IGVFFI2578BIPG

1{
2    "@context": "/terms/",
3    "@id": "/tabular-files/IGVFFI2578BIPG/",
4    "@type": [
5        "TabularFile",
6        "File",
7        "Item"
8    ],
9    "accession": "IGVFFI2578BIPG",
10    "aliases": [
11        "ansuman-satpathy:igvf11_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": "b70bd9aadf31f7d1e583b8426591196a",
25    "content_type": "fragments",
26    "controlled_access": false,
27    "creation_timestamp": "2025-01-28T06:08:20.046915+00:00",
28    "derived_from": [
29        "/sequence-files/IGVFFI4060KMTU/",
30        "/sequence-files/IGVFFI2693CLMF/",
31        "/sequence-files/IGVFFI2826OTFN/",
32        "/sequence-files/IGVFFI4248CJOB/",
33        "/sequence-files/IGVFFI2024VPLF/",
34        "/sequence-files/IGVFFI0980ARAR/",
35        "/sequence-files/IGVFFI2806AYVZ/",
36        "/sequence-files/IGVFFI8036LAGY/",
37        "/sequence-files/IGVFFI1472UONJ/",
38        "/sequence-files/IGVFFI7126FBUP/",
39        "/sequence-files/IGVFFI1407KJFX/",
40        "/sequence-files/IGVFFI2910ZQKO/",
41        "/sequence-files/IGVFFI3244YCDF/",
42        "/sequence-files/IGVFFI3256ARWG/",
43        "/sequence-files/IGVFFI1493XNIC/",
44        "/sequence-files/IGVFFI2015MKVY/"
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/IGVFDS7903FOXV/",
55        "@type": [
56            "AnalysisSet",
57            "FileSet",
58            "Item"
59        ],
60        "accession": "IGVFDS7903FOXV",
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/IGVFSM6160ZDRZ/",
69                "@type": [
70                    "MultiplexedSample",
71                    "Sample",
72                    "Item"
73                ],
74                "accession": "IGVFSM6160ZDRZ",
75                "classifications": [
76                    "differentiated cell specimen",
77                    "multiplexed sample"
78                ],
79                "disease_terms": [],
80                "modifications": [],
81                "sample_terms": [
82                    {
83                        "@id": "/sample-terms/EFO_0005904/",
84                        "status": "released",
85                        "term_name": "H7-hESC"
86                    },
87                    {
88                        "@id": "/sample-terms/EFO_0009747/",
89                        "status": "released",
90                        "term_name": "GM25256 (WTC-11)"
91                    }
92                ],
93                "status": "released",
94                "summary": "multiplexed sample: Homo sapiens (female) H7-hESC differentiated cell specimen; Homo sapiens (male) GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 6 days; ... and 10 more samples",
95                "taxa": "Homo sapiens",
96                "treatments": []
97            }
98        ],
99        "status": "released",
100        "summary": "single-nucleus ATAC-seq (10x multiome with MULTI-seq), single-nucleus RNA sequencing assay (10x multiome with MULTI-seq)"
101    },
102    "file_size": 4483649178,
103    "gene_list_for": [],
104    "href": "/tabular-files/IGVFFI2578BIPG/@@download/IGVFFI2578BIPG.tsv.gz",
105    "input_file_for": [
106        "/index-files/IGVFFI0347BCEG/",
107        "/tabular-files/IGVFFI7472XTOL/"
108    ],
109    "integrated_in": [],
110    "lab": {
111        "@id": "/labs/ansuman-satpathy/",
112        "title": "Ansuman Satpathy, Stanford"
113    },
114    "loci_list_for": [],
115    "md5sum": "b9602d94e86bb2de9f6c05d97fea0524",
116    "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\"",
117    "primer_design_for": [],
118    "quality_metrics": [],
119    "release_timestamp": "2025-03-07T06:05:05.988898+00:00",
120    "s3_uri": "s3://igvf-files/2025/01/28/0ccbb81a-9a30-464b-89b4-fc557bad8e02/IGVFFI2578BIPG.tsv.gz",
121    "schema_version": "15",
122    "status": "released",
123    "submitted_by": {
124        "@id": "/users/353655bc-31a1-4cd9-bac3-c7d34faf722f/",
125        "title": "Christopher Mcginnis"
126    },
127    "submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf11/e11l3_fragments.tsv.gz",
128    "summary": "fragments",
129    "upload_status": "validation exempted",
130    "uuid": "0ccbb81a-9a30-464b-89b4-fc557bad8e02",
131    "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\"]}}",
132    "workflow": {
133        "@id": "/workflows/IGVFWF1453HVEC/",
134        "name": "Satpathy Cell Ranger",
135        "uniform_pipeline": false
136    }
137}