IGVFFI3666KZJE

released
validated
1{
2    "@context": "/terms/",
3    "@id": "/sequence-files/IGVFFI3666KZJE/",
4    "@type": [
5        "SequenceFile",
6        "File",
7        "Item"
8    ],
9    "accession": "IGVFFI3666KZJE",
10    "aliases": [
11        "ansuman-satpathy:igvf_exp2_multi_10x1_NGS1_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": "00577cf0b9789b1f7dc619282384ffb6",
22    "content_type": "reads",
23    "controlled_access": false,
24    "creation_timestamp": "2024-07-21T22:28:31.946606+00:00",
25    "externally_hosted": false,
26    "file_format": "fastq",
27    "file_set": {
28        "@id": "/auxiliary-sets/IGVFDS9860EXKL/",
29        "@type": [
30            "AuxiliarySet",
31            "FileSet",
32            "Item"
33        ],
34        "accession": "IGVFDS9860EXKL",
35        "file_set_type": "lipid-conjugated oligo sequencing",
36        "samples": [
37            {
38                "@id": "/multiplexed-samples/IGVFSM3646QLDO/",
39                "@type": [
40                    "MultiplexedSample",
41                    "Sample",
42                    "Item"
43                ],
44                "accession": "IGVFSM3646QLDO",
45                "classifications": [
46                    "cell line",
47                    "multiplexed sample"
48                ],
49                "disease_terms": [],
50                "modifications": [],
51                "sample_terms": [
52                    {
53                        "@id": "/sample-terms/NTR_0000753/",
54                        "status": "released",
55                        "term_name": "TeloHAEC"
56                    }
57                ],
58                "status": "released",
59                "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",
60                "taxa": "Homo sapiens",
61                "treatments": [
62                    {
63                        "@id": "/treatments/d2d49540-dd91-49e2-b877-ce9aa0af8bb0/",
64                        "purpose": "perturbation",
65                        "status": "in progress",
66                        "summary": "Treatment of 10 ng/mL tumor necrosis factor alpha for 4 hours",
67                        "treatment_term_name": "tumor necrosis factor alpha"
68                    },
69                    {
70                        "@id": "/treatments/de8a9e87-d0e1-4ecb-bc9d-08e61b4ff368/",
71                        "purpose": "perturbation",
72                        "status": "in progress",
73                        "summary": "Treatment of 10 ng/mL tumor necrosis factor alpha for 1 day",
74                        "treatment_term_name": "tumor necrosis factor alpha"
75                    }
76                ]
77            }
78        ],
79        "status": "released",
80        "summary": "lipid-conjugated oligo sequencing for single-nucleus RNA sequencing assay (10x multiome with MULTI-seq), single-nucleus ATAC-seq (10x multiome with MULTI-seq)"
81    },
82    "file_size": 1478702519,
83    "flowcell_id": "2257H3LT3",
84    "gene_list_for": [],
85    "href": "/sequence-files/IGVFFI3666KZJE/@@download/IGVFFI3666KZJE.fastq.gz",
86    "illumina_read_type": "R2",
87    "input_file_for": [
88        "/tabular-files/IGVFFI1936ETPF/"
89    ],
90    "integrated_in": [],
91    "lab": {
92        "@id": "/labs/ansuman-satpathy/",
93        "title": "Ansuman Satpathy, Stanford"
94    },
95    "lane": 7,
96    "loci_list_for": [],
97    "maximum_read_length": 90,
98    "md5sum": "af71c096aa11956957c0a52719e16efa",
99    "mean_read_length": 90,
100    "minimum_read_length": 90,
101    "quality_metrics": [],
102    "read_count": 32393937,
103    "release_timestamp": "2025-03-07T01:10:41.928060+00:00",
104    "s3_uri": "s3://igvf-files/2024/07/21/2ac48ef4-4001-49e3-8ff0-0bc9ea5f975d/IGVFFI3666KZJE.fastq.gz",
105    "schema_version": "15",
106    "seqspecs": [
107        "/configuration-files/IGVFFI4120EDXM/"
108    ],
109    "sequencing_kit": "NovaSeq X Series 10B Reagent Kit",
110    "sequencing_platform": {
111        "@id": "/platform-terms/EFO_0022840/",
112        "status": "released",
113        "term_name": "Illumina NovaSeq X"
114    },
115    "sequencing_run": 1,
116    "status": "released",
117    "submitted_by": {
118        "@id": "/users/353655bc-31a1-4cd9-bac3-c7d34faf722f/",
119        "title": "Christopher Mcginnis"
120    },
121    "submitted_file_name": "/oak/stanford/projects/igvf/Projects/230522_IGVF2_McGinnis/MULTI/FASTQ/MULTI_3_S46_L007_R2_001.fastq.gz",
122    "summary": "R2 reads from sequencing run 1",
123    "upload_status": "validated",
124    "uuid": "2ac48ef4-4001-49e3-8ff0-0bc9ea5f975d"
125}