IGVFFI3624BMMT

1{
2    "@context": "/terms/",
3    "@id": "/tabular-files/IGVFFI3624BMMT/",
4    "@type": [
5        "TabularFile",
6        "File",
7        "Item"
8    ],
9    "accession": "IGVFFI3624BMMT",
10    "aliases": [
11        "ansuman-satpathy:igvf16_fragments_10x4"
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": "9a45fefc1a94273bfe0bf41184367e86",
25    "content_type": "fragments",
26    "controlled_access": true,
27    "creation_timestamp": "2025-02-14T22:53:34.714393+00:00",
28    "derived_from": [
29        "/sequence-files/IGVFFI1334NGIQ/",
30        "/sequence-files/IGVFFI7549ELIJ/",
31        "/sequence-files/IGVFFI6990DAGO/",
32        "/sequence-files/IGVFFI4799XAAS/",
33        "/sequence-files/IGVFFI4398SJEH/",
34        "/sequence-files/IGVFFI6637TZUR/",
35        "/sequence-files/IGVFFI1725INMI/",
36        "/sequence-files/IGVFFI4829LKAY/",
37        "/sequence-files/IGVFFI4765QWOK/",
38        "/sequence-files/IGVFFI4412BLAG/",
39        "/sequence-files/IGVFFI4406LHJI/",
40        "/sequence-files/IGVFFI8370XUWJ/",
41        "/sequence-files/IGVFFI1430EQDU/",
42        "/sequence-files/IGVFFI9695AFJV/",
43        "/sequence-files/IGVFFI1065UBIT/",
44        "/sequence-files/IGVFFI9885TJZC/"
45    ],
46    "file_format": "tsv",
47    "file_format_specifications": [
48        "/documents/43920105-5f77-430a-9bcd-f00180ff2b1d/"
49    ],
50    "file_set": {
51        "@id": "/analysis-sets/IGVFDS4570PZIO/",
52        "@type": [
53            "AnalysisSet",
54            "FileSet",
55            "Item"
56        ],
57        "accession": "IGVFDS4570PZIO",
58        "file_set_type": "intermediate analysis",
59        "samples": [
60            {
61                "@id": "/multiplexed-samples/IGVFSM5245KVZO/",
62                "@type": [
63                    "MultiplexedSample",
64                    "Sample",
65                    "Item"
66                ],
67                "accession": "IGVFSM5245KVZO",
68                "classifications": [
69                    "differentiated cell specimen",
70                    "multiplexed sample"
71                ],
72                "disease_terms": [],
73                "modifications": [],
74                "sample_terms": [
75                    {
76                        "@id": "/sample-terms/EFO_0004905/",
77                        "status": "released",
78                        "term_name": "induced pluripotent stem cell"
79                    }
80                ],
81                "status": "released",
82                "summary": "multiplexed sample: Homo sapiens (mixed sex) induced pluripotent stem differentiated cell specimen induced to islet of Langerhans for 11 days; Homo sapiens (mixed sex) induced pluripotent stem differentiated cell specimen induced to islet of Langerhans for 3 days; ... and 6 more samples",
83                "taxa": "Homo sapiens",
84                "treatments": []
85            }
86        ],
87        "status": "released",
88        "summary": "10x multiome with MULTI-seq: cell hashing barcodes, fragments, index, peaks, raw feature barcode matrix"
89    },
90    "file_size": 5728734455,
91    "gene_list_for": [],
92    "href": "/tabular-files/IGVFFI3624BMMT/@@download/IGVFFI3624BMMT.tsv.gz",
93    "input_file_for": [
94        "/tabular-files/IGVFFI6588PJQU/",
95        "/index-files/IGVFFI2658BEID/"
96    ],
97    "integrated_in": [],
98    "lab": {
99        "@id": "/labs/ansuman-satpathy/",
100        "title": "Ansuman Satpathy, Stanford"
101    },
102    "loci_list_for": [],
103    "md5sum": "474838b2ef8bbc9e7e7db4d8affc5b43",
104    "notes": "The file starts with # in the first multiple lines. Because this file came straight from cell ranger, we'll validation exempt it.",
105    "quality_metrics": [],
106    "release_timestamp": "2025-03-22T00:44:34.579042+00:00",
107    "s3_uri": "s3://igvf-restricted-files/2025/02/14/0edbddb5-ce8e-4854-8238-5ddd3405a575/IGVFFI3624BMMT.tsv.gz",
108    "schema_version": "15",
109    "status": "released",
110    "submitted_by": {
111        "@id": "/users/353655bc-31a1-4cd9-bac3-c7d34faf722f/",
112        "title": "Christopher Mcginnis"
113    },
114    "submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf16/e16l4_fragments.tsv.gz",
115    "summary": "fragments",
116    "upload_status": "validation exempted",
117    "uuid": "0edbddb5-ce8e-4854-8238-5ddd3405a575",
118    "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\"]}}",
119    "workflow": {
120        "@id": "/workflows/IGVFWF1453HVEC/",
121        "name": "Satpathy Cell Ranger",
122        "uniform_pipeline": false
123    }
124}