IGVFFI1809CHBB

released
validated
1{
2    "@context": "/terms/",
3    "@id": "/matrix-files/IGVFFI1809CHBB/",
4    "@type": [
5        "MatrixFile",
6        "File",
7        "Item"
8    ],
9    "accession": "IGVFFI1809CHBB",
10    "aliases": [
11        "ansuman-satpathy:igvf16_raw_rna_counts_10x2"
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 [IGVFFI1809CHBB](/matrix-files/IGVFFI1809CHBB/) has in progress subobject reference file [IGVFFI3944QOJF](/reference-files/IGVFFI3944QOJF/).",
22                "level": 30,
23                "level_name": "INTERNAL_ACTION",
24                "name": "audit_item_status",
25                "path": "/matrix-files/IGVFFI1809CHBB/"
26            },
27            {
28                "category": "mismatched status",
29                "detail": "Released matrix file [IGVFFI1809CHBB](/matrix-files/IGVFFI1809CHBB/) has in progress subobject reference file [IGVFFI8311QXYM](/reference-files/IGVFFI8311QXYM/).",
30                "level": 30,
31                "level_name": "INTERNAL_ACTION",
32                "name": "audit_item_status",
33                "path": "/matrix-files/IGVFFI1809CHBB/"
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": "2025-02-14T23:12:56.808376+00:00",
45    "derived_from": [
46        "/sequence-files/IGVFFI6209GSWP/",
47        "/sequence-files/IGVFFI6922CLIB/",
48        "/sequence-files/IGVFFI8195YWLT/",
49        "/sequence-files/IGVFFI0765RDEL/",
50        "/sequence-files/IGVFFI9470XEKG/",
51        "/sequence-files/IGVFFI9163ECSS/",
52        "/sequence-files/IGVFFI8701QMPV/",
53        "/sequence-files/IGVFFI5243NHEP/",
54        "/sequence-files/IGVFFI9293IUWX/",
55        "/sequence-files/IGVFFI8076ANRG/",
56        "/sequence-files/IGVFFI9826UQQN/",
57        "/sequence-files/IGVFFI6908OOED/",
58        "/sequence-files/IGVFFI4111XPBA/",
59        "/sequence-files/IGVFFI4969WLCP/",
60        "/sequence-files/IGVFFI7168ZXLB/",
61        "/sequence-files/IGVFFI9518ZKNO/"
62    ],
63    "file_format": "hdf5",
64    "file_format_specifications": [
65        "/documents/e18648f3-63a8-47e0-be86-2670f0cb68f0/"
66    ],
67    "file_set": {
68        "@id": "/analysis-sets/IGVFDS7649PCRX/",
69        "@type": [
70            "AnalysisSet",
71            "FileSet",
72            "Item"
73        ],
74        "accession": "IGVFDS7649PCRX",
75        "file_set_type": "intermediate analysis",
76        "samples": [
77            {
78                "@id": "/multiplexed-samples/IGVFSM9574RAZA/",
79                "@type": [
80                    "MultiplexedSample",
81                    "Sample",
82                    "Item"
83                ],
84                "accession": "IGVFSM9574RAZA",
85                "classifications": [
86                    "differentiated cell specimen",
87                    "multiplexed sample"
88                ],
89                "disease_terms": [],
90                "modifications": [],
91                "sample_terms": [
92                    {
93                        "@id": "/sample-terms/EFO_0004905/",
94                        "status": "released",
95                        "term_name": "induced pluripotent stem cell"
96                    }
97                ],
98                "status": "released",
99                "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",
100                "taxa": "Homo sapiens",
101                "treatments": []
102            }
103        ],
104        "status": "released",
105        "summary": "10x multiome with MULTI-seq: cell hashing barcodes, fragments, index, peaks, raw feature barcode matrix"
106    },
107    "file_size": 225493229,
108    "gene_list_for": [],
109    "href": "/matrix-files/IGVFFI1809CHBB/@@download/IGVFFI1809CHBB.h5",
110    "input_file_for": [],
111    "integrated_in": [],
112    "lab": {
113        "@id": "/labs/ansuman-satpathy/",
114        "title": "Ansuman Satpathy, Stanford"
115    },
116    "loci_list_for": [],
117    "md5sum": "a8b3f002cdfd93dc6741b7ac6e57edd7",
118    "principal_dimension": "cell",
119    "quality_metrics": [],
120    "reference_files": [
121        "/reference-files/IGVFFI8311QXYM/",
122        "/reference-files/IGVFFI3944QOJF/"
123    ],
124    "release_timestamp": "2025-03-22T00:44:18.324380+00:00",
125    "s3_uri": "s3://igvf-files/2025/02/14/2cbe0411-f62c-4781-bee7-014d8a31bd4c/IGVFFI1809CHBB.h5",
126    "schema_version": "7",
127    "secondary_dimensions": [
128        "gene"
129    ],
130    "status": "released",
131    "submitted_by": {
132        "@id": "/users/353655bc-31a1-4cd9-bac3-c7d34faf722f/",
133        "title": "Christopher Mcginnis"
134    },
135    "submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf16/e16l2_raw_feature_bc_matrix.h5",
136    "summary": "cell by gene in raw feature barcode matrix",
137    "upload_status": "validated",
138    "uuid": "2cbe0411-f62c-4781-bee7-014d8a31bd4c",
139    "workflow": {
140        "@id": "/workflows/IGVFWF1453HVEC/",
141        "name": "Satpathy Cell Ranger",
142        "uniform_pipeline": false
143    }
144}