IGVFFI9001PEQP

released
validated
1{
2    "@context": "/terms/",
3    "@id": "/sequence-files/IGVFFI9001PEQP/",
4    "@type": [
5        "SequenceFile",
6        "File",
7        "Item"
8    ],
9    "accession": "IGVFFI9001PEQP",
10    "aliases": [
11        "ansuman-satpathy:igvf_exp12_atac_10x2_NGS7_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": "011e5e1a43d4e1cae4dff6064e6b1979",
22    "content_type": "reads",
23    "controlled_access": true,
24    "creation_timestamp": "2024-07-23T22:10:44.934653+00:00",
25    "externally_hosted": false,
26    "file_format": "fastq",
27    "file_set": {
28        "@id": "/measurement-sets/IGVFDS7359TFTN/",
29        "@type": [
30            "MeasurementSet",
31            "FileSet",
32            "Item"
33        ],
34        "accession": "IGVFDS7359TFTN",
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/IGVFSM5189FTFS/",
43                "@type": [
44                    "MultiplexedSample",
45                    "Sample",
46                    "Item"
47                ],
48                "accession": "IGVFSM5189FTFS",
49                "classifications": [
50                    "differentiated cell specimen",
51                    "tissue",
52                    "multiplexed sample"
53                ],
54                "disease_terms": [],
55                "modifications": [],
56                "sample_terms": [
57                    {
58                        "@id": "/sample-terms/CL_0000236/",
59                        "status": "released",
60                        "term_name": "B cell"
61                    },
62                    {
63                        "@id": "/sample-terms/UBERON_0002371/",
64                        "status": "released",
65                        "term_name": "bone marrow"
66                    }
67                ],
68                "status": "released",
69                "summary": "multiplexed sample: Homo sapiens (female) B differentiated cell specimen induced to plasmablast for 6 days; Homo sapiens (female) B differentiated cell specimen induced to plasmablast for 5 days; ... and 10 more samples",
70                "taxa": "Homo sapiens",
71                "treatments": []
72            }
73        ],
74        "status": "released",
75        "summary": "single-nucleus ATAC-seq (10x multiome with MULTI-seq)"
76    },
77    "file_size": 2841358298,
78    "flowcell_id": "225JCCLT3",
79    "gene_list_for": [],
80    "href": "/sequence-files/IGVFFI9001PEQP/@@download/IGVFFI9001PEQP.fastq.gz",
81    "illumina_read_type": "R2",
82    "input_file_for": [
83        "/tabular-files/IGVFFI2013BVRU/"
84    ],
85    "integrated_in": [],
86    "lab": {
87        "@id": "/labs/ansuman-satpathy/",
88        "title": "Ansuman Satpathy, Stanford"
89    },
90    "lane": 7,
91    "loci_list_for": [],
92    "maximum_read_length": 24,
93    "md5sum": "657eacc56c1cc03be4d89f7a7dac4096",
94    "mean_read_length": 24,
95    "minimum_read_length": 24,
96    "quality_metrics": [],
97    "read_count": 173577800,
98    "read_names": [
99        "Barcode index"
100    ],
101    "release_timestamp": "2025-03-22T00:39:01.872832+00:00",
102    "s3_uri": "s3://igvf-restricted-files/2024/07/23/ec74d2aa-61c6-44fa-b37b-e6e81d9fffc8/IGVFFI9001PEQP.fastq.gz",
103    "schema_version": "15",
104    "seqspecs": [
105        "/configuration-files/IGVFFI1578KBVE/"
106    ],
107    "sequencing_kit": "NovaSeq X Series 10B Reagent Kit",
108    "sequencing_platform": {
109        "@id": "/platform-terms/EFO_0022840/",
110        "status": "released",
111        "term_name": "Illumina NovaSeq X"
112    },
113    "sequencing_run": 1,
114    "status": "released",
115    "submitted_by": {
116        "@id": "/users/353655bc-31a1-4cd9-bac3-c7d34faf722f/",
117        "title": "Christopher Mcginnis"
118    },
119    "submitted_file_name": "/oak/stanford/projects/igvf/Projects/240425_IGVF12_McGinnis/ATAC/FASTQ/ATAC2_S6_L007_R2_001.fastq.gz",
120    "summary": "R2 reads from sequencing run 1",
121    "upload_status": "validated",
122    "uuid": "ec74d2aa-61c6-44fa-b37b-e6e81d9fffc8"
123}