IGVFFI3640SGYN

released
validated
1{
2    "@context": "/terms/",
3    "@id": "/sequence-files/IGVFFI3640SGYN/",
4    "@type": [
5        "SequenceFile",
6        "File",
7        "Item"
8    ],
9    "accession": "IGVFFI3640SGYN",
10    "aliases": [
11        "ansuman-satpathy:igvf_exp2_atac_10x1_NGS2_r2"
12    ],
13    "assay_titles": [
14        "10x multiome with MULTI-seq"
15    ],
16    "audit": {},
17    "award": {
18        "@id": "/awards/HG012076/",
19        "component": "mapping"
20    },
21    "content_md5sum": "af642ac3475b958637dc28d25777d66e",
22    "content_type": "reads",
23    "controlled_access": false,
24    "creation_timestamp": "2024-07-19T22:51:41.044080+00:00",
25    "externally_hosted": false,
26    "file_format": "fastq",
27    "file_set": {
28        "@id": "/measurement-sets/IGVFDS6369SLCB/",
29        "@type": [
30            "MeasurementSet",
31            "FileSet",
32            "Item"
33        ],
34        "accession": "IGVFDS6369SLCB",
35        "assay_term": {
36            "@id": "/assay-terms/OBI_0002762/",
37            "term_name": "single-nucleus ATAC-seq"
38        },
39        "file_set_type": "experimental data",
40        "samples": [
41            {
42                "@id": "/multiplexed-samples/IGVFSM3646QLDO/",
43                "@type": [
44                    "MultiplexedSample",
45                    "Sample",
46                    "Item"
47                ],
48                "accession": "IGVFSM3646QLDO",
49                "classifications": [
50                    "cell line",
51                    "multiplexed sample"
52                ],
53                "disease_terms": [],
54                "modifications": [],
55                "sample_terms": [
56                    {
57                        "@id": "/sample-terms/NTR_0000753/",
58                        "status": "released",
59                        "term_name": "TeloHAEC"
60                    }
61                ],
62                "status": "released",
63                "summary": "multiplexed sample: Homo sapiens (female) TeloHAEC cell line treated with 10 ng/mL tumor necrosis factor alpha for 4 hours; Homo sapiens (female) TeloHAEC cell line; ... and 7 more samples",
64                "taxa": "Homo sapiens",
65                "treatments": [
66                    {
67                        "@id": "/treatments/d2d49540-dd91-49e2-b877-ce9aa0af8bb0/",
68                        "purpose": "perturbation",
69                        "status": "in progress",
70                        "summary": "Treatment of 10 ng/mL tumor necrosis factor alpha for 4 hours",
71                        "treatment_term_name": "tumor necrosis factor alpha"
72                    },
73                    {
74                        "@id": "/treatments/de8a9e87-d0e1-4ecb-bc9d-08e61b4ff368/",
75                        "purpose": "perturbation",
76                        "status": "in progress",
77                        "summary": "Treatment of 10 ng/mL tumor necrosis factor alpha for 1 day",
78                        "treatment_term_name": "tumor necrosis factor alpha"
79                    }
80                ]
81            }
82        ],
83        "status": "released",
84        "summary": "single-nucleus ATAC-seq (10x multiome with MULTI-seq)"
85    },
86    "file_size": 8829064282,
87    "flowcell_id": "2257H3LT3",
88    "gene_list_for": [],
89    "href": "/sequence-files/IGVFFI3640SGYN/@@download/IGVFFI3640SGYN.fastq.gz",
90    "illumina_read_type": "R2",
91    "input_file_for": [
92        "/tabular-files/IGVFFI6774RPHJ/"
93    ],
94    "integrated_in": [],
95    "lab": {
96        "@id": "/labs/ansuman-satpathy/",
97        "title": "Ansuman Satpathy, Stanford"
98    },
99    "lane": 8,
100    "loci_list_for": [],
101    "maximum_read_length": 24,
102    "md5sum": "d971888c87b71c980a4f1644ca56733d",
103    "mean_read_length": 24,
104    "minimum_read_length": 24,
105    "quality_metrics": [],
106    "read_count": 552165744,
107    "read_names": [
108        "Barcode index"
109    ],
110    "release_timestamp": "2025-03-07T01:10:41.744102+00:00",
111    "s3_uri": "s3://igvf-files/2024/07/19/8af0b01f-686b-4028-a5f1-4578287ebe5a/IGVFFI3640SGYN.fastq.gz",
112    "schema_version": "15",
113    "seqspecs": [
114        "/configuration-files/IGVFFI0680WESH/"
115    ],
116    "sequencing_kit": "NovaSeq X Series 10B Reagent Kit",
117    "sequencing_platform": {
118        "@id": "/platform-terms/EFO_0022840/",
119        "status": "released",
120        "term_name": "Illumina NovaSeq X"
121    },
122    "sequencing_run": 1,
123    "status": "released",
124    "submitted_by": {
125        "@id": "/users/353655bc-31a1-4cd9-bac3-c7d34faf722f/",
126        "title": "Christopher Mcginnis"
127    },
128    "submitted_file_name": "/oak/stanford/projects/igvf/Projects/230522_IGVF2_McGinnis/ATAC/FASTQ/ATAC_3_S360_L008_R2_001.fastq.gz",
129    "summary": "R2 reads from sequencing run 1",
130    "upload_status": "validated",
131    "uuid": "8af0b01f-686b-4028-a5f1-4578287ebe5a"
132}