IGVFFI3092VBKJ

1{
2    "@context": "/terms/",
3    "@id": "/tabular-files/IGVFFI3092VBKJ/",
4    "@type": [
5        "TabularFile",
6        "File",
7        "Item"
8    ],
9    "accession": "IGVFFI3092VBKJ",
10    "aliases": [
11        "ansuman-satpathy:igvf13_fragments_10x1"
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": "d39e470bef127f429a42e42af817a2d5",
25    "content_type": "fragments",
26    "controlled_access": true,
27    "creation_timestamp": "2025-01-28T06:23:16.240916+00:00",
28    "derived_from": [
29        "/sequence-files/IGVFFI3017ZKLK/",
30        "/sequence-files/IGVFFI8899OCMF/",
31        "/sequence-files/IGVFFI3923LTFP/",
32        "/sequence-files/IGVFFI9872ZCYZ/",
33        "/sequence-files/IGVFFI0244DQNM/",
34        "/sequence-files/IGVFFI3455XARV/",
35        "/sequence-files/IGVFFI9561YTLI/",
36        "/sequence-files/IGVFFI8966HZNP/",
37        "/sequence-files/IGVFFI9734XMHY/",
38        "/sequence-files/IGVFFI9768MFHS/",
39        "/sequence-files/IGVFFI8922GVCO/",
40        "/sequence-files/IGVFFI6086MFMD/"
41    ],
42    "file_format": "tsv",
43    "file_format_specifications": [
44        "/documents/43920105-5f77-430a-9bcd-f00180ff2b1d/"
45    ],
46    "file_set": {
47        "@id": "/analysis-sets/IGVFDS5901DVUG/",
48        "@type": [
49            "AnalysisSet",
50            "FileSet",
51            "Item"
52        ],
53        "accession": "IGVFDS5901DVUG",
54        "file_set_type": "intermediate analysis",
55        "samples": [
56            {
57                "@id": "/multiplexed-samples/IGVFSM6422YWWA/",
58                "@type": [
59                    "MultiplexedSample",
60                    "Sample",
61                    "Item"
62                ],
63                "accession": "IGVFSM6422YWWA",
64                "classifications": [
65                    "tissue",
66                    "multiplexed sample"
67                ],
68                "disease_terms": [
69                    {
70                        "@id": "/phenotype-terms/MONDO_0005010/",
71                        "@type": [
72                            "PhenotypeTerm",
73                            "OntologyTerm",
74                            "Item"
75                        ],
76                        "status": "released",
77                        "summary": "coronary artery disorder",
78                        "term_name": "coronary artery disorder"
79                    }
80                ],
81                "modifications": [],
82                "sample_terms": [
83                    {
84                        "@id": "/sample-terms/UBERON_0001626/",
85                        "status": "released",
86                        "term_name": "left coronary artery"
87                    }
88                ],
89                "status": "released",
90                "summary": "multiplexed sample: Homo sapiens (female, 48 years) left coronary artery tissue associated with coronary artery disorder; Homo sapiens (female, 73 years) left coronary artery tissue associated with coronary artery disorder; ... and 2 more samples",
91                "taxa": "Homo sapiens",
92                "treatments": []
93            }
94        ],
95        "status": "released",
96        "summary": "10x multiome with MULTI-seq: cell hashing barcodes, fragments, index, peaks, raw feature barcode matrix"
97    },
98    "file_size": 5327641058,
99    "gene_list_for": [],
100    "href": "/tabular-files/IGVFFI3092VBKJ/@@download/IGVFFI3092VBKJ.tsv.gz",
101    "input_file_for": [
102        "/index-files/IGVFFI0641CLXM/",
103        "/tabular-files/IGVFFI9273HUJF/"
104    ],
105    "integrated_in": [],
106    "lab": {
107        "@id": "/labs/ansuman-satpathy/",
108        "title": "Ansuman Satpathy, Stanford"
109    },
110    "loci_list_for": [],
111    "md5sum": "ba05e6e14de94a162099df30c3800e4c",
112    "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\"",
113    "quality_metrics": [],
114    "release_timestamp": "2025-03-22T00:41:57.830738+00:00",
115    "s3_uri": "s3://igvf-restricted-files/2025/01/28/eacb87f8-bb2e-41c6-b518-3f0405806c92/IGVFFI3092VBKJ.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/igvf13/e13l1_fragments.tsv.gz",
123    "summary": "fragments",
124    "upload_status": "validation exempted",
125    "uuid": "eacb87f8-bb2e-41c6-b518-3f0405806c92",
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}