IGVFFI5965MEPA

released
validated
1{
2    "@context": "/terms/",
3    "@id": "/matrix-files/IGVFFI5965MEPA/",
4    "@type": [
5        "MatrixFile",
6        "File",
7        "Item"
8    ],
9    "accession": "IGVFFI5965MEPA",
10    "aliases": [
11        "ansuman-satpathy:igvf16_raw_rna_counts_10x3"
12    ],
13    "analysis_step_version": "/analysis-step-versions/072beaf9-db5c-4bb3-9d63-e5cf7ee29dd6/",
14    "assay_titles": [
15        "10x multiome with MULTI-seq"
16    ],
17    "audit": {
18        "INTERNAL_ACTION": [
19            {
20                "category": "mismatched status",
21                "detail": "Released matrix file [IGVFFI5965MEPA](/matrix-files/IGVFFI5965MEPA/) has in progress subobject reference file [IGVFFI8311QXYM](/reference-files/IGVFFI8311QXYM/).",
22                "level": 30,
23                "level_name": "INTERNAL_ACTION",
24                "name": "audit_item_status",
25                "path": "/matrix-files/IGVFFI5965MEPA/"
26            },
27            {
28                "category": "mismatched status",
29                "detail": "Released matrix file [IGVFFI5965MEPA](/matrix-files/IGVFFI5965MEPA/) has in progress subobject reference file [IGVFFI3944QOJF](/reference-files/IGVFFI3944QOJF/).",
30                "level": 30,
31                "level_name": "INTERNAL_ACTION",
32                "name": "audit_item_status",
33                "path": "/matrix-files/IGVFFI5965MEPA/"
34            }
35        ]
36    },
37    "award": {
38        "@id": "/awards/HG011972/",
39        "component": "functional characterization"
40    },
41    "checkfiles_version": "v14",
42    "content_summary": "cell by gene in raw feature barcode matrix",
43    "content_type": "raw feature barcode matrix",
44    "creation_timestamp": "2025-02-14T23:13:11.871177+00:00",
45    "derived_from": [
46        "/sequence-files/IGVFFI6874AEZE/",
47        "/sequence-files/IGVFFI6854ZJPO/",
48        "/sequence-files/IGVFFI2269VTGT/",
49        "/sequence-files/IGVFFI1963GDHF/",
50        "/sequence-files/IGVFFI7617SZMU/",
51        "/sequence-files/IGVFFI3088IKKB/",
52        "/sequence-files/IGVFFI9998DEEX/",
53        "/sequence-files/IGVFFI5562BVNR/",
54        "/sequence-files/IGVFFI7969SWCF/",
55        "/sequence-files/IGVFFI8907EJIL/",
56        "/sequence-files/IGVFFI6723PXEN/",
57        "/sequence-files/IGVFFI2119WWMF/",
58        "/sequence-files/IGVFFI4167EJPY/",
59        "/sequence-files/IGVFFI1632QOXZ/",
60        "/sequence-files/IGVFFI8492QLRN/",
61        "/sequence-files/IGVFFI2040BEUK/"
62    ],
63    "file_format": "hdf5",
64    "file_format_specifications": [
65        "/documents/e18648f3-63a8-47e0-be86-2670f0cb68f0/"
66    ],
67    "file_set": {
68        "@id": "/analysis-sets/IGVFDS9825AFPQ/",
69        "accession": "IGVFDS9825AFPQ",
70        "file_set_type": "intermediate analysis",
71        "samples": [
72            {
73                "@id": "/multiplexed-samples/IGVFSM5332SKYG/",
74                "accession": "IGVFSM5332SKYG",
75                "classifications": [
76                    "differentiated cell specimen",
77                    "multiplexed sample"
78                ],
79                "disease_terms": [],
80                "modifications": [],
81                "sample_terms": [
82                    {
83                        "@id": "/sample-terms/EFO_0004905/",
84                        "status": "released",
85                        "term_name": "induced pluripotent stem cell"
86                    }
87                ],
88                "status": "released",
89                "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",
90                "taxa": "Homo sapiens",
91                "treatments": []
92            }
93        ],
94        "status": "released",
95        "summary": "10x multiome with MULTI-seq: cell hashing barcodes, fragments, index, peaks, raw feature barcode matrix"
96    },
97    "file_size": 216109405,
98    "gene_list_for": [],
99    "href": "/matrix-files/IGVFFI5965MEPA/@@download/IGVFFI5965MEPA.h5",
100    "input_file_for": [],
101    "integrated_in": [],
102    "lab": {
103        "@id": "/labs/ansuman-satpathy/",
104        "title": "Ansuman Satpathy, Stanford"
105    },
106    "loci_list_for": [],
107    "md5sum": "77b38c1056d1d70a99036efa9d3205df",
108    "principal_dimension": "cell",
109    "quality_metrics": [],
110    "reference_files": [
111        "/reference-files/IGVFFI8311QXYM/",
112        "/reference-files/IGVFFI3944QOJF/"
113    ],
114    "release_timestamp": "2025-03-22T00:44:27.068845+00:00",
115    "s3_uri": "s3://igvf-files/2025/02/14/aba4eeef-646a-4373-9d13-41ec0503a38b/IGVFFI5965MEPA.h5",
116    "schema_version": "7",
117    "secondary_dimensions": [
118        "gene"
119    ],
120    "status": "released",
121    "submitted_by": {
122        "@id": "/users/353655bc-31a1-4cd9-bac3-c7d34faf722f/",
123        "title": "Christopher Mcginnis"
124    },
125    "submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf16/e16l3_raw_feature_bc_matrix.h5",
126    "summary": "cell by gene in raw feature barcode matrix",
127    "upload_status": "validated",
128    "uuid": "aba4eeef-646a-4373-9d13-41ec0503a38b",
129    "workflow": {
130        "@id": "/workflows/IGVFWF1453HVEC/",
131        "name": "Satpathy Cell Ranger",
132        "uniform_pipeline": false
133    }
134}