IGVFFI5048OHPW

released
validated
1{
2    "@context": "/terms/",
3    "@id": "/sequence-files/IGVFFI5048OHPW/",
4    "@type": [
5        "SequenceFile",
6        "File",
7        "Item"
8    ],
9    "accession": "IGVFFI5048OHPW",
10    "aliases": [
11        "ansuman-satpathy:igvf_exp5_rna_10x3_NGS1_r1"
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": "b672b36045f2e655ed258271f3c3037d",
22    "content_type": "reads",
23    "controlled_access": false,
24    "creation_timestamp": "2024-07-21T23:58:59.409605+00:00",
25    "externally_hosted": false,
26    "file_format": "fastq",
27    "file_set": {
28        "@id": "/measurement-sets/IGVFDS6262VTZI/",
29        "@type": [
30            "MeasurementSet",
31            "FileSet",
32            "Item"
33        ],
34        "accession": "IGVFDS6262VTZI",
35        "assay_term": {
36            "@id": "/assay-terms/OBI_0003109/",
37            "term_name": "single-nucleus RNA sequencing assay"
38        },
39        "controlled_access": false,
40        "data_use_limitation_summaries": [
41            "No limitations"
42        ],
43        "file_set_type": "experimental data",
44        "samples": [
45            {
46                "@id": "/multiplexed-samples/IGVFSM7875RUGJ/",
47                "@type": [
48                    "MultiplexedSample",
49                    "Sample",
50                    "Item"
51                ],
52                "accession": "IGVFSM7875RUGJ",
53                "classifications": [
54                    "cell line",
55                    "differentiated cell specimen",
56                    "gastruloid",
57                    "multiplexed sample"
58                ],
59                "disease_terms": [],
60                "modifications": [],
61                "sample_terms": [
62                    {
63                        "@id": "/sample-terms/EFO_0001184/",
64                        "status": "released",
65                        "term_name": "HEK293T"
66                    },
67                    {
68                        "@id": "/sample-terms/EFO_0003042/",
69                        "status": "released",
70                        "term_name": "H1-hESC"
71                    },
72                    {
73                        "@id": "/sample-terms/EFO_0003045/",
74                        "status": "released",
75                        "term_name": "H9"
76                    },
77                    {
78                        "@id": "/sample-terms/EFO_0009747/",
79                        "status": "released",
80                        "term_name": "GM25256 (WTC-11)"
81                    }
82                ],
83                "status": "released",
84                "summary": "multiplexed sample: Homo sapiens (female) H9 differentiated cell specimen induced to neuron for 6 days; Homo sapiens (female) H9 differentiated cell specimen induced to neuron for 6 days; ... and 6 more samples",
85                "taxa": "Homo sapiens",
86                "treatments": []
87            }
88        ],
89        "status": "released",
90        "summary": "single-nucleus RNA sequencing assay (10x multiome with MULTI-seq)"
91    },
92    "file_size": 2834760133,
93    "flowcell_id": "223JJCLT3",
94    "gene_list_for": [],
95    "href": "/sequence-files/IGVFFI5048OHPW/@@download/IGVFFI5048OHPW.fastq.gz",
96    "illumina_read_type": "R1",
97    "input_file_for": [
98        "/matrix-files/IGVFFI0296TMZO/"
99    ],
100    "integrated_in": [],
101    "lab": {
102        "@id": "/labs/ansuman-satpathy/",
103        "title": "Ansuman Satpathy, Stanford"
104    },
105    "lane": 5,
106    "loci_list_for": [],
107    "maximum_read_length": 28,
108    "md5sum": "9fa78d6f12de77f8aa94b6bfff3b1b91",
109    "mean_read_length": 28,
110    "minimum_read_length": 28,
111    "quality_metrics": [],
112    "read_count": 138052685,
113    "read_names": [
114        "Read 1"
115    ],
116    "release_timestamp": "2025-03-07T01:12:28.759254+00:00",
117    "s3_uri": "s3://igvf-files/2024/07/21/a76db38a-1c39-4f6e-a175-11fa471b4e49/IGVFFI5048OHPW.fastq.gz",
118    "schema_version": "15",
119    "seqspecs": [
120        "/configuration-files/IGVFFI2338JGPU/"
121    ],
122    "sequencing_kit": "NovaSeq X Series 10B Reagent Kit",
123    "sequencing_platform": {
124        "@id": "/platform-terms/EFO_0022840/",
125        "status": "released",
126        "term_name": "Illumina NovaSeq X"
127    },
128    "sequencing_run": 1,
129    "status": "released",
130    "submitted_by": {
131        "@id": "/users/353655bc-31a1-4cd9-bac3-c7d34faf722f/",
132        "title": "Christopher Mcginnis"
133    },
134    "submitted_file_name": "/oak/stanford/projects/igvf/Projects/230522_IGVF5_McGinnis/GEX/FASTQ/GEX_3_S19_L005_R1_001.fastq.gz",
135    "summary": "R1 reads from sequencing run 1",
136    "upload_status": "validated",
137    "uuid": "a76db38a-1c39-4f6e-a175-11fa471b4e49"
138}