IGVFFI1003AFXX

preview
validated
1{
2    "@context": "/terms/",
3    "@id": "/sequence-files/IGVFFI1003AFXX/",
4    "@type": [
5        "SequenceFile",
6        "File",
7        "Item"
8    ],
9    "accession": "IGVFFI1003AFXX",
10    "aliases": [
11        "jimmie-ye:XX8-SC3_snATAC_S2_R3"
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": "1d938c2d518151d2e417b02a9d075538",
23    "content_type": "reads",
24    "controlled_access": true,
25    "creation_timestamp": "2025-03-11T17:18:35.963521+00:00",
26    "externally_hosted": false,
27    "file_format": "fastq",
28    "file_set": {
29        "@id": "/measurement-sets/IGVFDS5526TAEF/",
30        "@type": [
31            "MeasurementSet",
32            "FileSet",
33            "Item"
34        ],
35        "accession": "IGVFDS5526TAEF",
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/IGVFSM6182MOLI/",
44                "@type": [
45                    "MultiplexedSample",
46                    "Sample",
47                    "Item"
48                ],
49                "accession": "IGVFSM6182MOLI",
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 (male, 26.0 years) peripheral blood mononuclear cell; Homo sapiens (male, 26.0 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": 8320974243,
73    "gene_list_for": [],
74    "href": "/sequence-files/IGVFFI1003AFXX/@@download/IGVFFI1003AFXX.fastq.gz",
75    "illumina_read_type": "R3",
76    "input_file_for": [
77        "/tabular-files/IGVFFI4832MEVK/"
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": 90,
86    "md5sum": "d9014b4bc3e5c4a382814e3e21d69de7",
87    "mean_read_length": 90,
88    "minimum_read_length": 90,
89    "quality_metrics": [],
90    "read_count": 172882534,
91    "read_names": [
92        "Read 2"
93    ],
94    "s3_uri": "s3://igvf-restricted-files/2025/03/11/d153f23c-c2b1-40fe-9f99-5525dc4a1cce/IGVFFI1003AFXX.fastq.gz",
95    "schema_version": "15",
96    "seqspecs": [
97        "/configuration-files/IGVFFI6688CSTH/"
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": 554,
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-XX8-SC3/BH2VM7DSX3/XHLT1-POOL-XX8-SC3-ATAC_S15_L002_R3_001.fastq.gz",
112    "summary": "R3 reads from sequencing run 554",
113    "upload_status": "validated",
114    "uuid": "d153f23c-c2b1-40fe-9f99-5525dc4a1cce"
115}