IGVFFI4386BDER

released
validated
1{
2    "@context": "/terms/",
3    "@id": "/sequence-files/IGVFFI4386BDER/",
4    "@type": [
5        "SequenceFile",
6        "File",
7        "Item"
8    ],
9    "accession": "IGVFFI4386BDER",
10    "aliases": [
11        "bradley-bernstein:SS-LS_2005_R2",
12        "bradley-bernstein:SS-LS_39_R2",
13        "buenrostro-bernstein:SS-LS_2005_R2",
14        "buenrostro-bernstein:SS-LS_39_R2"
15    ],
16    "assay_titles": [
17        "SHARE-seq"
18    ],
19    "audit": {},
20    "award": {
21        "@id": "/awards/HG011986/",
22        "component": "mapping"
23    },
24    "content_md5sum": "5026188061432a0b567343a5fcd8456a",
25    "content_type": "reads",
26    "controlled_access": false,
27    "creation_timestamp": "2023-08-28T18:21:07.331449+00:00",
28    "externally_hosted": false,
29    "file_format": "fastq",
30    "file_set": {
31        "@id": "/measurement-sets/IGVFDS3032KHHX/",
32        "@type": [
33            "MeasurementSet",
34            "FileSet",
35            "Item"
36        ],
37        "accession": "IGVFDS3032KHHX",
38        "assay_term": {
39            "@id": "/assay-terms/OBI_0002764/",
40            "term_name": "single-cell ATAC-seq"
41        },
42        "file_set_type": "experimental data",
43        "samples": [
44            {
45                "@id": "/tissues/IGVFSM8719IQYM/",
46                "@type": [
47                    "Tissue",
48                    "Biosample",
49                    "Sample",
50                    "Item"
51                ],
52                "accession": "IGVFSM8719IQYM",
53                "classifications": [
54                    "tissue"
55                ],
56                "sample_terms": [
57                    {
58                        "@id": "/sample-terms/UBERON_0000955/",
59                        "status": "released",
60                        "term_name": "brain"
61                    }
62                ],
63                "status": "released",
64                "summary": "Mus musculus C57BL/6 (female) brain tissue (cellular sub pool: SS-PKR 130)",
65                "taxa": "Mus musculus"
66            }
67        ],
68        "status": "released",
69        "summary": "single-cell ATAC-seq (SHARE-seq)"
70    },
71    "file_size": 211585168,
72    "gene_list_for": [],
73    "href": "/sequence-files/IGVFFI4386BDER/@@download/IGVFFI4386BDER.fastq.gz",
74    "illumina_read_type": "R2",
75    "input_file_for": [
76        "/alignment-files/IGVFFI0876EPIM/",
77        "/tabular-files/IGVFFI6441PWQZ/"
78    ],
79    "integrated_in": [],
80    "lab": {
81        "@id": "/labs/jason-buenrostro/",
82        "title": "Jason Buenrostro, Broad"
83    },
84    "loci_list_for": [],
85    "maximum_read_length": 149,
86    "md5sum": "8c1a5485d640e7ea3e4df4e810426c22",
87    "mean_read_length": 149,
88    "minimum_read_length": 149,
89    "quality_metrics": [],
90    "read_count": 4307852,
91    "read_names": [
92        "Read 2",
93        "Barcode index"
94    ],
95    "release_timestamp": "2025-03-28T21:18:47.517648+00:00",
96    "s3_uri": "s3://igvf-files/2023/08/28/0550d9ce-c0df-48c5-98ef-0baae5f48fb6/IGVFFI4386BDER.fastq.gz",
97    "schema_version": "15",
98    "seqspecs": [
99        "/configuration-files/IGVFFI9756RDEZ/"
100    ],
101    "sequencing_kit": "NovaSeq 6000 S4 Reagent Kit v1.5",
102    "sequencing_platform": {
103        "@id": "/platform-terms/EFO_0008637/",
104        "status": "released",
105        "term_name": "Illumina NovaSeq 6000"
106    },
107    "sequencing_run": 39,
108    "status": "released",
109    "submitted_by": {
110        "@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
111        "title": "Siddarth Wekhande"
112    },
113    "submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-158_L1_SS-PKR-130_SS-V1-LEFT-HALF_R2.fastq.gz",
114    "summary": "R2 reads from sequencing run 39",
115    "upload_status": "validated",
116    "uuid": "0550d9ce-c0df-48c5-98ef-0baae5f48fb6"
117}