IGVFFI0207GMGR

released
validated
1{
2    "@context": "/terms/",
3    "@id": "/sequence-files/IGVFFI0207GMGR/",
4    "@type": [
5        "SequenceFile",
6        "File",
7        "Item"
8    ],
9    "accession": "IGVFFI0207GMGR",
10    "aliases": [
11        "charles-gersbach:cd8-tcells-atac-seq-acute-activation-batf3-rep2-fastq-R1"
12    ],
13    "assay_titles": [
14        "ATAC-seq"
15    ],
16    "audit": {},
17    "award": {
18        "@id": "/awards/HG012053/",
19        "component": "functional characterization"
20    },
21    "content_md5sum": "db80e1ecf48b4578013a6e9ae071ac91",
22    "content_type": "reads",
23    "controlled_access": false,
24    "creation_timestamp": "2023-11-08T20:58:53.781777+00:00",
25    "externally_hosted": false,
26    "file_format": "fastq",
27    "file_set": {
28        "@id": "/measurement-sets/IGVFDS2737CQNK/",
29        "@type": [
30            "MeasurementSet",
31            "FileSet",
32            "Item"
33        ],
34        "accession": "IGVFDS2737CQNK",
35        "assay_term": {
36            "@id": "/assay-terms/OBI_0003089/",
37            "term_name": "bulk assay for transposase-accessible chromatin using sequencing"
38        },
39        "file_set_type": "experimental data",
40        "samples": [
41            {
42                "@id": "/primary-cells/IGVFSM4716FORO/",
43                "@type": [
44                    "PrimaryCell",
45                    "Biosample",
46                    "Sample",
47                    "Item"
48                ],
49                "accession": "IGVFSM4716FORO",
50                "classifications": [
51                    "primary cell"
52                ],
53                "sample_terms": [
54                    {
55                        "@id": "/sample-terms/CL_0000909/",
56                        "status": "released",
57                        "term_name": "CD8-positive, alpha-beta memory T cell"
58                    }
59                ],
60                "status": "released",
61                "summary": "Homo sapiens CD8-positive, alpha-beta memory T cell treated with 300 percent Antibody Coated Bead, transduced (lentivirus) with a expression vector library",
62                "taxa": "Homo sapiens",
63                "treatments": [
64                    {
65                        "@id": "/treatments/725c21b1-d202-4a6c-89a4-e4fc05a001e8/",
66                        "purpose": "stimulation",
67                        "status": "in progress",
68                        "summary": "Treatment of 300 percent Antibody Coated Bead",
69                        "treatment_term_name": "Antibody Coated Bead"
70                    }
71                ]
72            }
73        ],
74        "status": "released",
75        "summary": "ATAC-seq integrating an expression vector library of BATF3"
76    },
77    "file_size": 1003979571,
78    "gene_list_for": [],
79    "href": "/sequence-files/IGVFFI0207GMGR/@@download/IGVFFI0207GMGR.fastq.gz",
80    "illumina_read_type": "R1",
81    "input_file_for": [
82        "/alignment-files/IGVFFI1198PNDA/"
83    ],
84    "integrated_in": [],
85    "lab": {
86        "@id": "/labs/charles-gersbach/",
87        "title": "Charles Gersbach, Duke"
88    },
89    "lane": 1,
90    "loci_list_for": [],
91    "maximum_read_length": 51,
92    "md5sum": "69448b4fc112720f6d2b694c7b77bd55",
93    "mean_read_length": 51,
94    "minimum_read_length": 51,
95    "quality_metrics": [],
96    "read_count": 31048657,
97    "release_timestamp": "2024-10-29T17:33:36.048468+00:00",
98    "s3_uri": "s3://igvf-files/2023/11/08/95aa8748-cb12-4fe6-96bd-2b36dc7371f5/IGVFFI0207GMGR.fastq.gz",
99    "schema_version": "15",
100    "seqspecs": [],
101    "sequencing_kit": "NextSeq 1000/2000 P2 Reagent Kit",
102    "sequencing_platform": {
103        "@id": "/platform-terms/EFO_0010963/",
104        "status": "released",
105        "term_name": "Illumina NextSeq 2000"
106    },
107    "sequencing_run": 2,
108    "status": "released",
109    "submitted_by": {
110        "@id": "/users/29f5f78d-ac90-421e-90c6-a90e1dc407a7/",
111        "title": "Alejandro Barrera"
112    },
113    "submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/raw_data/AIM_2_T_cell_project_1/70-2_S10_L001_R1_001.fastq.gz",
114    "summary": "R1 reads from sequencing run 2",
115    "upload_status": "validated",
116    "uuid": "95aa8748-cb12-4fe6-96bd-2b36dc7371f5"
117}