IGVFFI2549NCMF

preview
validated
1{
2    "@context": "/terms/",
3    "@id": "/sequence-files/IGVFFI2549NCMF/",
4    "@type": [
5        "SequenceFile",
6        "File",
7        "Item"
8    ],
9    "accession": "IGVFFI2549NCMF",
10    "aliases": [
11        "jimmie-ye:XX6-SC1_snATAC_S0_R2"
12    ],
13    "assay_titles": [
14        "10x multiome"
15    ],
16    "audit": {},
17    "award": {
18        "@id": "/awards/HG012076/",
19        "component": "mapping"
20    },
21    "checkfiles_version": "v17",
22    "content_md5sum": "af0e5c71ef2f6f1f80b05c0484c78965",
23    "content_type": "reads",
24    "controlled_access": true,
25    "creation_timestamp": "2025-03-11T12:53:17.546363+00:00",
26    "externally_hosted": false,
27    "file_format": "fastq",
28    "file_set": {
29        "@id": "/measurement-sets/IGVFDS9590YCER/",
30        "@type": [
31            "MeasurementSet",
32            "FileSet",
33            "Item"
34        ],
35        "accession": "IGVFDS9590YCER",
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/IGVFSM2228XCXF/",
44                "@type": [
45                    "MultiplexedSample",
46                    "Sample",
47                    "Item"
48                ],
49                "accession": "IGVFSM2228XCXF",
50                "classifications": [
51                    "primary cell",
52                    "multiplexed sample"
53                ],
54                "disease_terms": [],
55                "modifications": [],
56                "sample_terms": [
57                    {
58                        "@id": "/sample-terms/CL_2000001/",
59                        "status": "released",
60                        "term_name": "peripheral blood mononuclear cell"
61                    }
62                ],
63                "status": "preview",
64                "summary": "multiplexed sample: Homo sapiens (female, 30.0 years) peripheral blood mononuclear cell; Homo sapiens (female, 18.0 years) peripheral blood mononuclear cell; ... and 17 more samples",
65                "taxa": "Homo sapiens",
66                "treatments": []
67            }
68        ],
69        "status": "preview",
70        "summary": "single-nucleus ATAC-seq (10x multiome)"
71    },
72    "file_size": 3932684647,
73    "gene_list_for": [],
74    "href": "/sequence-files/IGVFFI2549NCMF/@@download/IGVFFI2549NCMF.fastq.gz",
75    "illumina_read_type": "R2",
76    "input_file_for": [
77        "/tabular-files/IGVFFI9658YEQH/"
78    ],
79    "integrated_in": [],
80    "lab": {
81        "@id": "/labs/jimmie-ye/",
82        "title": "Jimmie Ye, UCSF"
83    },
84    "loci_list_for": [],
85    "maximum_read_length": 24,
86    "md5sum": "5cd518fa66ed673b6060c36cc083efe9",
87    "mean_read_length": 24,
88    "minimum_read_length": 24,
89    "quality_metrics": [],
90    "read_count": 229375056,
91    "read_names": [
92        "Barcode index"
93    ],
94    "s3_uri": "s3://igvf-restricted-files/2025/03/11/7513aefc-89f5-46ec-b801-0d852e5edf05/IGVFFI2549NCMF.fastq.gz",
95    "schema_version": "15",
96    "seqspecs": [
97        "/configuration-files/IGVFFI8376ILEW/"
98    ],
99    "sequencing_kit": "NovaSeq 6000 S4 Reagent Kit v1.5",
100    "sequencing_platform": {
101        "@id": "/platform-terms/EFO_0008637/",
102        "status": "released",
103        "term_name": "Illumina NovaSeq 6000"
104    },
105    "sequencing_run": 472,
106    "status": "preview",
107    "submitted_by": {
108        "@id": "/users/6df823a5-62f2-4562-94ba-e9285afcfcf4/",
109        "title": "Marcus Alvarez"
110    },
111    "submitted_file_name": "production_data/xhlt1/data/single_cell_ATAC/raw/XHLT1-POOL-XX6-SC1/AH2YMLDSX3_ICJY04/XHLT1-POOL-XX6-SC1-ATAC_S5_L004_R2_001.fastq.gz",
112    "summary": "R2 reads from sequencing run 472",
113    "upload_status": "validated",
114    "uuid": "7513aefc-89f5-46ec-b801-0d852e5edf05"
115}