-b1b7-0ae7dd353fb6/IGVFFI3960XUKA.fastq.gz",
94    "schema_version": "15",
95    "seqspecs": [],
96    "sequencing_kit": "NovaSeq 6000 S4 Reagent Kit v1.5",
97    "sequencing_platform": {
98        "@id": "/platform-terms/EFO_0008637/",
99        "status": "released",
100        "term_name": "Illumina NovaSeq 6000"
101    },
102    "sequencing_run": 1,
103    "status": "preview",
104    "submitted_by": {
105        "@id": "/users/2bebcf9d-414f-4058-8d97-00020741a419/",
106        "title": "Shouvik Mani"
107    },
108    "submitted_file_name": "/users/shouvikm/data/Scale/SCALE_leukemia_01202023/fastqs_after_scATAC_Scale_pipeline/S701-S706/S702/S702P_S2_L003_I2_001.fastq.gz",
109    "summary": "I2 reads from sequencing run 1",
110    "upload_status": "validated",
111    "uuid": "54d97e26-49aa-4719-b1b7-0ae7dd353fb6"
112}