IGVFFI8360SRWO

1{
2    "@context": "/terms/",
3    "@id": "/tabular-files/IGVFFI8360SRWO/",
4    "@type": [
5        "TabularFile",
6        "File",
7        "Item"
8    ],
9    "accession": "IGVFFI8360SRWO",
10    "aliases": [
11        "ansuman-satpathy:igvf17_fragments_10x3"
12    ],
13    "analysis_step_version": "/analysis-step-versions/4e4a3f0b-c3bc-477c-bc53-c3091bc56756/",
14    "assay_titles": [
15        "10x multiome with MULTI-seq"
16    ],
17    "audit": {},
18    "award": {
19        "@id": "/awards/HG011972/",
20        "component": "functional characterization"
21    },
22    "barcode_map_for": [],
23    "checkfiles_version": "v14",
24    "content_md5sum": "094763ab3f469c603def7aa785512bc7",
25    "content_type": "fragments",
26    "controlled_access": false,
27    "creation_timestamp": "2025-01-28T06:32:05.828644+00:00",
28    "derived_from": [
29        "/sequence-files/IGVFFI3832ITNZ/",
30        "/sequence-files/IGVFFI3965NAFA/",
31        "/sequence-files/IGVFFI7047SZBO/",
32        "/sequence-files/IGVFFI0767RWRM/",
33        "/sequence-files/IGVFFI3290KMXW/",
34        "/sequence-files/IGVFFI7682FQQC/",
35        "/sequence-files/IGVFFI4704BEZU/",
36        "/sequence-files/IGVFFI5130TSUS/",
37        "/sequence-files/IGVFFI5962EVJS/",
38        "/sequence-files/IGVFFI6695URBV/",
39        "/sequence-files/IGVFFI7164YQMH/",
40        "/sequence-files/IGVFFI4013PTIR/",
41        "/sequence-files/IGVFFI9202GNDI/",
42        "/sequence-files/IGVFFI9643WXMN/",
43        "/sequence-files/IGVFFI6887BEUB/",
44        "/sequence-files/IGVFFI4912TWRK/"
45    ],
46    "file_format": "tsv",
47    "file_format_specifications": [
48        {
49            "@id": "/documents/43920105-5f77-430a-9bcd-f00180ff2b1d/",
50            "description": "10X Genomics Fragment File"
51        }
52    ],
53    "file_set": {
54        "@id": "/analysis-sets/IGVFDS3457PPSX/",
55        "@type": [
56            "AnalysisSet",
57            "FileSet",
58            "Item"
59        ],
60        "accession": "IGVFDS3457PPSX",
61        "controlled_access": false,
62        "data_use_limitation_summaries": [
63            "No limitations"
64        ],
65        "file_set_type": "intermediate analysis",
66        "samples": [
67            {
68                "@id": "/multiplexed-samples/IGVFSM6345RLEH/",
69                "@type": [
70                    "MultiplexedSample",
71                    "Sample",
72                    "Item"
73                ],
74                "accession": "IGVFSM6345RLEH",
75                "classifications": [
76                    "differentiated cell specimen",
77                    "multiplexed sample"
78                ],
79                "disease_terms": [],
80                "modifications": [],
81                "sample_terms": [
82                    {
83                        "@id": "/sample-terms/EFO_0009320/",
84                        "status": "released",
85                        "term_name": "RUES2"
86                    }
87                ],
88                "status": "released",
89                "summary": "multiplexed sample: Homo sapiens (female) RUES2 differentiated cell specimen induced to gastrula for 2 days; Homo sapiens (female) RUES2 differentiated cell specimen induced to gastrula for 1 day; ... and 10 more samples",
90                "taxa": "Homo sapiens",
91                "treatments": []
92            }
93        ],
94        "status": "released",
95        "summary": "single-nucleus ATAC-seq (10x multiome with MULTI-seq), single-nucleus RNA sequencing assay (10x multiome with MULTI-seq)"
96    },
97    "file_size": 5101000778,
98    "gene_list_for": [],
99    "href": "/tabular-files/IGVFFI8360SRWO/@@download/IGVFFI8360SRWO.tsv.gz",
100    "input_file_for": [
101        "/index-files/IGVFFI3180EJTY/",
102        "/tabular-files/IGVFFI9112WEDK/"
103    ],
104    "integrated_in": [],
105    "lab": {
106        "@id": "/labs/ansuman-satpathy/",
107        "title": "Ansuman Satpathy, Stanford"
108    },
109    "loci_list_for": [],
110    "md5sum": "42b13bab5d0969db756b6d6d64cfafeb",
111    "notes": "File has # in headers, the current version of checkfiles does not allow for that but this is a valid file output from cell ranger. Therefore, we have patched the upload_status to \"validation exempted\"",
112    "primer_design_for": [],
113    "quality_metrics": [],
114    "release_timestamp": "2025-03-07T06:05:21.542968+00:00",
115    "s3_uri": "s3://igvf-files/2025/01/28/a7c9c3df-e5cf-4518-ac6f-8778c0c2b68c/IGVFFI8360SRWO.tsv.gz",
116    "schema_version": "15",
117    "status": "released",
118    "submitted_by": {
119        "@id": "/users/353655bc-31a1-4cd9-bac3-c7d34faf722f/",
120        "title": "Christopher Mcginnis"
121    },
122    "submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf17/e17l3_fragments.tsv.gz",
123    "summary": "fragments",
124    "upload_status": "validation exempted",
125    "uuid": "a7c9c3df-e5cf-4518-ac6f-8778c0c2b68c",
126    "validation_error_detail": "{\"tabular_file_error\": {\"schema\": null, \"error_number_limit\": 1000, \"number_of_errors\": 1000, \"extra-cell\": {\"count\": 1000, \"description\": \"This row has more values compared to the header row (the first row in the data source). A key concept is that all the rows in tabular data must have the same number of columns.\", \"details\": [{\"row_number\": 52, \"field_number\": 2, \"note\": \"\"}, {\"row_number\": 52, \"field_number\": 3, \"note\": \"\"}]}, \"error_types\": [\"extra-cell\"]}}",
127    "workflow": {
128        "@id": "/workflows/IGVFWF1453HVEC/",
129        "name": "Satpathy Cell Ranger",
130        "uniform_pipeline": false
131    }
132}