IGVFFI0315UORM

released
validated
1{
2    "@context": "/terms/",
3    "@id": "/matrix-files/IGVFFI0315UORM/",
4    "@type": [
5        "MatrixFile",
6        "File",
7        "Item"
8    ],
9    "accession": "IGVFFI0315UORM",
10    "aliases": [
11        "buenrostro-bernstein:surya-mouse-colitis-organoid-rna-matrix"
12    ],
13    "analysis_step_version": "/analysis-step-versions/45d73e29-280a-4faf-9762-c1b4c655b689/",
14    "assay_titles": [
15        "SHARE-seq"
16    ],
17    "audit": {
18        "INTERNAL_ACTION": [
19            {
20                "category": "mismatched status",
21                "detail": "Released matrix file [IGVFFI0315UORM](/matrix-files/IGVFFI0315UORM/) has in progress subobject reference file [IGVFFI6909ZBPJ](/reference-files/IGVFFI6909ZBPJ/).",
22                "level": 30,
23                "level_name": "INTERNAL_ACTION",
24                "name": "audit_item_status",
25                "path": "/matrix-files/IGVFFI0315UORM/"
26            },
27            {
28                "category": "mismatched status",
29                "detail": "Released matrix file [IGVFFI0315UORM](/matrix-files/IGVFFI0315UORM/) has in progress subobject reference file [IGVFFI4319MSMI](/reference-files/IGVFFI4319MSMI/).",
30                "level": 30,
31                "level_name": "INTERNAL_ACTION",
32                "name": "audit_item_status",
33                "path": "/matrix-files/IGVFFI0315UORM/"
34            }
35        ]
36    },
37    "award": {
38        "@id": "/awards/HG011986/",
39        "component": "mapping"
40    },
41    "checkfiles_version": "v17",
42    "content_summary": "cell by gene in sparse gene count matrix",
43    "content_type": "sparse gene count matrix",
44    "creation_timestamp": "2025-03-06T16:38:18.620373+00:00",
45    "derived_from": [
46        "/sequence-files/IGVFFI8469AYWW/",
47        "/sequence-files/IGVFFI4332PNYO/",
48        "/sequence-files/IGVFFI5138TGVX/",
49        "/sequence-files/IGVFFI1779UNVR/",
50        "/sequence-files/IGVFFI4885KWUD/",
51        "/sequence-files/IGVFFI0961MKPO/",
52        "/sequence-files/IGVFFI7632WZNX/",
53        "/sequence-files/IGVFFI2979RGGQ/"
54    ],
55    "file_format": "h5ad",
56    "file_format_specifications": [
57        "/documents/cae4f4ad-b937-4694-b5b7-028917c8dbab/"
58    ],
59    "file_set": {
60        "@id": "/analysis-sets/IGVFDS5536ZQMO/",
61        "@type": [
62            "AnalysisSet",
63            "FileSet",
64            "Item"
65        ],
66        "accession": "IGVFDS5536ZQMO",
67        "file_set_type": "intermediate analysis",
68        "samples": [
69            {
70                "@id": "/in-vitro-systems/IGVFSM4239FRER/",
71                "@type": [
72                    "InVitroSystem",
73                    "Biosample",
74                    "Sample",
75                    "Item"
76                ],
77                "accession": "IGVFSM4239FRER",
78                "classifications": [
79                    "organoid"
80                ],
81                "sample_terms": [
82                    {
83                        "@id": "/sample-terms/UBERON_0000397/",
84                        "status": "released",
85                        "term_name": "colonic epithelium"
86                    }
87                ],
88                "status": "released",
89                "summary": "Mus musculus C57BL/6J colonic epithelium organoid induced to colon for 27 days",
90                "targeted_sample_term": {
91                    "@id": "/sample-terms/UBERON_0001155/",
92                    "status": "released",
93                    "term_name": "colon"
94                },
95                "taxa": "Mus musculus"
96            }
97        ],
98        "status": "released",
99        "summary": "SHARE-seq: fragments, sparse gene count matrix"
100    },
101    "file_size": 282446983,
102    "filtered": false,
103    "gene_list_for": [],
104    "href": "/matrix-files/IGVFFI0315UORM/@@download/IGVFFI0315UORM.h5ad",
105    "input_file_for": [],
106    "integrated_in": [],
107    "lab": {
108        "@id": "/labs/jason-buenrostro/",
109        "title": "Jason Buenrostro, Broad"
110    },
111    "loci_list_for": [],
112    "md5sum": "d99b8ab309161a8ff391b85a4dc74d4d",
113    "principal_dimension": "cell",
114    "quality_metrics": [],
115    "reference_files": [
116        "/reference-files/IGVFFI6909ZBPJ/",
117        "/reference-files/IGVFFI4319MSMI/"
118    ],
119    "release_timestamp": "2025-03-26T19:25:49.852410+00:00",
120    "s3_uri": "s3://igvf-files/2025/03/06/e170e021-c397-4b37-8b4d-887a0af04eff/IGVFFI0315UORM.h5ad",
121    "schema_version": "7",
122    "secondary_dimensions": [
123        "gene"
124    ],
125    "status": "released",
126    "submitted_by": {
127        "@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
128        "title": "Siddarth Wekhande"
129    },
130    "submitted_file_name": "gs://sw-igvf-submission/surya-mouse-colitis/processed-data/mouse_organoids.RNA.raw_counts.h5",
131    "summary": "unfiltered cell by gene in sparse gene count matrix",
132    "upload_status": "validated",
133    "uuid": "e170e021-c397-4b37-8b4d-887a0af04eff",
134    "workflow": {
135        "@id": "/workflows/IGVFWF0507XZOR/",
136        "name": "SHARE-seq-alignmentV2",
137        "uniform_pipeline": false
138    }
139}